############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/mzR_2.28.0.tar.gz && rm -rf mzR.buildbin-libdir && mkdir mzR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mzR.buildbin-libdir mzR_2.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL mzR_2.28.0.zip && rm mzR_2.28.0.tar.gz mzR_2.28.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 12 4778k 12 589k 0 0 634k 0 0:00:07 --:--:-- 0:00:07 634k 44 4778k 44 2122k 0 0 1103k 0 0:00:04 0:00:01 0:00:03 1103k 95 4778k 95 4573k 0 0 1565k 0 0:00:03 0:00:02 0:00:01 1566k 100 4778k 100 4778k 0 0 1610k 0 0:00:02 0:00:02 --:--:-- 1610k install for i386 * installing *source* package 'mzR' ... ** using staged installation ** libs rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./pwiz/data/msdata/ramp/wglob.o ./boost_aux/boost/nowide/iostream.o rampR.o find . -name \*~ -exec rm {} \; ## from cleanup find . -name \*.o -exec rm {} \; ## from cleanup find . -name "#*#" -exec rm {} \; ## from cleanup "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cramp.cpp -o cramp.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from random_access_gzFile.h:21, from ramp.h:72, from cramp.h:33, from cramp.cpp:49: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from cramp.cpp:49: cramp.h: In copy constructor 'rampScanInfo::rampScanInfo(rampScanInfo&)': cramp.h:261:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampScanInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(this,&rhs,sizeof(rhs)); ^ In file included from cramp.cpp:49: cramp.h:251:7: note: 'class rampScanInfo' declared here class rampScanInfo: public rampInfo ^~~~~~~~~~~~ In file included from cramp.cpp:49: cramp.h: In copy constructor 'rampRunInfo::rampRunInfo(const rampRunInfo&)': cramp.h:315:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampRunInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(this,&rhs,sizeof(rhs)); ^ cramp.h:305:7: note: 'class rampRunInfo' declared here class rampRunInfo: public rampInfo ^~~~~~~~~~~ In file included from cramp.cpp:49: cramp.h: In constructor 'cRamp::cRamp(const char*, bool)': cramp.h:149:10: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder] bool m_declaredScansOnly; // if true, suppress RAMP's habit of adding scans to fill in between declared scans ^~~~~~~~~~~~~~~~~~~ cramp.h:148:18: warning: 'rampRunInfo* cRamp::m_runInfo' [-Wreorder] rampRunInfo *m_runInfo; // scan count etc ^~~~~~~~~ cramp.cpp:72:1: warning: when initialized here [-Wreorder] cRamp::cRamp( const char* fileName,bool declaredScansOnly ) : ^~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ramp_base64.cpp -o ramp_base64.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ramp.cpp -o ramp.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from random_access_gzFile.h:21, from ramp.h:72, from ramp.cpp:44: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)': ramp.cpp:248:23: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(buf,sizeof(buf)-1,result); ^~~~ ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)': ramp.cpp:451:12: warning: unused variable 'nread' [-Wunused-variable] size_t nread = ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI); ^~~~~ ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)': ramp.cpp:650:31: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(buf, SIZE_BUF, pFI); ^~~~ ramp.cpp:692:31: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(buf, SIZE_BUF, pFI); ^~~~ ramp.cpp:729:27: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(buf, SIZE_BUF, pFI); ^~~~ ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)': ramp.cpp:1446:27: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)': ramp.cpp:1532:15: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp:1528:11: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)': ramp.cpp:2090:28: warning: unused variable 'nread' [-Wunused-variable] size_t nread = ramp_fread(pData+partial,(int)(peaksLen-partial), pFI); ^~~~~ ramp.cpp:2293:27: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(buf, sizeof(buf)-1 , pFI); ^~~~ ramp.cpp:2340:24: warning: unused variable 'nread' [-Wunused-variable] size_t nread = ramp_fread(pData+partial,peaksLen-partial, pFI); ^~~~~ ramp.cpp:2394:21: warning: variable 'err' set but not used [-Wunused-but-set-variable] int err; ^~~ ramp.cpp:2212:19: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(buf, sizeof(buf)-1, pFI); ^~~~ ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)': ramp.cpp:2520:15: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp:2544:15: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp:2516:11: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)': ramp.cpp:2695:19: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp:2731:19: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp:2682:11: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp: In function 'int rampSelfTest(char*)': ramp.cpp:2799:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation] strncpy(buf,testname[i],sizeof(buf)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ramp.cpp:2812:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation] strncpy(buf,filename,sizeof(buf)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ ramp.cpp:2816:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation] strncpy(buf,filename,sizeof(buf)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppRamp.cpp -o RcppRamp.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from random_access_gzFile.h:21, from ramp.h:72, from cramp.h:33, from RcppRamp.h:14, from RcppRamp.cpp:1: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from RcppRamp.h:14, from RcppRamp.cpp:1: cramp.h: In copy constructor 'rampScanInfo::rampScanInfo(rampScanInfo&)': cramp.h:261:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampScanInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(this,&rhs,sizeof(rhs)); ^ In file included from RcppRamp.h:14, from RcppRamp.cpp:1: cramp.h:251:7: note: 'class rampScanInfo' declared here class rampScanInfo: public rampInfo ^~~~~~~~~~~~ In file included from RcppRamp.h:14, from RcppRamp.cpp:1: cramp.h: In copy constructor 'rampRunInfo::rampRunInfo(const rampRunInfo&)': cramp.h:315:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampRunInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(this,&rhs,sizeof(rhs)); ^ cramp.h:305:7: note: 'class rampRunInfo' declared here class rampRunInfo: public rampInfo ^~~~~~~~~~~ RcppRamp.cpp: In member function 'Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo()': RcppRamp.cpp:215:27: warning: unused variable 'info' [-Wunused-variable] rampScanInfo *info = ramp->getScanHeaderInfo( 1 ); ^~~~ RcppRamp.cpp: In member function 'Rcpp::NumericMatrix RcppRamp::get3DMap(std::vector, double, double, double)': RcppRamp.cpp:388:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i < scanNumbers.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppRampModule.cpp -o RcppRampModule.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from random_access_gzFile.h:21, from ramp.h:72, from cramp.h:33, from RcppRamp.h:14, from RcppRampModule.cpp:2: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from RcppRamp.h:14, from RcppRampModule.cpp:2: cramp.h: In copy constructor 'rampScanInfo::rampScanInfo(rampScanInfo&)': cramp.h:261:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampScanInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(this,&rhs,sizeof(rhs)); ^ In file included from RcppRamp.h:14, from RcppRampModule.cpp:2: cramp.h:251:7: note: 'class rampScanInfo' declared here class rampScanInfo: public rampInfo ^~~~~~~~~~~~ In file included from RcppRamp.h:14, from RcppRampModule.cpp:2: cramp.h: In copy constructor 'rampRunInfo::rampRunInfo(const rampRunInfo&)': cramp.h:315:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampRunInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(this,&rhs,sizeof(rhs)); ^ cramp.h:305:7: note: 'class rampRunInfo' declared here class rampRunInfo: public rampInfo ^~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppPwiz.cpp -o RcppPwiz.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from RcppPwiz.h:12, from RcppPwiz.cpp:1: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Std.hpp:31, from RcppPwiz.h:20, from RcppPwiz.cpp:1: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from pwiz/utility/misc/Std.hpp:32, from RcppPwiz.h:20, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from ./boost/boost/iostreams/filtering_stream.hpp:22, from RcppPwiz.h:23, from RcppPwiz.cpp:1: ./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base::push_impl(const T&, std::streamsize, std::streamsize)': ./boost/boost/iostreams/chain.hpp:256:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getScanHeaderInfo(Rcpp::IntegerVector)': RcppPwiz.cpp:133:9: warning: unused variable 'N' [-Wunused-variable] int N = slp->size(); ^ RcppPwiz.cpp: In member function 'void RcppPwiz::addSpectrumList(pwiz::msdata::MSData&, Rcpp::DataFrame&, Rcpp::List&, bool)': RcppPwiz.cpp:745:29: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] if (precursorScanNum[i] > 0 | precursorMZ[i] > 0) { RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)': RcppPwiz.cpp:820:49: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) { ~~~~~~~~~~~^~~~~~~~~~~~~ RcppPwiz.cpp:830:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i < pairs.size(); i++) { ~~^~~~~~~~~~~~~~ RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo(Rcpp::IntegerVector)': RcppPwiz.cpp:850:10: warning: unused variable 'nativeIdFormat_' [-Wunused-variable] CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd); ^~~~~~~~~~~~~~~ RcppPwiz.cpp: In member function 'Rcpp::NumericMatrix RcppPwiz::get3DMap(std::vector, double, double, double)': RcppPwiz.cpp:981:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i < scanNumbers.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~ RcppPwiz.cpp:987:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k < pairs.size(); k++) ~~^~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppPwizModule.cpp -o RcppPwizModule.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from RcppPwiz.h:12, from RcppPwizModule.cpp:2: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Std.hpp:31, from RcppPwiz.h:20, from RcppPwizModule.cpp:2: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from pwiz/utility/misc/Std.hpp:32, from RcppPwiz.h:20, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from ./boost/boost/iostreams/filtering_stream.hpp:22, from RcppPwiz.h:23, from RcppPwizModule.cpp:2: ./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base::push_impl(const T&, std::streamsize, std::streamsize)': ./boost/boost/iostreams/chain.hpp:256:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppIdent.cpp -o RcppIdent.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Std.hpp:31, from RcppIdent.h:14, from RcppIdent.cpp:1: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from pwiz/utility/misc/Std.hpp:32, from RcppIdent.h:14, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ RcppIdent.cpp: In member function 'Rcpp::DataFrame RcppIdent::getScore()': RcppIdent.cpp:293:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] for (size_t j = 0; j < nCvParams; j++) { ~~^~~~~~~~~~~ RcppIdent.cpp: In member function 'Rcpp::List RcppIdent::getPara()': RcppIdent.cpp:382:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i = 0 ; i < sip[0]->additionalSearchParams.cvParams.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RcppIdent.cpp:388:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppIdentModule.cpp -o RcppIdentModule.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Std.hpp:31, from RcppIdent.h:14, from RcppIdentModule.cpp:2: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from pwiz/utility/misc/Std.hpp:32, from RcppIdent.h:14, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/system/config.hpp:13, from ./boost/boost/system/error_code.hpp:14, from boost/libs/system/src/error_code.cpp:16: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/posix_api.cpp:21: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/fileiter.cpp -o boost/libs/regex/src/fileiter.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/fileiter.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex_raw_buffer.cpp -o boost/libs/regex/src/regex_raw_buffer.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/regex_raw_buffer.cpp:21: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/cregex.cpp -o boost/libs/regex/src/cregex.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from ./boost/boost/regex.hpp:28, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from boost/libs/regex/src/regex_debug.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/instances.cpp -o boost/libs/regex/src/instances.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from boost/libs/regex/src/instances.cpp:21: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/icu.cpp -o boost/libs/regex/src/icu.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from boost/libs/regex/src/icu.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/usinstances.cpp -o boost/libs/regex/src/usinstances.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/detail/workaround.hpp:41, from boost/libs/regex/src/usinstances.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/regex.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from boost/libs/regex/src/wide_posix_api.cpp:21: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex_traits_defaults.cpp -o boost/libs/regex/src/regex_traits_defaults.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from ./boost/boost/regex/regex_traits.hpp:23, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/winstances.cpp -o boost/libs/regex/src/winstances.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from boost/libs/regex/src/winstances.cpp:21: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/wc_regex_traits.cpp -o boost/libs/regex/src/wc_regex_traits.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/detail/workaround.hpp:41, from boost/libs/regex/src/wc_regex_traits.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/c_regex_traits.cpp -o boost/libs/regex/src/c_regex_traits.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/c_regex_traits.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/cpp_regex_traits.cpp -o boost/libs/regex/src/cpp_regex_traits.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/cpp_regex_traits.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/static_mutex.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/w32_regex_traits.cpp -o boost/libs/regex/src/w32_regex_traits.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from boost/libs/regex/src/w32_regex_traits.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/range/iterator_range.hpp:13, from ./boost/boost/iostreams/traits.hpp:39, from ./boost/boost/iostreams/detail/dispatch.hpp:17, from ./boost/boost/iostreams/read.hpp:19, from ./boost/boost/iostreams/detail/buffer.hpp:20, from ./boost/boost/iostreams/filter/symmetric.hpp:49, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o In file included from ./boost/boost/config.hpp:57, from boost/libs/iostreams/src/file_descriptor.cpp:16: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/filesystem/operations.hpp:18, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/filesystem/path.hpp:28, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o In file included from ./boost/boost/config.hpp:57, from boost/libs/filesystem/src/path.cpp:12: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/filesystem/path.hpp:28, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/filesystem/config.hpp:28, from boost/libs/filesystem/src/utf8_codecvt_facet.cpp:15: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/chrono/config.hpp:15, from ./boost/boost/chrono/duration.hpp:33, from ./boost/boost/chrono/chrono.hpp:11, from ./boost/boost/chrono/detail/inlined/chrono.hpp:13, from boost/libs/chrono/src/chrono.cpp:14: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/chrono/config.hpp:15, from ./boost/boost/chrono/detail/inlined/process_cpu_clocks.hpp:15, from boost/libs/chrono/src/process_cpu_clocks.cpp:17: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/chrono/config.hpp:15, from ./boost/boost/chrono/detail/inlined/thread_clock.hpp:14, from boost/libs/chrono/src/thread_clock.cpp:18: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/MemoryIndex.cpp:26: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/MemoryIndex.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/common/MemoryIndex.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/checked_delete.hpp:15, from ./boost/boost/smart_ptr/shared_ptr.hpp:26, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::MemoryIndex::Impl]': ./boost/boost/smart_ptr/detail/shared_count.hpp:134:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::MemoryIndex::Impl]' ./boost/boost/smart_ptr/shared_ptr.hpp:271:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, boost::detail::shared_count&) [with T = pwiz::data::MemoryIndex::Impl; Y = pwiz::data::MemoryIndex::Impl]' ./boost/boost/smart_ptr/shared_ptr.hpp:349:44: required from 'boost::shared_ptr::shared_ptr(Y*) [with Y = pwiz::data::MemoryIndex::Impl; T = pwiz::data::MemoryIndex::Impl]' pwiz/data/common/MemoryIndex.cpp:73:58: required from here ./boost/boost/core/checked_delete.hpp:34:5: warning: deleting object of polymorphic class type 'pwiz::data::MemoryIndex::Impl' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete x; ^~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/range/iterator_range.hpp:13, from ./boost/boost/range/as_literal.hpp:22, from ./boost/boost/algorithm/string/predicate.hpp:19, from pwiz/data/common/CVTranslator.cpp:28: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/CVTranslator.cpp:29: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/common/CVTranslator.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)': pwiz/data/common/CVTranslator.cpp:133:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses] return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ pwiz/data/common/CVTranslator.cpp:135:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ pwiz/data/common/CVTranslator.cpp:136:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from pwiz/data/common/cv.cpp:24765: pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)': pwiz/data/common/cv.inl:102:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int o=0;o: note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/ParamTypes.cpp:28: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/common/ParamTypes.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/spirit/home/karma/string.hpp:13, from ./boost/boost/spirit/home/karma.hpp:14, from ./boost/boost/spirit/include/karma.hpp:16, from pwiz/data/common/ParamTypes.cpp:29: ./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const': ./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs] extracted_string_type; ^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/BinaryIndexStream.cpp:26: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/BinaryIndexStream.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/common/BinaryIndexStream.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from pwiz/data/common/BinaryIndexStream.cpp:27: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from pwiz/data/common/BinaryIndexStream.cpp:27: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ In file included from ./boost/boost/checked_delete.hpp:15, from ./boost/boost/smart_ptr/shared_ptr.hpp:26, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::BinaryIndexStream::Impl]': ./boost/boost/smart_ptr/detail/shared_count.hpp:134:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl]' ./boost/boost/smart_ptr/shared_ptr.hpp:271:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, boost::detail::shared_count&) [with T = pwiz::data::BinaryIndexStream::Impl; Y = pwiz::data::BinaryIndexStream::Impl]' ./boost/boost/smart_ptr/shared_ptr.hpp:349:44: required from 'boost::shared_ptr::shared_ptr(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl; T = pwiz::data::BinaryIndexStream::Impl]' pwiz/data/common/BinaryIndexStream.cpp:402:103: required from here ./boost/boost/core/checked_delete.hpp:34:5: warning: deleting object of polymorphic class type 'pwiz::data::BinaryIndexStream::Impl' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete x; ^~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from pwiz/data/common/diff_std.cpp:27: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost_aux/boost/enum/iterator.hpp:18, from ./boost_aux/boost/enum.hpp:18, from pwiz/data/common/Unimod.hpp:31, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost_aux/boost/enum/bitfield.hpp:22, from ./boost_aux/boost/enum.hpp:20, from pwiz/data/common/Unimod.hpp:31, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/common/Unimod.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/function/detail/maybe_include.hpp:23, from ./boost/boost/function/detail/function_iterate.hpp:14, from ./boost/boost/preprocessor/iteration/detail/iter/forward1.hpp:57, from ./boost/boost/function.hpp:64, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost_aux/boost/enum/bitfield.hpp:22, from ./boost_aux/boost/enum.hpp:20, from pwiz/data/common/Unimod.hpp:31, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/function/function_template.hpp: In instantiation of 'void boost::detail::function::basic_vtable2::assign_functor(FunctionObj, boost::detail::function::function_buffer&, mpl_::true_) const [with FunctionObj = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >; mpl_::true_ = mpl_::bool_]': ./boost/boost/function/function_template.hpp:608:13: required from 'bool boost::detail::function::basic_vtable2::assign_to(FunctionObj, boost::detail::function::function_buffer&, boost::detail::function::function_obj_tag) const [with FunctionObj = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:498:45: required from 'bool boost::detail::function::basic_vtable2::assign_to(F, boost::detail::function::function_buffer&) const [with F = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:942:7: required from 'void boost::function2::assign_to(Functor) [with Functor = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:728:7: required from 'boost::function2::function2(Functor, typename boost::enable_if_c::value>::value, int>::type) [with Functor = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >; typename boost::enable_if_c::value>::value, int>::type = int]' ./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36: required from 'boost::algorithm::detail::find_iterator_base::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::token_finderF; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/find_iterator.hpp:265:29: required from 'boost::algorithm::split_iterator::split_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::token_finderF; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/iter_find.hpp:170:21: required from 'SequenceSequenceT& boost::algorithm::iter_split(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector >; RangeT = const std::__cxx11::basic_string; FinderT = boost::algorithm::detail::token_finderF]' ./boost/boost/algorithm/string/split.hpp:146:50: required from 'SequenceSequenceT& boost::algorithm::split(SequenceSequenceT&, RangeT&, PredicateT, boost::algorithm::token_compress_mode_type) [with SequenceSequenceT = std::vector >; RangeT = const std::__cxx11::basic_string; PredicateT = boost::algorithm::detail::is_classifiedF]' pwiz/data/common/Unimod.cpp:129:71: required from here ./boost/boost/function/function_template.hpp:572:49: warning: placement new constructing an object of type 'boost::algorithm::detail::token_finderF' and size '12' in a region of type 'char' and size '1' [-Wplacement-new=] new (reinterpret_cast(&functor.data)) FunctionObj(f); ~~~~~~~~^~~~ In file included from ./boost/boost/function/detail/prologue.hpp:17, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost_aux/boost/enum/bitfield.hpp:22, from ./boost_aux/boost/enum.hpp:20, from pwiz/data/common/Unimod.hpp:31, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/function/function_base.hpp: In instantiation of 'static void boost::detail::function::functor_manager_common::manage_small(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::token_finderF]': ./boost/boost/function/function_base.hpp:364:56: required from 'static void boost::detail::function::functor_manager::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, mpl_::true_) [with Functor = boost::algorithm::detail::token_finderF; mpl_::true_ = mpl_::bool_]' ./boost/boost/function/function_base.hpp:412:18: required from 'static void boost::detail::function::functor_manager::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, boost::detail::function::function_obj_tag) [with Functor = boost::algorithm::detail::token_finderF]' ./boost/boost/function/function_base.hpp:440:20: required from 'static void boost::detail::function::functor_manager::manage(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::token_finderF]' ./boost/boost/function/function_template.hpp:940:13: required from 'void boost::function2::assign_to(Functor) [with Functor = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:728:7: required from 'boost::function2::function2(Functor, typename boost::enable_if_c::value>::value, int>::type) [with Functor = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >; typename boost::enable_if_c::value>::value, int>::type = int]' ./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36: required from 'boost::algorithm::detail::find_iterator_base::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::token_finderF; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/find_iterator.hpp:265:29: required from 'boost::algorithm::split_iterator::split_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::token_finderF; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/iter_find.hpp:170:21: required from 'SequenceSequenceT& boost::algorithm::iter_split(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector >; RangeT = const std::__cxx11::basic_string; FinderT = boost::algorithm::detail::token_finderF]' ./boost/boost/algorithm/string/split.hpp:146:50: required from 'SequenceSequenceT& boost::algorithm::split(SequenceSequenceT&, RangeT&, PredicateT, boost::algorithm::token_compress_mode_type) [with SequenceSequenceT = std::vector >; RangeT = const std::__cxx11::basic_string; PredicateT = boost::algorithm::detail::is_classifiedF]' pwiz/data/common/Unimod.cpp:129:71: required from here ./boost/boost/function/function_base.hpp:318:54: warning: placement new constructing an object of type 'boost::detail::function::functor_manager_common >::functor_type' {aka 'boost::algorithm::detail::token_finderF'} and size '12' in a region of type 'char' and size '1' [-Wplacement-new=] new (reinterpret_cast(&out_buffer.data)) functor_type(*in_functor); ~~~~~~~~~~~^~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/smart_ptr.hpp:19, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32, from pwiz/data/msdata/mz5/Connection_mz5.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/smart_ptr.hpp:19, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/smart_ptr.hpp:19, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/smart_ptr.hpp:19, from ./pwiz/data/msdata/SpectrumWorkerThreads.hpp:27, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_MGF.cpp:28: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumList_MGF.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_MGF.cpp:29: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_MGF.cpp:29: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mzML.cpp:31: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/ChromatogramList_mzML.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/examples.cpp:26: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/examples.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mzML.cpp:33: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Serializer_mzML.cpp:33: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/msdata/Serializer_MSn.cpp:28: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Serializer_MSn.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/msdata/Reader.cpp:27: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Reader.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/msdata/Serializer_MGF.cpp:27: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Serializer_MGF.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/spirit/home/karma/string.hpp:13, from ./boost/boost/spirit/home/karma.hpp:14, from ./boost/boost/spirit/include/karma.hpp:16, from pwiz/data/msdata/Serializer_MGF.cpp:29: ./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const': ./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs] extracted_string_type; ^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:33: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Serializer_mzXML.cpp:34: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mzML.cpp:30: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumList_mzML.cpp:30: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mzML.cpp:32: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mzML.cpp:32: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_MSn.cpp:28: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumList_MSn.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_MSn.cpp:31: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_MSn.cpp:31: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mz5.cpp:29: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mz5.cpp:29: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/range/iterator_range.hpp:13, from ./boost/boost/iostreams/traits.hpp:39, from ./boost/boost/iostreams/pipeline.hpp:18, from ./boost/boost/iostreams/detail/push.hpp:22, from ./boost/boost/iostreams/chain.hpp:29, from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.cpp:30: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.cpp:30: ./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base::push_impl(const T&, std::streamsize, std::streamsize)': ./boost/boost/iostreams/chain.hpp:256:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/bind/bind.hpp:26, from ./boost/boost/bind.hpp:22, from ./boost/boost/iostreams/copy.hpp:26, from pwiz/data/msdata/BinaryDataEncoder.cpp:32: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/BinaryDataEncoder.cpp:38: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::__cxx11::string&, size_t*)': pwiz/data/msdata/BinaryDataEncoder.cpp:280:37: warning: 'byteCount' may be used uninitialized in this function [-Wmaybe-uninitialized] filterArray(byteBuffer, byteCount,compressed); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/BinaryDataEncoder.cpp:280:37: warning: 'byteBuffer' may be used uninitialized in this function [-Wmaybe-uninitialized] "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Diff.cpp:28: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Diff.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/MSData.cpp:26: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/MSData.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/References.cpp:26: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/References.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mzXML.cpp:29: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumList_mzXML.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mzXML.cpp:30: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/msdata/SpectrumList_mzXML.cpp: In constructor 'pwiz::msdata::{anonymous}::SpectrumList_mzXMLImpl::SpectrumList_mzXMLImpl(boost::shared_ptr >, const pwiz::msdata::MSData&, bool)': pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=] } catch (index_not_found e){ ^ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mzXML.cpp:30: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': pwiz/data/msdata/SpectrumList_mzXML.cpp:730:46: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] spectrumIdentity->sourceFilePosition = lexical_cast(text); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': pwiz/data/msdata/SpectrumList_mzXML.cpp:683:22: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] indexOffset_ = lexical_cast(text); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/msdata/IO.cpp:29: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/IO.cpp:30: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerBinaryDataArray::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': pwiz/data/msdata/IO.cpp:1727:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!dataProcessingRef.empty()) ^~ pwiz/data/msdata/IO.cpp:1730:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' getAttribute(attributes, "encodedLength", encodedLength_, NoXMLUnescape); ^~~~~~~~~~~~ pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': pwiz/data/msdata/IO.cpp:2020:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses] else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': pwiz/data/msdata/IO.cpp:2731:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_BTDX.cpp:29: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumList_BTDX.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_BTDX.cpp:30: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_BTDX.cpp:30: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumInfo.cpp:29: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumInfo.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:27: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/RAMPAdapter.cpp:31: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/RAMPAdapter.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)', inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:283:25: pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation] strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)', inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:284:25: pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation] strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)', inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:285:25: pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation] strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)', inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:286:25: pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation] strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/LegacyAdapter.cpp:31: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/LegacyAdapter.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumIterator.cpp:29: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumIterator.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::equal(const pwiz::msdata::SpectrumIterator::Impl&) const': pwiz/data/msdata/SpectrumIterator.cpp:125:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] return (done() && &that.spectrumList_==&pastEndMarker_ || ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses] &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::done() const': pwiz/data/msdata/SpectrumIterator.cpp:141:34: warning: suggest parentheses around '&&' within '||' [-Wparentheses] return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() || ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:36: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/MSDataFile.cpp:37: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from ./boost/boost/iostreams/filtering_stream.hpp:22, from pwiz/data/msdata/MSDataFile.cpp:41: ./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base::push_impl(const T&, std::streamsize, std::streamsize)': ./boost/boost/iostreams/chain.hpp:256:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] } else if (init == mask) { ~~~~~^~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/bind/bind.hpp:26, from ./boost/boost/bind.hpp:22, from ./boost/boost/multi_index/sequenced_index.hpp:49, from ./pwiz/utility/misc/mru_list.hpp:30, from pwiz/data/msdata/MemoryMRUCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.hpp:28, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumListCache.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Index_mzML.cpp:25: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Index_mzML.cpp:25: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:28: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:28: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:30: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/IdentDataFile.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from ./boost/boost/iostreams/filtering_stream.hpp:22, from pwiz/data/identdata/IdentDataFile.cpp:34: ./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base::push_impl(const T&, std::streamsize, std::streamsize)': ./boost/boost/iostreams/chain.hpp:256:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/identdata/Reader.cpp:27: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/Reader.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/Serializer_protXML.cpp:31: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/Serializer_protXML.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/identdata/Serializer_protXML.cpp: In constructor 'pwiz::identdata::{anonymous}::Handler_protXML::Handler_protXML(pwiz::identdata::IdentData&, const pwiz::util::IterationListenerRegistry*, bool, std::vector >*)': pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: 'pwiz::identdata::{anonymous}::Handler_protXML::strict' will be initialized after [-Wreorder] bool strict; ^~~~~~ pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning: 'int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides' [-Wreorder] int nPeptides; ^~~~~~~~~ pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning: when initialized here [-Wreorder] Handler_protXML(IdentData& mzid, ^~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/Serializer_pepXML.cpp:28: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/Serializer_pepXML.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp: In function 'void pwiz::identdata::{anonymous}::write_spectrum_queries(pwiz::minimxml::XMLWriter&, const pwiz::identdata::IdentData&, const string&, const pwiz::util::IterationListenerRegistry*)': pwiz/data/identdata/Serializer_pepXML.cpp:800:52: warning: 'lastSpectrumIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] if (sii.chargeState != lastChargeState || spectrumIndex != lastSpectrumIndex) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/Serializer_mzid.cpp:30: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/Serializer_mzid.cpp:30: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/identdata/IO.cpp:30: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/IO.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/References.cpp:27: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/References.cpp:27: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/identdata/References.cpp: In function 'void pwiz::identdata::References::resolve(std::vector >&, pwiz::identdata::IdentData&)': pwiz/data/identdata/References.cpp:148:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] else if (dynamic_cast(c.get())) ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/proteome/Modification.cpp:30: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/proteome/Modification.cpp:30: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/proteome/Modification.cpp:30: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/proteome/Modification.cpp:89:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr formula_; ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/proteome/Digestion.cpp:32: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/proteome/Digestion.cpp:32: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/proteome/Digestion.cpp:32: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/function/detail/maybe_include.hpp:23, from ./boost/boost/function/detail/function_iterate.hpp:14, from ./boost/boost/preprocessor/iteration/detail/iter/forward1.hpp:57, from ./boost/boost/function.hpp:64, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/proteome/Digestion.cpp:32: ./boost/boost/function/function_template.hpp: In instantiation of 'void boost::detail::function::basic_vtable2::assign_functor(FunctionObj, boost::detail::function::function_buffer&, mpl_::true_) const [with FunctionObj = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >; mpl_::true_ = mpl_::bool_]': ./boost/boost/function/function_template.hpp:608:13: required from 'bool boost::detail::function::basic_vtable2::assign_to(FunctionObj, boost::detail::function::function_buffer&, boost::detail::function::function_obj_tag) const [with FunctionObj = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:498:45: required from 'bool boost::detail::function::basic_vtable2::assign_to(F, boost::detail::function::function_buffer&) const [with F = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:942:7: required from 'void boost::function2::assign_to(Functor) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:728:7: required from 'boost::function2::function2(Functor, typename boost::enable_if_c::value>::value, int>::type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >; typename boost::enable_if_c::value>::value, int>::type = int]' ./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36: required from 'boost::algorithm::detail::find_iterator_base::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/find_iterator.hpp:100:26: required from 'boost::algorithm::find_iterator::find_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/iter_find.hpp:100:21: required from 'SequenceSequenceT& boost::algorithm::iter_find(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector > > >; RangeT = const std::__cxx11::basic_string; FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>]' ./boost/boost/algorithm/string/split.hpp:67:49: required from 'SequenceSequenceT& boost::algorithm::find_all(SequenceSequenceT&, Range1T&, const Range2T&) [with SequenceSequenceT = std::vector > > >; Range1T = const std::__cxx11::basic_string; Range2T = std::__cxx11::basic_string]' pwiz/data/proteome/Digestion.cpp:472:63: required from here ./boost/boost/function/function_template.hpp:572:49: warning: placement new constructing an object of type 'boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>' and size '12' in a region of type 'char' and size '1' [-Wplacement-new=] new (reinterpret_cast(&functor.data)) FunctionObj(f); ~~~~~~~~^~~~ In file included from ./boost/boost/function/detail/prologue.hpp:17, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/proteome/Digestion.cpp:32: ./boost/boost/function/function_base.hpp: In instantiation of 'static void boost::detail::function::functor_manager_common::manage_small(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>]': ./boost/boost/function/function_base.hpp:364:56: required from 'static void boost::detail::function::functor_manager::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, mpl_::true_) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; mpl_::true_ = mpl_::bool_]' ./boost/boost/function/function_base.hpp:412:18: required from 'static void boost::detail::function::functor_manager::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, boost::detail::function::function_obj_tag) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>]' ./boost/boost/function/function_base.hpp:440:20: required from 'static void boost::detail::function::functor_manager::manage(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>]' ./boost/boost/function/function_template.hpp:940:13: required from 'void boost::function2::assign_to(Functor) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:728:7: required from 'boost::function2::function2(Functor, typename boost::enable_if_c::value>::value, int>::type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >; typename boost::enable_if_c::value>::value, int>::type = int]' ./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36: required from 'boost::algorithm::detail::find_iterator_base::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/find_iterator.hpp:100:26: required from 'boost::algorithm::find_iterator::find_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/iter_find.hpp:100:21: required from 'SequenceSequenceT& boost::algorithm::iter_find(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector > > >; RangeT = const std::__cxx11::basic_string; FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>]' ./boost/boost/algorithm/string/split.hpp:67:49: required from 'SequenceSequenceT& boost::algorithm::find_all(SequenceSequenceT&, Range1T&, const Range2T&) [with SequenceSequenceT = std::vector > > >; Range1T = const std::__cxx11::basic_string; Range2T = std::__cxx11::basic_string]' pwiz/data/proteome/Digestion.cpp:472:63: required from here ./boost/boost/function/function_base.hpp:318:54: warning: placement new constructing an object of type 'boost::detail::function::functor_manager_common >, boost::algorithm::is_equal> >::functor_type' {aka 'boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>'} and size '12' in a region of type 'char' and size '1' [-Wplacement-new=] new (reinterpret_cast(&out_buffer.data)) functor_type(*in_functor); ~~~~~~~~~~~^~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/proteome/Peptide.cpp:31: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/proteome/Peptide.cpp:31: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/proteome/Peptide.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:27: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/proteome/AminoAcid.cpp:27: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/proteome/AminoAcid.cpp:27: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/minimxml/XMLWriter.cpp:26: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/minimxml/XMLWriter.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from ./boost/boost/iostreams/filtering_stream.hpp:22, from pwiz/utility/minimxml/XMLWriter.cpp:27: ./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base::push_impl(const T&, std::streamsize, std::streamsize)': ./boost/boost/iostreams/chain.hpp:256:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/spirit/home/karma/string.hpp:13, from ./boost/boost/spirit/home/karma.hpp:14, from ./boost/boost/spirit/include/karma.hpp:16, from pwiz/utility/minimxml/XMLWriter.cpp:29: ./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const': ./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs] extracted_string_type; ^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:29: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, pwiz::minimxml::SAXParser::Handler&)': pwiz/utility/minimxml/SAXParser.cpp:431:20: warning: offset '1' outside bounds of constant string [-Warray-bounds] PWIZ_API_DECL void parse(istream& is, Handler& handler) ^~~~~ pwiz/utility/minimxml/SAXParser.cpp:517:17: warning: 'inCDATA' may be used uninitialized in this function [-Wmaybe-uninitialized] if (inCDATA) ^~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/Chemistry.cpp:28: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/Chemistry.cpp:28: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/chemistry/Chemistry.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const': pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses] return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/MSIHandler.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/MSIHandler.cpp:25: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/MSIHandler.cpp:25: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/algorithm/string/std_containers_traits.hpp:18, from ./boost/boost/algorithm/string.hpp:18, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition pwiz/utility/misc/Filesystem.cpp:39: warning: "_WIN32_WINNT" redefined #define _WIN32_WINNT 0x0400 In file included from C:/rtools40/mingw32/i686-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw32/i686-w64-mingw32/include/wchar.h:9, from C:/rtools40/mingw32/include/c++/8.3.0/cwchar:44, from C:/rtools40/mingw32/include/c++/8.3.0/bits/postypes.h:40, from C:/rtools40/mingw32/include/c++/8.3.0/bits/char_traits.h:40, from C:/rtools40/mingw32/include/c++/8.3.0/string:40, from pwiz/utility/misc/String.hpp:27, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw32/i686-w64-mingw32/include/_mingw.h:225: note: this is the location of the previous definition #define _WIN32_WINNT 0x502 In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/range/iterator_range.hpp:13, from ./boost/boost/range/as_literal.hpp:22, from ./boost/boost/algorithm/string/trim.hpp:19, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/TabReader.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/TabReader.cpp:25: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/TabReader.cpp:25: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/static_assert.hpp:17, from pwiz/utility/misc/endian.hpp:28, from pwiz/utility/misc/SHA1.cpp:10: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/filesystem/path.hpp:28, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/interprocess/errors.hpp:41, from ./boost/boost/interprocess/exceptions.hpp:24, from ./boost/boost/interprocess/file_mapping.hpp:30, from pwiz/utility/misc/SHA1.cpp:20: ./boost_aux/boost/interprocess/detail/win32_api.hpp: In instantiation of 'static void* boost::interprocess::winapi::function_address_holder::get(unsigned int) [with int Dummy = 0]': ./boost_aux/boost/interprocess/detail/win32_api.hpp:1617:20: required from here ./boost_aux/boost/interprocess/detail/win32_api.hpp:1544:31: warning: invalid conversion from 'boost::interprocess::winapi::farproc_t' {aka 'int (__attribute__((stdcall)) *)()'} to 'void*' [-fpermissive] return FunctionAddresses[id]; ~~~~~~~~~~~~~~~~~^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/static_assert.hpp:17, from pwiz/utility/misc/endian.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/SHA1Calculator.cpp:33: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/SHA1Calculator.cpp:33: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/SHA1Calculator.cpp:33: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/algorithm/string/replace.hpp:16, from ./boost/boost/date_time/date_facet.hpp:17, from ./boost/boost/date_time/gregorian/gregorian_io.hpp:16, from ./boost/boost/date_time/gregorian/gregorian.hpp:31, from ./boost/boost/date_time/posix_time/time_formatters.hpp:12, from ./boost/boost/date_time/posix_time/posix_time.hpp:24, from ./boost/boost/date_time/local_time/local_time.hpp:11, from pwiz/utility/misc/DateTime.hpp:25, from pwiz/utility/misc/unit.hpp:29, from pwiz/utility/misc/sha1calc.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/unit.hpp:30, from pwiz/utility/misc/sha1calc.cpp:25: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/sha1calc.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c random_access_gzFile.cpp -o random_access_gzFile.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from random_access_gzFile.h:21, from random_access_gzFile.cpp:21: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/filesystem/config.hpp:28, from boost/libs/filesystem/src/path_traits.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/filesystem/config.hpp:28, from boost/libs/filesystem/src/windows_file_codecvt.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/filesystem/config.hpp:28, from boost/libs/filesystem/src/codecvt_error_category.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/thread/src/win32/tss_pe.cpp -o boost/libs/thread/src/win32/tss_pe.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/thread/detail/config.hpp:11, from boost/libs/thread/src/win32/tss_pe.cpp:10: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/thread/src/win32/tss_dll.cpp -o boost/libs/thread/src/win32/tss_dll.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/thread/detail/config.hpp:11, from boost/libs/thread/src/win32/tss_dll.cpp:6: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/thread/src/win32/thread.cpp -o boost/libs/thread/src/win32/thread.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/thread/detail/platform.hpp:14, from ./boost/boost/thread/thread_only.hpp:12, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/bind/bind.hpp:26, from ./boost/boost/bind.hpp:22, from ./boost/boost/thread/detail/thread.hpp:30, from ./boost/boost/thread/thread_only.hpp:22, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/ramp/wglob.cpp -o pwiz/data/msdata/ramp/wglob.o pwiz/data/msdata/ramp/wglob.cpp: In function 'int glob(const char*, int, int*, glob_t*)': pwiz/data/msdata/ramp/wglob.cpp:63:9: warning: unused variable 'fileList' [-Wunused-variable] char** fileList= NULL; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_aux/boost/nowide/iostream.cpp -o boost_aux/boost/nowide/iostream.o In file included from ./boost/boost/config.hpp:57, from ./boost_aux/boost/nowide/config.hpp:11, from ./boost_aux/boost/nowide/iostream.hpp:11, from boost_aux/boost/nowide/iostream.cpp:9: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/iostream.hpp:12, from boost_aux/boost/nowide/iostream.cpp:9: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/iostream.hpp:12, from boost_aux/boost/nowide/iostream.cpp:9: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ boost_aux/boost/nowide/iostream.cpp: In member function 'virtual int boost::nowide::details::console_input_buffer::underflow()': boost_aux/boost/nowide/iostream.cpp:189:13: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized] if(c==uf::incomplete) { ^~ boost_aux/boost/nowide/iostream.cpp:178:28: note: 'c' was declared here uf::code_point c; ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rampR.cpp -o rampR.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from random_access_gzFile.h:21, from ramp.h:72, from rampR.cpp:15: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./pwiz/data/msdata/ramp/wglob.o ./boost_aux/boost/nowide/iostream.o rampR.o -lpthread -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -lws2_32 -lz -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/mzR.buildbin-libdir/00LOCK-mzR/00new/mzR/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'mzR' finding HTML links ... done copyWriteMSData html isolationWindow-methods html metadata html mzR-class html finding level-2 HTML links ... done openMSfile html peaks html pwiz-version html writeMSData html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'mzR' ... ** libs rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./pwiz/data/msdata/ramp/wglob.o ./boost_aux/boost/nowide/iostream.o rampR.o find . -name \*~ -exec rm {} \; ## from cleanup find . -name \*.o -exec rm {} \; ## from cleanup find . -name "#*#" -exec rm {} \; ## from cleanup "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cramp.cpp -o cramp.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from random_access_gzFile.h:21, from ramp.h:72, from cramp.h:33, from cramp.cpp:49: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from cramp.cpp:49: cramp.h: In copy constructor 'rampScanInfo::rampScanInfo(rampScanInfo&)': cramp.h:261:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampScanInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(this,&rhs,sizeof(rhs)); ^ In file included from cramp.cpp:49: cramp.h:251:7: note: 'class rampScanInfo' declared here class rampScanInfo: public rampInfo ^~~~~~~~~~~~ In file included from cramp.cpp:49: cramp.h: In copy constructor 'rampRunInfo::rampRunInfo(const rampRunInfo&)': cramp.h:315:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampRunInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(this,&rhs,sizeof(rhs)); ^ cramp.h:305:7: note: 'class rampRunInfo' declared here class rampRunInfo: public rampInfo ^~~~~~~~~~~ In file included from cramp.cpp:49: cramp.h: In constructor 'cRamp::cRamp(const char*, bool)': cramp.h:149:10: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder] bool m_declaredScansOnly; // if true, suppress RAMP's habit of adding scans to fill in between declared scans ^~~~~~~~~~~~~~~~~~~ cramp.h:148:18: warning: 'rampRunInfo* cRamp::m_runInfo' [-Wreorder] rampRunInfo *m_runInfo; // scan count etc ^~~~~~~~~ cramp.cpp:72:1: warning: when initialized here [-Wreorder] cRamp::cRamp( const char* fileName,bool declaredScansOnly ) : ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ramp_base64.cpp -o ramp_base64.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ramp.cpp -o ramp.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from random_access_gzFile.h:21, from ramp.h:72, from ramp.cpp:44: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/msdata/RAMPAdapter.hpp:30, from ramp.cpp:60: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from ramp.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)': ramp.cpp:248:23: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(buf,sizeof(buf)-1,result); ^~~~ ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)': ramp.cpp:451:12: warning: unused variable 'nread' [-Wunused-variable] size_t nread = ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI); ^~~~~ ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)': ramp.cpp:650:31: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(buf, SIZE_BUF, pFI); ^~~~ ramp.cpp:692:31: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(buf, SIZE_BUF, pFI); ^~~~ ramp.cpp:729:27: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(buf, SIZE_BUF, pFI); ^~~~ ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)': ramp.cpp:1446:27: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)': ramp.cpp:1532:15: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp:1528:11: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)': ramp.cpp:2090:28: warning: unused variable 'nread' [-Wunused-variable] size_t nread = ramp_fread(pData+partial,(int)(peaksLen-partial), pFI); ^~~~~ ramp.cpp:2293:27: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(buf, sizeof(buf)-1 , pFI); ^~~~ ramp.cpp:2340:24: warning: unused variable 'nread' [-Wunused-variable] size_t nread = ramp_fread(pData+partial,peaksLen-partial, pFI); ^~~~~ ramp.cpp:2394:21: warning: variable 'err' set but not used [-Wunused-but-set-variable] int err; ^~~ ramp.cpp:2212:19: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(buf, sizeof(buf)-1, pFI); ^~~~ ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)': ramp.cpp:2520:15: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp:2544:15: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp:2516:11: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)': ramp.cpp:2695:19: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp:2731:19: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp:2682:11: warning: unused variable 'fgot' [-Wunused-variable] char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI); ^~~~ ramp.cpp: In function 'int rampSelfTest(char*)': ramp.cpp:2799:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation] strncpy(buf,testname[i],sizeof(buf)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ramp.cpp:2812:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation] strncpy(buf,filename,sizeof(buf)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ ramp.cpp:2816:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 256 equals destination size [-Wstringop-truncation] strncpy(buf,filename,sizeof(buf)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppRamp.cpp -o RcppRamp.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from random_access_gzFile.h:21, from ramp.h:72, from cramp.h:33, from RcppRamp.h:14, from RcppRamp.cpp:1: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from RcppRamp.h:14, from RcppRamp.cpp:1: cramp.h: In copy constructor 'rampScanInfo::rampScanInfo(rampScanInfo&)': cramp.h:261:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampScanInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(this,&rhs,sizeof(rhs)); ^ In file included from RcppRamp.h:14, from RcppRamp.cpp:1: cramp.h:251:7: note: 'class rampScanInfo' declared here class rampScanInfo: public rampInfo ^~~~~~~~~~~~ In file included from RcppRamp.h:14, from RcppRamp.cpp:1: cramp.h: In copy constructor 'rampRunInfo::rampRunInfo(const rampRunInfo&)': cramp.h:315:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampRunInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(this,&rhs,sizeof(rhs)); ^ cramp.h:305:7: note: 'class rampRunInfo' declared here class rampRunInfo: public rampInfo ^~~~~~~~~~~ RcppRamp.cpp: In member function 'Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo()': RcppRamp.cpp:215:27: warning: unused variable 'info' [-Wunused-variable] rampScanInfo *info = ramp->getScanHeaderInfo( 1 ); ^~~~ RcppRamp.cpp: In member function 'Rcpp::NumericMatrix RcppRamp::get3DMap(std::vector, double, double, double)': RcppRamp.cpp:388:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < scanNumbers.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppRampModule.cpp -o RcppRampModule.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from random_access_gzFile.h:21, from ramp.h:72, from cramp.h:33, from RcppRamp.h:14, from RcppRampModule.cpp:2: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from RcppRamp.h:14, from RcppRampModule.cpp:2: cramp.h: In copy constructor 'rampScanInfo::rampScanInfo(rampScanInfo&)': cramp.h:261:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampScanInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(this,&rhs,sizeof(rhs)); ^ In file included from RcppRamp.h:14, from RcppRampModule.cpp:2: cramp.h:251:7: note: 'class rampScanInfo' declared here class rampScanInfo: public rampInfo ^~~~~~~~~~~~ In file included from RcppRamp.h:14, from RcppRampModule.cpp:2: cramp.h: In copy constructor 'rampRunInfo::rampRunInfo(const rampRunInfo&)': cramp.h:315:38: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class rampRunInfo' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(this,&rhs,sizeof(rhs)); ^ cramp.h:305:7: note: 'class rampRunInfo' declared here class rampRunInfo: public rampInfo ^~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppPwiz.cpp -o RcppPwiz.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from RcppPwiz.h:12, from RcppPwiz.cpp:1: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Std.hpp:31, from RcppPwiz.h:20, from RcppPwiz.cpp:1: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from pwiz/utility/misc/Std.hpp:32, from RcppPwiz.h:20, from RcppPwiz.cpp:1: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from ./boost/boost/iostreams/filtering_stream.hpp:22, from RcppPwiz.h:23, from RcppPwiz.cpp:1: ./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base::push_impl(const T&, std::streamsize, std::streamsize)': ./boost/boost/iostreams/chain.hpp:256:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwiz.h:4, from RcppPwiz.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getScanHeaderInfo(Rcpp::IntegerVector)': RcppPwiz.cpp:133:9: warning: unused variable 'N' [-Wunused-variable] int N = slp->size(); ^ RcppPwiz.cpp: In member function 'void RcppPwiz::addSpectrumList(pwiz::msdata::MSData&, Rcpp::DataFrame&, Rcpp::List&, bool)': RcppPwiz.cpp:745:29: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] if (precursorScanNum[i] > 0 | precursorMZ[i] > 0) { RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)': RcppPwiz.cpp:820:49: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) { ~~~~~~~~~~~^~~~~~~~~~~~~ RcppPwiz.cpp:830:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < pairs.size(); i++) { ~~^~~~~~~~~~~~~~ RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo(Rcpp::IntegerVector)': RcppPwiz.cpp:850:10: warning: unused variable 'nativeIdFormat_' [-Wunused-variable] CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd); ^~~~~~~~~~~~~~~ RcppPwiz.cpp: In member function 'Rcpp::NumericMatrix RcppPwiz::get3DMap(std::vector, double, double, double)': RcppPwiz.cpp:981:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < scanNumbers.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~ RcppPwiz.cpp:987:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int k=0; k < pairs.size(); k++) ~~^~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppPwizModule.cpp -o RcppPwizModule.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from RcppPwiz.h:11, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from RcppPwiz.h:12, from RcppPwizModule.cpp:2: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Std.hpp:31, from RcppPwiz.h:20, from RcppPwizModule.cpp:2: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from pwiz/utility/misc/Std.hpp:32, from RcppPwiz.h:20, from RcppPwizModule.cpp:2: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from ./boost/boost/iostreams/filtering_stream.hpp:22, from RcppPwiz.h:23, from RcppPwizModule.cpp:2: ./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base::push_impl(const T&, std::streamsize, std::streamsize)': ./boost/boost/iostreams/chain.hpp:256:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppPwizModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppIdent.cpp -o RcppIdent.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdent.cpp:1: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Std.hpp:31, from RcppIdent.h:14, from RcppIdent.cpp:1: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from pwiz/utility/misc/Std.hpp:32, from RcppIdent.h:14, from RcppIdent.cpp:1: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdent.h:4, from RcppIdent.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ RcppIdent.cpp: In member function 'Rcpp::DataFrame RcppIdent::getScore()': RcppIdent.cpp:293:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] for (size_t j = 0; j < nCvParams; j++) { ~~^~~~~~~~~~~ RcppIdent.cpp: In member function 'Rcpp::List RcppIdent::getPara()': RcppIdent.cpp:382:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i = 0 ; i < sip[0]->additionalSearchParams.cvParams.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RcppIdent.cpp:388:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppIdentModule.cpp -o RcppIdentModule.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/IdentDataFile.hpp:29, from RcppIdent.h:11, from RcppIdentModule.cpp:2: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Std.hpp:31, from RcppIdent.h:14, from RcppIdentModule.cpp:2: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from pwiz/utility/misc/Std.hpp:32, from RcppIdent.h:14, from RcppIdentModule.cpp:2: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:27, from RcppIdentModule.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/system/config.hpp:13, from ./boost/boost/system/error_code.hpp:14, from boost/libs/system/src/error_code.cpp:16: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/posix_api.cpp:21: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/posix_api.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/fileiter.cpp -o boost/libs/regex/src/fileiter.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/fileiter.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from boost/libs/regex/src/fileiter.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from boost/libs/regex/src/fileiter.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex_raw_buffer.cpp -o boost/libs/regex/src/regex_raw_buffer.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/regex_raw_buffer.cpp:21: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/cregex.cpp -o boost/libs/regex/src/cregex.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from ./boost/boost/regex.hpp:28, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/cregex.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from boost/libs/regex/src/regex_debug.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/instances.cpp -o boost/libs/regex/src/instances.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from boost/libs/regex/src/instances.cpp:21: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/icu.cpp -o boost/libs/regex/src/icu.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from boost/libs/regex/src/icu.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/usinstances.cpp -o boost/libs/regex/src/usinstances.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/detail/workaround.hpp:41, from boost/libs/regex/src/usinstances.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/regex.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/regex.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from boost/libs/regex/src/wide_posix_api.cpp:21: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex.hpp:32, from ./boost/boost/regex.hpp:31, from boost/libs/regex/src/wide_posix_api.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/regex_traits_defaults.cpp -o boost/libs/regex/src/regex_traits_defaults.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from ./boost/boost/regex/regex_traits.hpp:23, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/regex_traits_defaults.cpp:20: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/winstances.cpp -o boost/libs/regex/src/winstances.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from boost/libs/regex/src/winstances.cpp:21: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/wc_regex_traits.cpp -o boost/libs/regex/src/wc_regex_traits.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/detail/workaround.hpp:41, from boost/libs/regex/src/wc_regex_traits.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/wc_regex_traits.cpp:76: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from boost/libs/regex/src/wc_regex_traits.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/c_regex_traits.cpp -o boost/libs/regex/src/c_regex_traits.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/c_regex_traits.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/c_regex_traits.hpp:26, from boost/libs/regex/src/c_regex_traits.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/cpp_regex_traits.cpp -o boost/libs/regex/src/cpp_regex_traits.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/cpp_regex_traits.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/regex/v4/regex_workaround.hpp:43, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/regex/v4/regex_workaround.hpp:41, from ./boost/boost/regex/v4/regex_traits.hpp:26, from ./boost/boost/regex/regex_traits.hpp:27, from boost/libs/regex/src/cpp_regex_traits.cpp:22: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o In file included from ./boost/boost/config.hpp:57, from boost/libs/regex/src/static_mutex.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/regex/src/w32_regex_traits.cpp -o boost/libs/regex/src/w32_regex_traits.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/regex/config.hpp:43, from boost/libs/regex/src/w32_regex_traits.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/range/iterator_range.hpp:13, from ./boost/boost/iostreams/traits.hpp:39, from ./boost/boost/iostreams/detail/dispatch.hpp:17, from ./boost/boost/iostreams/read.hpp:19, from ./boost/boost/iostreams/detail/buffer.hpp:20, from ./boost/boost/iostreams/filter/symmetric.hpp:49, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/filter/symmetric.hpp:60, from ./boost/boost/iostreams/filter/zlib.hpp:31, from boost/libs/iostreams/src/zlib.cpp:19: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/iostreams/filter/zlib.hpp:20, from boost/libs/iostreams/src/zlib.cpp:19: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o In file included from ./boost/boost/config.hpp:57, from boost/libs/iostreams/src/file_descriptor.cpp:16: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from boost/libs/iostreams/src/file_descriptor.cpp:23: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ./boost/boost/iostreams/device/file_descriptor.hpp:27, from boost/libs/iostreams/src/file_descriptor.cpp:23: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/filesystem/operations.hpp:18, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/filesystem/path.hpp:28, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from ./boost/boost/filesystem/operations.hpp:25, from boost/libs/filesystem/src/operations.cpp:44: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o In file included from ./boost/boost/config.hpp:57, from boost/libs/filesystem/src/path.cpp:12: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/filesystem/path.hpp:28, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from boost/libs/filesystem/src/path.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/filesystem/path_traits.hpp:29, from ./boost/boost/filesystem/path.hpp:25, from boost/libs/filesystem/src/path.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/filesystem/config.hpp:28, from boost/libs/filesystem/src/utf8_codecvt_facet.cpp:15: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/chrono/config.hpp:15, from ./boost/boost/chrono/duration.hpp:33, from ./boost/boost/chrono/chrono.hpp:11, from ./boost/boost/chrono/detail/inlined/chrono.hpp:13, from boost/libs/chrono/src/chrono.cpp:14: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/chrono/config.hpp:15, from ./boost/boost/chrono/detail/inlined/process_cpu_clocks.hpp:15, from boost/libs/chrono/src/process_cpu_clocks.cpp:17: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/chrono/config.hpp:15, from ./boost/boost/chrono/detail/inlined/thread_clock.hpp:14, from boost/libs/chrono/src/thread_clock.cpp:18: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/MemoryIndex.cpp:26: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/MemoryIndex.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/common/MemoryIndex.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/checked_delete.hpp:15, from ./boost/boost/smart_ptr/shared_ptr.hpp:26, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/MemoryIndex.hpp:26, from pwiz/data/common/MemoryIndex.cpp:25: ./boost/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::MemoryIndex::Impl]': ./boost/boost/smart_ptr/detail/shared_count.hpp:134:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::MemoryIndex::Impl]' ./boost/boost/smart_ptr/shared_ptr.hpp:271:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, boost::detail::shared_count&) [with T = pwiz::data::MemoryIndex::Impl; Y = pwiz::data::MemoryIndex::Impl]' ./boost/boost/smart_ptr/shared_ptr.hpp:349:44: required from 'boost::shared_ptr::shared_ptr(Y*) [with Y = pwiz::data::MemoryIndex::Impl; T = pwiz::data::MemoryIndex::Impl]' pwiz/data/common/MemoryIndex.cpp:73:58: required from here ./boost/boost/core/checked_delete.hpp:34:5: warning: deleting object of polymorphic class type 'pwiz::data::MemoryIndex::Impl' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete x; ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/range/iterator_range.hpp:13, from ./boost/boost/range/as_literal.hpp:22, from ./boost/boost/algorithm/string/predicate.hpp:19, from pwiz/data/common/CVTranslator.cpp:28: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/CVTranslator.cpp:29: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/common/CVTranslator.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/CVTranslator.hpp:31, from pwiz/data/common/CVTranslator.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)': pwiz/data/common/CVTranslator.cpp:133:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses] return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ pwiz/data/common/CVTranslator.cpp:135:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ pwiz/data/common/CVTranslator.cpp:136:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/common/cv.cpp:34: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/cv.cpp:34: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from pwiz/data/common/cv.cpp:24765: pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)': pwiz/data/common/cv.inl:102:23: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] for (int o=0;o: note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/ParamTypes.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/ParamTypes.cpp:28: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/common/ParamTypes.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/ParamTypes.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/spirit/home/karma/string.hpp:13, from ./boost/boost/spirit/home/karma.hpp:14, from ./boost/boost/spirit/include/karma.hpp:16, from pwiz/data/common/ParamTypes.cpp:29: ./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const': ./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs] extracted_string_type; ^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/common/BinaryIndexStream.cpp:26: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/common/BinaryIndexStream.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/common/BinaryIndexStream.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from pwiz/data/common/BinaryIndexStream.cpp:27: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/data/common/Index.hpp:29, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from pwiz/data/common/BinaryIndexStream.cpp:27: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ In file included from ./boost/boost/checked_delete.hpp:15, from ./boost/boost/smart_ptr/shared_ptr.hpp:26, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/Index.hpp:30, from pwiz/data/common/BinaryIndexStream.hpp:26, from pwiz/data/common/BinaryIndexStream.cpp:25: ./boost/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::BinaryIndexStream::Impl]': ./boost/boost/smart_ptr/detail/shared_count.hpp:134:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl]' ./boost/boost/smart_ptr/shared_ptr.hpp:271:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, boost::detail::shared_count&) [with T = pwiz::data::BinaryIndexStream::Impl; Y = pwiz::data::BinaryIndexStream::Impl]' ./boost/boost/smart_ptr/shared_ptr.hpp:349:44: required from 'boost::shared_ptr::shared_ptr(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl; T = pwiz::data::BinaryIndexStream::Impl]' pwiz/data/common/BinaryIndexStream.cpp:402:103: required from here ./boost/boost/core/checked_delete.hpp:34:5: warning: deleting object of polymorphic class type 'pwiz::data::BinaryIndexStream::Impl' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete x; ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from pwiz/data/common/diff_std.cpp:27: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/common/diff_std.hpp:33, from pwiz/data/common/diff_std.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost_aux/boost/enum/iterator.hpp:18, from ./boost_aux/boost/enum.hpp:18, from pwiz/data/common/Unimod.hpp:31, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost_aux/boost/enum/bitfield.hpp:22, from ./boost_aux/boost/enum.hpp:20, from pwiz/data/common/Unimod.hpp:31, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/common/Unimod.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/common/Unimod.hpp:28, from pwiz/data/common/Unimod.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/function/detail/maybe_include.hpp:23, from ./boost/boost/function/detail/function_iterate.hpp:14, from ./boost/boost/preprocessor/iteration/detail/iter/forward1.hpp:57, from ./boost/boost/function.hpp:64, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost_aux/boost/enum/bitfield.hpp:22, from ./boost_aux/boost/enum.hpp:20, from pwiz/data/common/Unimod.hpp:31, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/function/function_template.hpp: In instantiation of 'void boost::detail::function::basic_vtable2::assign_functor(FunctionObj, boost::detail::function::function_buffer&, mpl_::true_) const [with FunctionObj = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >; mpl_::true_ = mpl_::bool_]': ./boost/boost/function/function_template.hpp:608:13: required from 'bool boost::detail::function::basic_vtable2::assign_to(FunctionObj, boost::detail::function::function_buffer&, boost::detail::function::function_obj_tag) const [with FunctionObj = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:498:45: required from 'bool boost::detail::function::basic_vtable2::assign_to(F, boost::detail::function::function_buffer&) const [with F = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:942:7: required from 'void boost::function2::assign_to(Functor) [with Functor = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:728:7: required from 'boost::function2::function2(Functor, typename boost::enable_if_c::value>::value, int>::type) [with Functor = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >; typename boost::enable_if_c::value>::value, int>::type = int]' ./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36: required from 'boost::algorithm::detail::find_iterator_base::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::token_finderF; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/find_iterator.hpp:265:29: required from 'boost::algorithm::split_iterator::split_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::token_finderF; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/iter_find.hpp:170:21: required from 'SequenceSequenceT& boost::algorithm::iter_split(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector >; RangeT = const std::__cxx11::basic_string; FinderT = boost::algorithm::detail::token_finderF]' ./boost/boost/algorithm/string/split.hpp:146:50: required from 'SequenceSequenceT& boost::algorithm::split(SequenceSequenceT&, RangeT&, PredicateT, boost::algorithm::token_compress_mode_type) [with SequenceSequenceT = std::vector >; RangeT = const std::__cxx11::basic_string; PredicateT = boost::algorithm::detail::is_classifiedF]' pwiz/data/common/Unimod.cpp:129:71: required from here ./boost/boost/function/function_template.hpp:572:49: warning: placement new constructing an object of type 'boost::algorithm::detail::token_finderF' and size '24' in a region of type 'char' and size '1' [-Wplacement-new=] new (reinterpret_cast(&functor.data)) FunctionObj(f); ~~~~~~~~^~~~ In file included from ./boost/boost/function/detail/prologue.hpp:17, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost_aux/boost/enum/bitfield.hpp:22, from ./boost_aux/boost/enum.hpp:20, from pwiz/data/common/Unimod.hpp:31, from pwiz/data/common/Unimod.cpp:25: ./boost/boost/function/function_base.hpp: In instantiation of 'static void boost::detail::function::functor_manager_common::manage_small(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::token_finderF]': ./boost/boost/function/function_base.hpp:364:56: required from 'static void boost::detail::function::functor_manager::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, mpl_::true_) [with Functor = boost::algorithm::detail::token_finderF; mpl_::true_ = mpl_::bool_]' ./boost/boost/function/function_base.hpp:412:18: required from 'static void boost::detail::function::functor_manager::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, boost::detail::function::function_obj_tag) [with Functor = boost::algorithm::detail::token_finderF]' ./boost/boost/function/function_base.hpp:440:20: required from 'static void boost::detail::function::functor_manager::manage(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::token_finderF]' ./boost/boost/function/function_template.hpp:940:13: required from 'void boost::function2::assign_to(Functor) [with Functor = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:728:7: required from 'boost::function2::function2(Functor, typename boost::enable_if_c::value>::value, int>::type) [with Functor = boost::algorithm::detail::token_finderF; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >; typename boost::enable_if_c::value>::value, int>::type = int]' ./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36: required from 'boost::algorithm::detail::find_iterator_base::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::token_finderF; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/find_iterator.hpp:265:29: required from 'boost::algorithm::split_iterator::split_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::token_finderF; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/iter_find.hpp:170:21: required from 'SequenceSequenceT& boost::algorithm::iter_split(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector >; RangeT = const std::__cxx11::basic_string; FinderT = boost::algorithm::detail::token_finderF]' ./boost/boost/algorithm/string/split.hpp:146:50: required from 'SequenceSequenceT& boost::algorithm::split(SequenceSequenceT&, RangeT&, PredicateT, boost::algorithm::token_compress_mode_type) [with SequenceSequenceT = std::vector >; RangeT = const std::__cxx11::basic_string; PredicateT = boost::algorithm::detail::is_classifiedF]' pwiz/data/common/Unimod.cpp:129:71: required from here ./boost/boost/function/function_base.hpp:318:54: warning: placement new constructing an object of type 'boost::detail::function::functor_manager_common >::functor_type' {aka 'boost::algorithm::detail::token_finderF'} and size '24' in a region of type 'char' and size '1' [-Wplacement-new=] new (reinterpret_cast(&out_buffer.data)) functor_type(*in_functor); ~~~~~~~~~~~^~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27, from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/smart_ptr.hpp:19, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32, from pwiz/data/msdata/mz5/Connection_mz5.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/../MSData.hpp:29, from pwiz/data/msdata/mz5/Connection_mz5.hpp:27, from pwiz/data/msdata/mz5/Connection_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/smart_ptr.hpp:19, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28, from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/smart_ptr.hpp:19, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:32, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:33, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost/boost/smart_ptr.hpp:19, from ./pwiz/data/msdata/SpectrumWorkerThreads.hpp:27, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28, from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_MGF.cpp:28: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumList_MGF.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_MGF.cpp:29: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MGF.hpp:30, from pwiz/data/msdata/SpectrumList_MGF.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_MGF.cpp:29: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mzML.cpp:31: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/ChromatogramList_mzML.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/ChromatogramListBase.hpp:28, from pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from pwiz/data/msdata/ChromatogramList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/ChromatogramList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/examples.cpp:26: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/examples.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/examples.hpp:29, from pwiz/data/msdata/examples.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mzML.cpp:33: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Serializer_mzML.cpp:33: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzML.hpp:29, from pwiz/data/msdata/Serializer_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/msdata/Serializer_MSn.cpp:28: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Serializer_MSn.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MSn.hpp:26, from pwiz/data/msdata/Serializer_MSn.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/msdata/Reader.cpp:27: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Reader.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Reader.hpp:28, from pwiz/data/msdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Serializer_mz5.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/Serializer_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/msdata/Serializer_MGF.cpp:27: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Serializer_MGF.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_MGF.hpp:27, from pwiz/data/msdata/Serializer_MGF.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/spirit/home/karma/string.hpp:13, from ./boost/boost/spirit/home/karma.hpp:14, from ./boost/boost/spirit/include/karma.hpp:16, from pwiz/data/msdata/Serializer_MGF.cpp:29: ./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const': ./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs] extracted_string_type; ^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:33: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Serializer_mzXML.cpp:34: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Serializer_mzXML.hpp:29, from pwiz/data/msdata/Serializer_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mzML.cpp:30: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumList_mzML.cpp:30: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mzML.cpp:32: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzML.hpp:29, from pwiz/data/msdata/SpectrumList_mzML.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mzML.cpp:32: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_MSn.cpp:28: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumList_MSn.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_MSn.cpp:31: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_MSn.hpp:29, from pwiz/data/msdata/SpectrumList_MSn.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_MSn.cpp:31: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mz5.cpp:29: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumList_mz5.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mz5.cpp:29: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/range/iterator_range.hpp:13, from ./boost/boost/iostreams/traits.hpp:39, from ./boost/boost/iostreams/pipeline.hpp:18, from ./boost/boost/iostreams/detail/push.hpp:22, from ./boost/boost/iostreams/chain.hpp:29, from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.cpp:30: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.cpp:30: ./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base::push_impl(const T&, std::streamsize, std::streamsize)': ./boost/boost/iostreams/chain.hpp:256:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/bind/bind.hpp:26, from ./boost/boost/bind.hpp:22, from ./boost/boost/iostreams/copy.hpp:26, from pwiz/data/msdata/BinaryDataEncoder.cpp:32: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/BinaryDataEncoder.cpp:38: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/BinaryDataEncoder.hpp:29, from pwiz/data/msdata/BinaryDataEncoder.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::__cxx11::string&, size_t*)': pwiz/data/msdata/BinaryDataEncoder.cpp:280:37: warning: 'byteCount' may be used uninitialized in this function [-Wmaybe-uninitialized] filterArray(byteBuffer, byteCount,compressed); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/BinaryDataEncoder.cpp:280:37: warning: 'byteBuffer' may be used uninitialized in this function [-Wmaybe-uninitialized] "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Diff.cpp:28: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Diff.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Diff.hpp:29, from pwiz/data/msdata/Diff.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/MSData.cpp:26: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/MSData.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/References.cpp:26: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/References.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/References.hpp:29, from pwiz/data/msdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_mzXML.cpp:29: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumList_mzXML.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mzXML.cpp:30: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_mzXML.hpp:29, from pwiz/data/msdata/SpectrumList_mzXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/msdata/SpectrumList_mzXML.cpp: In constructor 'pwiz::msdata::{anonymous}::SpectrumList_mzXMLImpl::SpectrumList_mzXMLImpl(boost::shared_ptr >, const pwiz::msdata::MSData&, bool)': pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=] } catch (index_not_found e){ ^ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_mzXML.cpp:30: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/msdata/IO.cpp:29: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/IO.cpp:30: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/IO.hpp:29, from pwiz/data/msdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerBinaryDataArray::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': pwiz/data/msdata/IO.cpp:1727:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!dataProcessingRef.empty()) ^~ pwiz/data/msdata/IO.cpp:1730:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' getAttribute(attributes, "encodedLength", encodedLength_, NoXMLUnescape); ^~~~~~~~~~~~ pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': pwiz/data/msdata/IO.cpp:2020:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses] else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': pwiz/data/msdata/IO.cpp:2731:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumList_BTDX.cpp:29: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumList_BTDX.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_BTDX.cpp:30: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from ./pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListBase.hpp:28, from pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from pwiz/data/msdata/SpectrumList_BTDX.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumList_BTDX.cpp:30: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumInfo.cpp:29: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumInfo.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumInfo.hpp:29, from pwiz/data/msdata/SpectrumInfo.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/data/msdata/RAMPAdapter.hpp:30, from pwiz/data/msdata/RAMPAdapter.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:27: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/RAMPAdapter.cpp:31: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/RAMPAdapter.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from ./random_access_gzFile.h:21, from ./ramp.h:72, from pwiz/data/msdata/RAMPAdapter.hpp:29, from pwiz/data/msdata/RAMPAdapter.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)', inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:283:25: pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation] strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)', inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:284:25: pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation] strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)', inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:285:25: pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation] strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void pwiz::msdata::{anonymous}::copyInstrumentString(char*, const string&)', inlined from 'void pwiz::msdata::RAMPAdapter::Impl::getInstrument(InstrumentStruct&) const' at pwiz/data/msdata/RAMPAdapter.cpp:286:25: pwiz/data/msdata/RAMPAdapter.cpp:267:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 2000 equals destination size [-Wstringop-truncation] strncpy(to, from.substr(0,INSTRUMENT_LENGTH-1).c_str(), INSTRUMENT_LENGTH); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/LegacyAdapter.cpp:31: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/LegacyAdapter.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/LegacyAdapter.hpp:30, from pwiz/data/msdata/LegacyAdapter.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumIterator.cpp:29: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumIterator.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumIterator.hpp:29, from pwiz/data/msdata/SpectrumIterator.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::equal(const pwiz::msdata::SpectrumIterator::Impl&) const': pwiz/data/msdata/SpectrumIterator.cpp:125:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] return (done() && &that.spectrumList_==&pastEndMarker_ || ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses] &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::done() const': pwiz/data/msdata/SpectrumIterator.cpp:141:34: warning: suggest parentheses around '&&' within '||' [-Wparentheses] return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() || ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:36: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/MSDataFile.cpp:37: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from ./boost/boost/iostreams/filtering_stream.hpp:22, from pwiz/data/msdata/MSDataFile.cpp:41: ./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base::push_impl(const T&, std::streamsize, std::streamsize)': ./boost/boost/iostreams/chain.hpp:256:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/MSDataFile.hpp:29, from pwiz/data/msdata/MSDataFile.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] } else if (init == mask) { ~~~~~^~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/bind/bind.hpp:26, from ./boost/boost/bind.hpp:22, from ./boost/boost/multi_index/sequenced_index.hpp:49, from ./pwiz/utility/misc/mru_list.hpp:30, from pwiz/data/msdata/MemoryMRUCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.hpp:28, from pwiz/data/msdata/SpectrumListCache.cpp:25: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumListCache.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/SpectrumListCache.hpp:27, from pwiz/data/msdata/SpectrumListCache.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/data/common/ParamTypes.hpp:33, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/Index_mzML.cpp:25: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/Index_mzML.cpp:25: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/msdata/MSData.hpp:29, from pwiz/data/msdata/Index_mzML.hpp:28, from pwiz/data/msdata/Index_mzML.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:28: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/data/msdata/SpectrumWorkerThreads.cpp:28: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:30: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/IdentDataFile.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from ./boost/boost/iostreams/filtering_stream.hpp:22, from pwiz/data/identdata/IdentDataFile.cpp:34: ./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base::push_impl(const T&, std::streamsize, std::streamsize)': ./boost/boost/iostreams/chain.hpp:256:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IdentDataFile.hpp:29, from pwiz/data/identdata/IdentDataFile.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/IdentData.cpp:25: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/IdentData.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/DefaultReaderList.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/DefaultReaderList.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/identdata/Reader.cpp:27: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/Reader.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Reader.hpp:28, from pwiz/data/identdata/Reader.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/Serializer_protXML.cpp:31: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/Serializer_protXML.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_protXML.hpp:29, from pwiz/data/identdata/Serializer_protXML.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/identdata/Serializer_protXML.cpp: In constructor 'pwiz::identdata::{anonymous}::Handler_protXML::Handler_protXML(pwiz::identdata::IdentData&, const pwiz::util::IterationListenerRegistry*, bool, std::vector >*)': pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: 'pwiz::identdata::{anonymous}::Handler_protXML::strict' will be initialized after [-Wreorder] bool strict; ^~~~~~ pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning: 'int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides' [-Wreorder] int nPeptides; ^~~~~~~~~ pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning: when initialized here [-Wreorder] Handler_protXML(IdentData& mzid, ^~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/Serializer_pepXML.cpp:28: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/Serializer_pepXML.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_pepXML.hpp:27, from pwiz/data/identdata/Serializer_pepXML.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/identdata/Serializer_pepXML.cpp: In function 'void pwiz::identdata::{anonymous}::write_spectrum_queries(pwiz::minimxml::XMLWriter&, const pwiz::identdata::IdentData&, const string&, const pwiz::util::IterationListenerRegistry*)': pwiz/data/identdata/Serializer_pepXML.cpp:800:52: warning: 'lastSpectrumIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] if (sii.chargeState != lastChargeState || spectrumIndex != lastSpectrumIndex) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/Serializer_mzid.cpp:30: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/Serializer_mzid.cpp:30: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/Serializer_mzid.hpp:28, from pwiz/data/identdata/Serializer_mzid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Filesystem.hpp:29, from pwiz/data/identdata/IO.cpp:30: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/IO.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/IO.hpp:27, from pwiz/data/identdata/IO.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/data/common/ParamTypes.hpp:29, from pwiz/data/identdata/IdentData.hpp:31, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/References.cpp:27: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/References.cpp:27: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from ./pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/identdata/IdentData.hpp:30, from pwiz/data/identdata/References.hpp:29, from pwiz/data/identdata/References.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/identdata/References.cpp: In function 'void pwiz::identdata::References::resolve(std::vector >&, pwiz::identdata::IdentData&)': pwiz/data/identdata/References.cpp:148:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] else if (dynamic_cast(c.get())) ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/identdata/MascotReader.cpp:25: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/identdata/MascotReader.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/proteome/Modification.cpp:30: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/proteome/Modification.cpp:30: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/proteome/Modification.cpp:30: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/data/proteome/Modification.cpp:89:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr formula_; ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Modification.hpp:30, from pwiz/data/proteome/Modification.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/proteome/Digestion.cpp:32: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/proteome/Digestion.cpp:32: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/proteome/Digestion.cpp:32: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Digestion.hpp:31, from pwiz/data/proteome/Digestion.cpp:27: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/function/detail/maybe_include.hpp:23, from ./boost/boost/function/detail/function_iterate.hpp:14, from ./boost/boost/preprocessor/iteration/detail/iter/forward1.hpp:57, from ./boost/boost/function.hpp:64, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/proteome/Digestion.cpp:32: ./boost/boost/function/function_template.hpp: In instantiation of 'void boost::detail::function::basic_vtable2::assign_functor(FunctionObj, boost::detail::function::function_buffer&, mpl_::true_) const [with FunctionObj = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >; mpl_::true_ = mpl_::bool_]': ./boost/boost/function/function_template.hpp:608:13: required from 'bool boost::detail::function::basic_vtable2::assign_to(FunctionObj, boost::detail::function::function_buffer&, boost::detail::function::function_obj_tag) const [with FunctionObj = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:498:45: required from 'bool boost::detail::function::basic_vtable2::assign_to(F, boost::detail::function::function_buffer&) const [with F = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:942:7: required from 'void boost::function2::assign_to(Functor) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:728:7: required from 'boost::function2::function2(Functor, typename boost::enable_if_c::value>::value, int>::type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >; typename boost::enable_if_c::value>::value, int>::type = int]' ./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36: required from 'boost::algorithm::detail::find_iterator_base::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/find_iterator.hpp:100:26: required from 'boost::algorithm::find_iterator::find_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/iter_find.hpp:100:21: required from 'SequenceSequenceT& boost::algorithm::iter_find(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector > > >; RangeT = const std::__cxx11::basic_string; FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>]' ./boost/boost/algorithm/string/split.hpp:67:49: required from 'SequenceSequenceT& boost::algorithm::find_all(SequenceSequenceT&, Range1T&, const Range2T&) [with SequenceSequenceT = std::vector > > >; Range1T = const std::__cxx11::basic_string; Range2T = std::__cxx11::basic_string]' pwiz/data/proteome/Digestion.cpp:472:63: required from here ./boost/boost/function/function_template.hpp:572:49: warning: placement new constructing an object of type 'boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>' and size '24' in a region of type 'char' and size '1' [-Wplacement-new=] new (reinterpret_cast(&functor.data)) FunctionObj(f); ~~~~~~~~^~~~ In file included from ./boost/boost/function/detail/prologue.hpp:17, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/proteome/Digestion.cpp:32: ./boost/boost/function/function_base.hpp: In instantiation of 'static void boost::detail::function::functor_manager_common::manage_small(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>]': ./boost/boost/function/function_base.hpp:364:56: required from 'static void boost::detail::function::functor_manager::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, mpl_::true_) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; mpl_::true_ = mpl_::bool_]' ./boost/boost/function/function_base.hpp:412:18: required from 'static void boost::detail::function::functor_manager::manager(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type, boost::detail::function::function_obj_tag) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>]' ./boost/boost/function/function_base.hpp:440:20: required from 'static void boost::detail::function::functor_manager::manage(const boost::detail::function::function_buffer&, boost::detail::function::function_buffer&, boost::detail::function::functor_manager_operation_type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>]' ./boost/boost/function/function_template.hpp:940:13: required from 'void boost::function2::assign_to(Functor) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >]' ./boost/boost/function/function_template.hpp:728:7: required from 'boost::function2::function2(Functor, typename boost::enable_if_c::value>::value, int>::type) [with Functor = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; R = boost::iterator_range<__gnu_cxx::__normal_iterator > >; T0 = __gnu_cxx::__normal_iterator >; T1 = __gnu_cxx::__normal_iterator >; typename boost::enable_if_c::value>::value, int>::type = int]' ./boost/boost/algorithm/string/detail/find_iterator.hpp:51:36: required from 'boost::algorithm::detail::find_iterator_base::find_iterator_base(FinderT, int) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/find_iterator.hpp:100:26: required from 'boost::algorithm::find_iterator::find_iterator(IteratorT, IteratorT, FinderT) [with FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>; IteratorT = __gnu_cxx::__normal_iterator >]' ./boost/boost/algorithm/string/iter_find.hpp:100:21: required from 'SequenceSequenceT& boost::algorithm::iter_find(SequenceSequenceT&, RangeT&, FinderT) [with SequenceSequenceT = std::vector > > >; RangeT = const std::__cxx11::basic_string; FinderT = boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>]' ./boost/boost/algorithm/string/split.hpp:67:49: required from 'SequenceSequenceT& boost::algorithm::find_all(SequenceSequenceT&, Range1T&, const Range2T&) [with SequenceSequenceT = std::vector > > >; Range1T = const std::__cxx11::basic_string; Range2T = std::__cxx11::basic_string]' pwiz/data/proteome/Digestion.cpp:472:63: required from here ./boost/boost/function/function_base.hpp:318:54: warning: placement new constructing an object of type 'boost::detail::function::functor_manager_common >, boost::algorithm::is_equal> >::functor_type' {aka 'boost::algorithm::detail::first_finderF<__gnu_cxx::__normal_iterator >, boost::algorithm::is_equal>'} and size '24' in a region of type 'char' and size '1' [-Wplacement-new=] new (reinterpret_cast(&out_buffer.data)) functor_type(*in_functor); ~~~~~~~~~~~^~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/proteome/Peptide.cpp:31: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/proteome/Peptide.cpp:31: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/proteome/Peptide.cpp:31: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/Peptide.hpp:29, from pwiz/data/proteome/Peptide.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:27: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/data/proteome/AminoAcid.cpp:27: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/data/proteome/AminoAcid.cpp:27: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/data/proteome/AminoAcid.hpp:29, from pwiz/data/proteome/AminoAcid.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/minimxml/XMLWriter.hpp:30, from pwiz/utility/minimxml/XMLWriter.cpp:25: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/minimxml/XMLWriter.cpp:26: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/minimxml/XMLWriter.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/iostreams/filtering_streambuf.hpp:17, from ./boost/boost/iostreams/filtering_stream.hpp:22, from pwiz/utility/minimxml/XMLWriter.cpp:27: ./boost/boost/iostreams/chain.hpp: In member function 'void boost::iostreams::detail::chain_base::push_impl(const T&, std::streamsize, std::streamsize)': ./boost/boost/iostreams/chain.hpp:256:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/XMLWriter.hpp:29, from pwiz/utility/minimxml/XMLWriter.cpp:25: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/spirit/home/karma/string.hpp:13, from ./boost/boost/spirit/home/karma.hpp:14, from ./boost/boost/spirit/include/karma.hpp:16, from pwiz/utility/minimxml/XMLWriter.cpp:29: ./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const': ./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs] extracted_string_type; ^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./pwiz/utility/misc/shared_map.hpp:28, from pwiz/utility/minimxml/SAXParser.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:28: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:29: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/minimxml/SAXParser.cpp:29: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from pwiz/utility/minimxml/SAXParser.hpp:31, from pwiz/utility/minimxml/SAXParser.cpp:28: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, pwiz::minimxml::SAXParser::Handler&)': pwiz/utility/minimxml/SAXParser.cpp:431:20: warning: offset '1' outside bounds of constant string [-Warray-bounds] PWIZ_API_DECL void parse(istream& is, Handler& handler) ^~~~~ pwiz/utility/minimxml/SAXParser.cpp:517:17: warning: 'inCDATA' may be used uninitialized in this function [-Wmaybe-uninitialized] if (inCDATA) ^~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/Chemistry.cpp:28: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/Chemistry.cpp:28: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/chemistry/Chemistry.cpp:28: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/Chemistry.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/chemistry/Chemistry.hpp:33, from pwiz/utility/chemistry/ChemistryData.hpp:29, from pwiz/utility/chemistry/ChemistryData.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/chemistry/MZTolerance.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/chemistry/MZTolerance.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/IntegerSet.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IntegerSet.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const': pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses] return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/Base64.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/Base64.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/lexical_cast.hpp:21, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/IterationListener.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp: At global scope: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/lexical_cast/detail/converter_lexical_streams.hpp:44, from ./boost/boost/lexical_cast/detail/converter_lexical.hpp:53, from ./boost/boost/lexical_cast/try_lexical_convert.hpp:34, from ./boost/boost/lexical_cast.hpp:32, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/IterationListener.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/MSIHandler.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/MSIHandler.cpp:25: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/MSIHandler.cpp:25: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/MSIHandler.hpp:28, from pwiz/utility/misc/MSIHandler.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/algorithm/string/std_containers_traits.hpp:18, from ./boost/boost/algorithm/string.hpp:18, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition pwiz/utility/misc/Filesystem.cpp:39: warning: "_WIN32_WINNT" redefined #define _WIN32_WINNT 0x0400 In file included from C:/rtools40/mingw64/x86_64-w64-mingw32/include/crtdefs.h:10, from C:/rtools40/mingw64/x86_64-w64-mingw32/include/wchar.h:9, from C:/rtools40/mingw64/include/c++/8.3.0/cwchar:44, from C:/rtools40/mingw64/include/c++/8.3.0/bits/postypes.h:40, from C:/rtools40/mingw64/include/c++/8.3.0/bits/char_traits.h:40, from C:/rtools40/mingw64/include/c++/8.3.0/string:40, from pwiz/utility/misc/String.hpp:27, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw64/x86_64-w64-mingw32/include/_mingw.h:225: note: this is the location of the previous definition #define _WIN32_WINNT 0x502 In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/range/iterator_range.hpp:13, from ./boost/boost/range/as_literal.hpp:22, from ./boost/boost/algorithm/string/trim.hpp:19, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/TabReader.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/TabReader.cpp:25: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/TabReader.cpp:25: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83: ./boost/boost/thread/detail/thread_group.hpp: In member function 'boost::thread* boost::thread_group::create_thread(F)': ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr new_thread(new thread(threadfunc)); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/thread/shared_mutex.hpp:18, from ./boost/boost/thread/detail/thread_group.hpp:9, from ./boost/boost/thread/thread.hpp:13, from ./boost/boost/thread.hpp:13, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83: ./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]': ./boost/boost/thread/win32/shared_mutex.hpp:130:103: required from here ./boost/boost/thread/win32/shared_mutex.hpp:51:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&new_value), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:52:63: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *reinterpret_cast(&comparand)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] return *reinterpret_cast(&res); ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/static_assert.hpp:17, from pwiz/utility/misc/endian.hpp:28, from pwiz/utility/misc/SHA1.cpp:10: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/filesystem/path.hpp:28, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/interprocess/errors.hpp:41, from ./boost/boost/interprocess/exceptions.hpp:24, from ./boost/boost/interprocess/file_mapping.hpp:30, from pwiz/utility/misc/SHA1.cpp:20: ./boost_aux/boost/interprocess/detail/win32_api.hpp: In instantiation of 'static void* boost::interprocess::winapi::function_address_holder::get(unsigned int) [with int Dummy = 0]': ./boost_aux/boost/interprocess/detail/win32_api.hpp:1617:20: required from here ./boost_aux/boost/interprocess/detail/win32_api.hpp:1544:31: warning: invalid conversion from 'boost::interprocess::winapi::farproc_t' {aka 'long long int (*)()'} to 'void*' [-fpermissive] return FunctionAddresses[id]; ~~~~~~~~~~~~~~~~~^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/static_assert.hpp:17, from pwiz/utility/misc/endian.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:25: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/lexical_cast.hpp:30, from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29, from ./pwiz/utility/misc/Environment.hpp:24, from ./pwiz/utility/misc/Std.hpp:29, from pwiz/utility/misc/SHA1Calculator.cpp:33: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/SHA1Calculator.cpp:33: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/SHA1Calculator.cpp:33: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/smart_ptr/shared_ptr.hpp:17, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/mpl/aux_/na_assert.hpp:23, from ./boost/boost/mpl/arg.hpp:25, from ./boost/boost/mpl/placeholders.hpp:24, from ./boost/boost/iterator/iterator_categories.hpp:17, from ./boost/boost/iterator/iterator_facade.hpp:14, from ./boost/boost/range/iterator_range_core.hpp:27, from ./boost/boost/algorithm/string/replace.hpp:16, from ./boost/boost/date_time/date_facet.hpp:17, from ./boost/boost/date_time/gregorian/gregorian_io.hpp:16, from ./boost/boost/date_time/gregorian/gregorian.hpp:31, from ./boost/boost/date_time/posix_time/time_formatters.hpp:12, from ./boost/boost/date_time/posix_time/posix_time.hpp:24, from ./boost/boost/date_time/local_time/local_time.hpp:11, from pwiz/utility/misc/DateTime.hpp:25, from pwiz/utility/misc/unit.hpp:29, from pwiz/utility/misc/sha1calc.cpp:25: ./boost/boost/mpl/assert.hpp: At global scope: ./boost/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ ./boost/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/unit.hpp:30, from pwiz/utility/misc/sha1calc.cpp:25: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/sha1calc.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c random_access_gzFile.cpp -o random_access_gzFile.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from random_access_gzFile.h:21, from random_access_gzFile.cpp:21: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/filesystem/config.hpp:28, from boost/libs/filesystem/src/path_traits.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/filesystem/config.hpp:28, from boost/libs/filesystem/src/windows_file_codecvt.cpp:20: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/filesystem/config.hpp:28, from boost/libs/filesystem/src/codecvt_error_category.cpp:22: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/thread/src/win32/tss_pe.cpp -o boost/libs/thread/src/win32/tss_pe.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/thread/detail/config.hpp:11, from boost/libs/thread/src/win32/tss_pe.cpp:10: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/thread/src/win32/tss_dll.cpp -o boost/libs/thread/src/win32/tss_dll.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/thread/detail/config.hpp:11, from boost/libs/thread/src/win32/tss_dll.cpp:6: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/thread/src/win32/thread.cpp -o boost/libs/thread/src/win32/thread.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/thread/detail/platform.hpp:14, from ./boost/boost/thread/thread_only.hpp:12, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/bind/bind.hpp:26, from ./boost/boost/bind.hpp:22, from ./boost/boost/thread/detail/thread.hpp:30, from ./boost/boost/thread/thread_only.hpp:22, from boost/libs/thread/src/win32/thread.cpp:17: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/win32/thread_data.hpp:10, from ./boost/boost/thread/thread_only.hpp:15, from boost/libs/thread/src/win32/thread.cpp:17: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwiz/data/msdata/ramp/wglob.cpp -o pwiz/data/msdata/ramp/wglob.o pwiz/data/msdata/ramp/wglob.cpp: In function 'int glob(const char*, int, int*, glob_t*)': pwiz/data/msdata/ramp/wglob.cpp:63:9: warning: unused variable 'fileList' [-Wunused-variable] char** fileList= NULL; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_aux/boost/nowide/iostream.cpp -o boost_aux/boost/nowide/iostream.o In file included from ./boost/boost/config.hpp:57, from ./boost_aux/boost/nowide/config.hpp:11, from ./boost_aux/boost/nowide/iostream.hpp:11, from boost_aux/boost/nowide/iostream.cpp:9: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition In file included from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/iostream.hpp:12, from boost_aux/boost/nowide/iostream.cpp:9: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/iostream.hpp:12, from boost_aux/boost/nowide/iostream.cpp:9: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ boost_aux/boost/nowide/iostream.cpp: In member function 'virtual int boost::nowide::details::console_input_buffer::underflow()': boost_aux/boost/nowide/iostream.cpp:189:13: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized] if(c==uf::incomplete) { ^~ boost_aux/boost/nowide/iostream.cpp:178:28: note: 'c' was declared here uf::code_point c; ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rampR.cpp -o rampR.o In file included from ./boost/boost/config.hpp:57, from ./boost/boost/iostreams/positioning.hpp:18, from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from random_access_gzFile.h:21, from ramp.h:72, from rampR.cpp:15: ./boost/boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined # define BOOST_HAS_WINTHREADS : note: this is the location of the previous definition C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./pwiz/data/msdata/ramp/wglob.o ./boost_aux/boost/nowide/iostream.o rampR.o -lpthread -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -lws2_32 -lz -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/mzR.buildbin-libdir/mzR/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'mzR' as mzR_2.28.0.zip * DONE (mzR) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'mzR' successfully unpacked and MD5 sums checked