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BioC 3.4: CHECK report for mzR on zin1

This page was generated on 2016-09-21 03:37:28 -0700 (Wed, 21 Sep 2016).

Package 803/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mzR 2.7.4
Bernd Fischer , Steffen Neumann , Laurent Gatto , Qiang Kou
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR
Last Changed Rev: 120458 / Revision: 121152
Last Changed Date: 2016-08-26 00:40:19 -0700 (Fri, 26 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  ERROR  ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: mzR
Version: 2.7.4
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings mzR_2.7.4.tar.gz
StartedAt: 2016-09-20 09:50:05 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:00:29 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 623.4 seconds
RetCode: 0
Status:  OK 
CheckDir: mzR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings mzR_2.7.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/mzR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mzR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzR’ version ‘2.7.4’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  src/win/i386/libpwiz.a src/win/x64/libnetcdf.a src/win/x64/libpwiz.a
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mzR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 80.0Mb
  sub-directories of 1Mb or more:
    libs  79.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/mzR.Rcheck/00check.log’
for details.

mzR.Rcheck/00install.out:

* installing *source* package ‘mzR’ ...
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/pthread/once.o ./boost/thread/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/chrono/src/chrono.o ./boost/chrono/src/process_cpu_clocks.o ./boost/chrono/src/thread_clock.o ./pwiz/data/msdata/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/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.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_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.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 rampR.o R_init_mzR.o
find . -name \*˜ -exec rm {} \;   ## from cleanup
find . -name \*.o -exec rm {} \;  ## from cleanup
find . -name "#*#" -exec rm {} \; ## from cleanup
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c cramp.cpp -o cramp.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c ramp_base64.cpp -o ramp_base64.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c ramp.cpp -o ramp.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from ramp.cpp:60:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ramp.cpp:33:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppRamp.cpp -o RcppRamp.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppRampModule.cpp -o RcppRampModule.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c rnetCDF.c -o rnetCDF.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppPwiz.cpp -o RcppPwiz.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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:19,
                 from RcppPwiz.cpp:1:
./boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/iostreams/filtering_streambuf.hpp:17:0,
                 from ./boost/iostreams/filtering_stream.hpp:22,
                 from RcppPwiz.h:22,
                 from RcppPwiz.cpp:1:
./boost/iostreams/chain.hpp: In member function ‘void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)’:
./boost/iostreams/chain.hpp:256:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppPwizModule.cpp -o RcppPwizModule.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from RcppPwiz.h:11,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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:19,
                 from RcppPwizModule.cpp:2:
./boost/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/iostreams/filtering_streambuf.hpp:17:0,
                 from ./boost/iostreams/filtering_stream.hpp:22,
                 from RcppPwiz.h:22,
                 from RcppPwizModule.cpp:2:
./boost/iostreams/chain.hpp: In member function ‘void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)’:
./boost/iostreams/chain.hpp:256:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppIdent.cpp -o RcppIdent.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdent.h:4,
                 from RcppIdent.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppIdentModule.cpp -o RcppIdentModule.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppIdentModule.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/posix_api.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from boost/regex/src/fileiter.cpp:28:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from boost/regex/src/fileiter.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from boost/regex/src/fileiter.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from boost/regex/src/fileiter.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from boost/regex/src/fileiter.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from boost/regex/src/fileiter.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from boost/regex/src/fileiter.cpp:28:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from boost/regex/src/fileiter.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/cregex.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/instances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/regex.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/wide_posix_api.cpp:25:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/regex_traits_defaults.cpp:20:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex.hpp:32,
                 from ./boost/regex.hpp:31,
                 from boost/regex/src/winstances.cpp:30:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/wc_regex_traits.cpp:76:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from boost/regex/src/wc_regex_traits.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/wc_regex_traits.cpp:76:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from boost/regex/src/wc_regex_traits.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/wc_regex_traits.cpp:76:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from boost/regex/src/wc_regex_traits.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/wc_regex_traits.cpp:76:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from boost/regex/src/wc_regex_traits.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/wc_regex_traits.cpp:76:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from boost/regex/src/wc_regex_traits.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/wc_regex_traits.cpp:76:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from boost/regex/src/wc_regex_traits.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/wc_regex_traits.cpp:76:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from boost/regex/src/wc_regex_traits.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/wc_regex_traits.cpp:76:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from boost/regex/src/wc_regex_traits.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/c_regex_traits.hpp:26,
                 from boost/regex/src/c_regex_traits.cpp:28:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/regex/v4/regex_workaround.hpp:43,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost/regex/v4/regex_workaround.hpp:41,
                 from ./boost/regex/v4/regex_traits.hpp:26,
                 from ./boost/regex/regex_traits.hpp:27,
                 from boost/regex/src/cpp_regex_traits.cpp:22:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/iostreams/filter/zlib.hpp:31,
                 from boost/iostreams/src/zlib.cpp:19:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/iostreams/filter/zlib.hpp:20,
                 from boost/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/iostreams/filter/zlib.hpp:31,
                 from boost/iostreams/src/zlib.cpp:19:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/iostreams/filter/zlib.hpp:20,
                 from boost/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/iostreams/filter/zlib.hpp:31,
                 from boost/iostreams/src/zlib.cpp:19:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/iostreams/filter/zlib.hpp:20,
                 from boost/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/iostreams/filter/zlib.hpp:31,
                 from boost/iostreams/src/zlib.cpp:19:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/iostreams/filter/zlib.hpp:20,
                 from boost/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/iostreams/filter/zlib.hpp:31,
                 from boost/iostreams/src/zlib.cpp:19:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/iostreams/filter/zlib.hpp:20,
                 from boost/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/iostreams/filter/zlib.hpp:31,
                 from boost/iostreams/src/zlib.cpp:19:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/iostreams/filter/zlib.hpp:20,
                 from boost/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/filter/symmetric.hpp:60,
                 from ./boost/iostreams/filter/zlib.hpp:31,
                 from boost/iostreams/src/zlib.cpp:19:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/iostreams/filter/zlib.hpp:20,
                 from boost/iostreams/src/zlib.cpp:19:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/iostreams/src/file_descriptor.cpp -o boost/iostreams/src/file_descriptor.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/iostreams/src/file_descriptor.cpp:23:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/iostreams/positioning.hpp:21,
                 from ./boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/iostreams/src/file_descriptor.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/iostreams/src/file_descriptor.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/iostreams/positioning.hpp:21,
                 from ./boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/iostreams/src/file_descriptor.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/iostreams/src/file_descriptor.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/iostreams/positioning.hpp:21,
                 from ./boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/iostreams/src/file_descriptor.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/iostreams/src/file_descriptor.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/iostreams/positioning.hpp:21,
                 from ./boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/iostreams/src/file_descriptor.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/iostreams/src/file_descriptor.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/iostreams/positioning.hpp:21,
                 from ./boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/iostreams/src/file_descriptor.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/iostreams/src/file_descriptor.cpp:23:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/iostreams/positioning.hpp:21,
                 from ./boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/iostreams/src/file_descriptor.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from boost/iostreams/src/file_descriptor.cpp:23:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/iostreams/positioning.hpp:21,
                 from ./boost/iostreams/device/file_descriptor.hpp:27,
                 from boost/iostreams/src/file_descriptor.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/thread/pthread/once.cpp -o boost/thread/pthread/once.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/thread/pthread/thread.cpp -o boost/thread/pthread/thread.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/date_time/time_clock.hpp:17,
                 from ./boost/thread/thread_time.hpp:9,
                 from ./boost/thread/lock_types.hpp:18,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread_only.hpp:17,
                 from boost/thread/pthread/thread.cpp:11:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/filesystem/src/operations.cpp -o boost/filesystem/src/operations.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from ./boost/filesystem/operations.hpp:25,
                 from boost/filesystem/src/operations.cpp:44:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/filesystem/src/path.cpp -o boost/filesystem/src/path.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/filesystem/path.hpp:29,
                 from boost/filesystem/src/path.cpp:26:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from boost/filesystem/src/path.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from boost/filesystem/src/path.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from boost/filesystem/src/path.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from boost/filesystem/src/path.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from boost/filesystem/src/path.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from boost/filesystem/src/path.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from boost/filesystem/src/path.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from boost/filesystem/src/path.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from boost/filesystem/src/path.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from boost/filesystem/src/path.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from boost/filesystem/src/path.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from boost/filesystem/src/path.cpp:26:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/filesystem/path_traits.hpp:29,
                 from ./boost/filesystem/path.hpp:25,
                 from boost/filesystem/src/path.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/filesystem/src/utf8_codecvt_facet.cpp -o boost/filesystem/src/utf8_codecvt_facet.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/chrono/src/chrono.cpp -o boost/chrono/src/chrono.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/chrono/src/process_cpu_clocks.cpp -o boost/chrono/src/process_cpu_clocks.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c boost/chrono/src/thread_clock.cpp -o boost/chrono/src/thread_clock.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/ParamTypes.cpp:26:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/thread/thread.hpp:13:0,
                 from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/thread/detail/thread_group.hpp: In member function ‘boost::thread* boost::thread_group::create_thread(F)’:
./boost/thread/detail/thread_group.hpp:78:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/common/diff_std.hpp:33,
                 from pwiz/data/common/diff_std.cpp:26:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/common/Unimod.hpp:28,
                 from pwiz/data/common/Unimod.cpp:25:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/thread/thread.hpp:13:0,
                 from ./boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:29:
./boost/thread/detail/thread_group.hpp: In member function ‘boost::thread* boost::thread_group::create_thread(F)’:
./boost/thread/detail/thread_group.hpp:78:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/thread/thread.hpp:13:0,
                 from ./boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:32:
./boost/thread/detail/thread_group.hpp: In member function ‘boost::thread* boost::thread_group::create_thread(F)’:
./boost/thread/detail/thread_group.hpp:78:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/thread/thread.hpp:13:0,
                 from ./boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:31:
./boost/thread/detail/thread_group.hpp: In member function ‘boost::thread* boost::thread_group::create_thread(F)’:
./boost/thread/detail/thread_group.hpp:78:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/iostreams/filtering_streambuf.hpp:17:0,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:30:
./boost/iostreams/chain.hpp: In member function ‘void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)’:
./boost/iostreams/chain.hpp:256:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/MSData.cpp:25:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/thread/thread.hpp:13:0,
                 from ./boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:30:
./boost/thread/detail/thread_group.hpp: In member function ‘boost::thread* boost::thread_group::create_thread(F)’:
./boost/thread/detail/thread_group.hpp:78:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/thread/thread.hpp:13:0,
                 from ./boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:30:
./boost/thread/detail/thread_group.hpp: In member function ‘boost::thread* boost::thread_group::create_thread(F)’:
./boost/thread/detail/thread_group.hpp:78:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/data/msdata/RAMPAdapter.hpp:30,
                 from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/iostreams/filtering_streambuf.hpp:17:0,
                 from ./boost/iostreams/filtering_stream.hpp:22,
                 from pwiz/data/msdata/MSDataFile.cpp:41:
./boost/iostreams/chain.hpp: In member function ‘void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)’:
./boost/iostreams/chain.hpp:256:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./boost/lexical_cast.hpp:32,
                 from ./pwiz/utility/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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/thread/thread.hpp:13:0,
                 from ./boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:28:
./boost/thread/detail/thread_group.hpp: In member function ‘boost::thread* boost::thread_group::create_thread(F)’:
./boost/thread/detail/thread_group.hpp:78:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/iostreams/filtering_streambuf.hpp:17:0,
                 from ./boost/iostreams/filtering_stream.hpp:22,
                 from pwiz/data/identdata/IdentDataFile.cpp:34:
./boost/iostreams/chain.hpp: In member function ‘void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)’:
./boost/iostreams/chain.hpp:256:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
pwiz/data/proteome/Modification.cpp:89:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     auto_ptr<Formula> formula_;
     ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Digestion.hpp:31,
                 from pwiz/data/proteome/Digestion.cpp:27:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Peptide.cpp:26:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/AminoAcid.hpp:29,
                 from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/minimxml/XMLWriter.hpp:30,
                 from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/iostreams/filtering_streambuf.hpp:17:0,
                 from ./boost/iostreams/filtering_stream.hpp:22,
                 from pwiz/utility/minimxml/XMLWriter.cpp:27:
./boost/iostreams/chain.hpp: In member function ‘void boost::iostreams::detail::chain_base<Self, Ch, Tr, Alloc, Mode>::push_impl(const T&, std::streamsize, std::streamsize)’:
./boost/iostreams/chain.hpp:256:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         std::auto_ptr<streambuf_t>
              ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./pwiz/utility/misc/shared_map.hpp:28,
                 from pwiz/utility/minimxml/SAXParser.hpp:32,
                 from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/ChemistryData.hpp:29,
                 from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from ./boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from ./boost/lexical_cast/try_lexical_convert.hpp:35,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/MSIHandler.hpp:28,
                 from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/algorithm/string/classification.hpp:15,
                 from ./boost/algorithm/string/trim.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/algorithm/string/classification.hpp:15,
                 from ./boost/algorithm/string/trim.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/algorithm/string/classification.hpp:15,
                 from ./boost/algorithm/string/trim.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/algorithm/string/classification.hpp:15,
                 from ./boost/algorithm/string/trim.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/algorithm/string/classification.hpp:15,
                 from ./boost/algorithm/string/trim.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/algorithm/string/classification.hpp:15,
                 from ./boost/algorithm/string/trim.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/format/alt_sstream.hpp:21,
                 from ./boost/format/internals.hpp:23,
                 from ./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/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/algorithm/string/classification.hpp:15,
                 from ./boost/algorithm/string/trim.hpp:23,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/iostreams/device/file_descriptor.hpp:28,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/thread/thread.hpp:13:0,
                 from ./boost/thread.hpp:13,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83:
./boost/thread/detail/thread_group.hpp: In member function ‘boost::thread* boost::thread_group::create_thread(F)’:
./boost/thread/detail/thread_group.hpp:78:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from ./boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./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:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
In file included from ./boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from ./boost/filesystem/path.hpp:29,
                 from ./boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from ./boost/config/no_tr1/memory.hpp:21,
                 from ./boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
In file included from ./boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/smart_ptr/detail/shared_count.hpp:396:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pwiz/utility/misc/sha1calc.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:249:65: warning: ‘template<class> 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pwiz/utility/misc/sha1calc.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:448:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pwiz/utility/misc/sha1calc.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:461:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pwiz/utility/misc/sha1calc.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:538:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pwiz/utility/misc/sha1calc.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/smart_ptr/shared_ptr.hpp:547:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pwiz/utility/misc/sha1calc.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/smart_ptr/shared_ptr.hpp:549:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pwiz/utility/misc/sha1calc.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from ./boost/scoped_ptr.hpp:14:0,
                 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/smart_ptr/scoped_ptr.hpp: At global scope:
./boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pwiz/utility/misc/sha1calc.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c random_access_gzFile.cpp -o random_access_gzFile.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c rampR.cpp -o rampR.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c R_init_mzR.c -o R_init_mzR.o
g++ -std=c++11 -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o mzR.so cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/pthread/once.o ./boost/thread/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/chrono/src/chrono.o ./boost/chrono/src/process_cpu_clocks.o ./boost/chrono/src/thread_clock.o ./pwiz/data/msdata/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/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.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_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.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 rampR.o R_init_mzR.o -lpthread -L/usr/local/lib -lnetcdf -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/mzR.Rcheck/mzR/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘close’ from package ‘base’ in package ‘mzR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mzR)

mzR.Rcheck/mzR-Ex.timings:

nameusersystemelapsed
metadata0.1000.0040.122
mzR-class0.0600.0040.063
openMSfile0.0840.0120.096
peaks0.0440.0040.046