############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Rbowtie ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'Rbowtie' ... ** this is package 'Rbowtie' version '1.47.0' ** using staged installation ** libs running 'src/Makefile.win' ... g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -Wall -mfpmath=sse -msse2 -mstackrealign \"" -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -Wall -mfpmath=sse -msse2 -mstackrealign \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2025-03-21T15:23:30\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party -I third_party \ -o bowtie-build-s ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp bowtie_build_main.cpp \ -lz cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ In file included from ebwt.h:41, from ebwt_build.cpp:10: In member function 'bool ProcessorSupport::POPCNTenabled()', inlined from 'Ebwt::Ebwt(TStr, bool, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, EList&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool, bool) [with TStr = S2bDnaString]' at ebwt.h:495:49, inlined from 'void driver(const std::string&, EList >&, const std::string&, bool) [with TStr = S2bDnaString]' at ebwt_build.cpp:420:7: processor_support.h:55:13: warning: 'regs.regs_t::ECX' may be used uninitialized [-Wmaybe-uninitialized] 55 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ processor_support.h: In function 'void driver(const std::string&, EList >&, const std::string&, bool) [with TStr = S2bDnaString]': processor_support.h:43:12: note: 'regs.regs_t::ECX' was declared here 43 | regs_t regs; | ^~~~ In member function 'bool ProcessorSupport::POPCNTenabled()', inlined from 'Ebwt::Ebwt(TStr, bool, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, EList&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool, bool) [with TStr = SString]' at ebwt.h:495:49, inlined from 'void driver(const std::string&, EList >&, const std::string&, bool) [with TStr = SString]' at ebwt_build.cpp:420:7: processor_support.h:55:13: warning: 'regs.regs_t::ECX' may be used uninitialized [-Wmaybe-uninitialized] 55 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ processor_support.h: In function 'void driver(const std::string&, EList >&, const std::string&, bool) [with TStr = SString]': processor_support.h:43:12: note: 'regs.regs_t::ECX' was declared here 43 | regs_t regs; | ^~~~ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -Wall -mfpmath=sse -msse2 -mstackrealign \"" -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -O2 -Wall -mfpmath=sse -msse2 -mstackrealign \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2025-03-21T15:23:54\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party -I third_party \ -o bowtie-align-s ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp hit.cpp bowtie_main.cpp \ -lz cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ In file included from ebwt.h:41, from aligner.h:18, from ebwt_search.cpp:17: In member function 'bool ProcessorSupport::POPCNTenabled()', inlined from 'Ebwt::Ebwt(const std::string&, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool)' at ebwt.h:421:49: processor_support.h:55:13: warning: 'regs.regs_t::ECX' may be used uninitialized [-Wmaybe-uninitialized] 55 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ processor_support.h: In constructor 'Ebwt::Ebwt(const std::string&, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool)': processor_support.h:43:12: note: 'regs.regs_t::ECX' was declared here 43 | regs_t regs; | ^~~~ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ cc1plus.exe: warning: command-line option '-std=gnu23' is valid for C/ObjC but not for C++ mkdir -p ../inst cp bowtie-align-s ../inst/bowtie cp bowtie-build-s ../inst/bowtie-build cd SpliceMap; \ make -f Makefile.win; \ echo "MAKE of SpliceMap DONE" g++ `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp -static-libgcc g++ `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp -static-libgcc g++ `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp -static-libgcc g++ `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o -static-libgcc runSpliceMap_QuasR.cpp: In function 'int main(int, char* const*)': runSpliceMap_QuasR.cpp:108:38: warning: variable 'chr_file_list_it' set but not used [-Wunused-but-set-variable] 108 | vector::iterator chr_file_list_it = chr_file_list.begin(); | ^~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp:537:47: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 537 | if (line.length() > head_clip_length) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp:595:47: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 595 | if (line.length() > head_clip_length) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp:716:47: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 716 | if (line.length() > head_clip_length) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp:841:43: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 841 | if (line.length() > head_clip_length) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp: In function 'void processbowtie(std::string&, std::string&)': runSpliceMap_QuasR.cpp:1327:9: warning: variable 'min_mismatch' set but not used [-Wunused-but-set-variable] 1327 | int min_mismatch; | ^~~~~~~~~~~~ g++ `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc sortsam.cpp: In function 'int main(int, char* const*)': sortsam.cpp:189:27: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long long unsigned int'} [-Wsign-compare] 189 | if (nmloc == string::npos) { // unaligned, no NM tag | ~~~~~~^~~~~~~~~~~~~~~ sortsam.cpp:194:32: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long long unsigned int'} [-Wsign-compare] 194 | if (nmloc2 == string::npos) { | ~~~~~~~^~~~~~~~~~~~~~~ sortsam.cpp:231:35: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long long unsigned int'} [-Wsign-compare] 231 | if (nmloc == string::npos) { // unaligned, no NM tag | ~~~~~~^~~~~~~~~~~~~~~ sortsam.cpp:236:40: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long long unsigned int'} [-Wsign-compare] 236 | if (nmloc2 == string::npos) { | ~~~~~~~^~~~~~~~~~~~~~~ g++ `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc amalgamateSAM.cpp: In function 'int extractId(const std::string&)': amalgamateSAM.cpp:19:18: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long long unsigned int'} [-Wsign-compare] 19 | if(start_pos != string::npos && end_pos != string::npos) | ~~~~~~~~~~^~~~~~~~~~~~~~~ amalgamateSAM.cpp:19:45: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long long unsigned int'} [-Wsign-compare] 19 | if(start_pos != string::npos && end_pos != string::npos) | ~~~~~~~~^~~~~~~~~~~~~~~ amalgamateSAM.cpp: In function 'void update_jun_coverage(std::map, std::map > >&, std::string, bool)': amalgamateSAM.cpp:695:31: warning: variable 'front_clip' set but not used [-Wunused-but-set-variable] 695 | uint_fast32_t front_clip = 0; | ^~~~~~~~~~ g++ `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp -static-libgcc getSpliceMapUnmapped.cpp: In function 'int extractNextId(const std::string&)': getSpliceMapUnmapped.cpp:88:18: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long long unsigned int'} [-Wsign-compare] 88 | if(start_pos != string::npos && end_pos != string::npos) | ~~~~~~~~~~^~~~~~~~~~~~~~~ getSpliceMapUnmapped.cpp:88:45: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long long unsigned int'} [-Wsign-compare] 88 | if(start_pos != string::npos && end_pos != string::npos) | ~~~~~~~~^~~~~~~~~~~~~~~ g++ `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp -static-libgcc g++ `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"E:/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o -static-libgcc MAKE of SpliceMap DONE mkdir -p ../inst cp SpliceMap/SpliceMap ../inst/SpliceMap cp SpliceMap/amalgamateSAM ../inst/amalgamateSAM cp SpliceMap/getSpliceMapUnmapped ../inst/getSpliceMapUnmapped cp SpliceMap/fuseReorder ../inst/fuseReorder cp SpliceMap/runSpliceMap_QuasR ../inst/runSpliceMap_QuasR cp SpliceMap/sortsam ../inst/sortsam ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rbowtie)