############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rbowtie ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' * installing *source* package 'Rbowtie' ... ** using staged installation ** libs running 'src/Makefile.win' ... c:/rtools40/mingw64/bin/g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY \"" -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2022-04-12T03:56:45\"" -DCOMPILER_VERSION="\"`c:/rtools40/mingw64/bin/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 c:/rtools40/mingw64/bin/g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY \"" -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2022-04-12T03:58:31\"" -DCOMPILER_VERSION="\"`c:/rtools40/mingw64/bin/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 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" c:/rtools40/mingw64/bin/g++ `"C:/Users/biocbuild/bbs-3.14-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp -static-libgcc c:/rtools40/mingw64/bin/g++ `"C:/Users/biocbuild/bbs-3.14-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp -static-libgcc c:/rtools40/mingw64/bin/g++ `"C:/Users/biocbuild/bbs-3.14-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp -static-libgcc c:/rtools40/mingw64/bin/g++ `"C:/Users/biocbuild/bbs-3.14-bioc/R/bin/R" CMD config LDFLAGS` `"C:/Users/biocbuild/bbs-3.14-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:108:31: warning: variable 'chr_file_list_it' set but not used [-Wunused-but-set-variable] vector::iterator chr_file_list_it = chr_file_list.begin(); ^~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp:537:26: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if (line.length() > head_clip_length) { ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp:595:26: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if (line.length() > head_clip_length) { ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp:716:26: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if (line.length() > head_clip_length) { ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp:841:22: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if (line.length() > head_clip_length) { ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp: In function 'void processbowtie(std::__cxx11::string&, std::__cxx11::string&)': runSpliceMap_QuasR.cpp:1327:9: warning: variable 'min_mismatch' set but not used [-Wunused-but-set-variable] int min_mismatch; ^~~~~~~~~~~~ c:/rtools40/mingw64/bin/g++ `"C:/Users/biocbuild/bbs-3.14-bioc/R/bin/R" CMD config LDFLAGS` `"C:/Users/biocbuild/bbs-3.14-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:189:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if (nmloc == string::npos) { // unaligned, no NM tag ~~~~~~^~~~~~~~~ sortsam.cpp:194:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if (nmloc2 == string::npos) { ~~~~~~~^~~~~~~~~ sortsam.cpp:231:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if (nmloc == string::npos) { // unaligned, no NM tag ~~~~~~^~~~~~~~~ sortsam.cpp:236:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if (nmloc2 == string::npos) { ~~~~~~~^~~~~~~~~ c:/rtools40/mingw64/bin/g++ `"C:/Users/biocbuild/bbs-3.14-bioc/R/bin/R" CMD config LDFLAGS` `"C:/Users/biocbuild/bbs-3.14-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 string&)': amalgamateSAM.cpp:19:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if(start_pos != string::npos && end_pos != string::npos) ~~~~~~~~~~^~~~~~~~~ amalgamateSAM.cpp:19:45: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if(start_pos != string::npos && end_pos != string::npos) ~~~~~~~~^~~~~~~~~ amalgamateSAM.cpp: In function 'void update_jun_coverage(std::map, std::map > >&, std::__cxx11::string, bool)': amalgamateSAM.cpp:695:17: warning: variable 'front_clip' set but not used [-Wunused-but-set-variable] uint_fast32_t front_clip = 0; ^~~~~~~~~~ c:/rtools40/mingw64/bin/g++ `"C:/Users/biocbuild/bbs-3.14-bioc/R/bin/R" CMD config LDFLAGS` `"C:/Users/biocbuild/bbs-3.14-bioc/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp -static-libgcc getSpliceMapUnmapped.cpp: In function 'int extractNextId(const string&)': getSpliceMapUnmapped.cpp:88:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if(start_pos != string::npos && end_pos != string::npos) ~~~~~~~~~~^~~~~~~~~ getSpliceMapUnmapped.cpp:88:45: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if(start_pos != string::npos && end_pos != string::npos) ~~~~~~~~^~~~~~~~~ c:/rtools40/mingw64/bin/g++ `"C:/Users/biocbuild/bbs-3.14-bioc/R/bin/R" CMD config LDFLAGS` `"C:/Users/biocbuild/bbs-3.14-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp -static-libgcc c:/rtools40/mingw64/bin/g++ `"C:/Users/biocbuild/bbs-3.14-bioc/R/bin/R" CMD config LDFLAGS` `"C:/Users/biocbuild/bbs-3.14-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 converting help for package 'Rbowtie' finding HTML links ... done Rbowtie-package html Rbowtie html SpliceMap html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rbowtie) Making 'packages.html' ... done