##############################################################################
##############################################################################
###
### 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="\"2025-03-18T15:27:32\"" -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<FileBuf*>&, EList<RefRecord>&, EList<unsigned int>&, 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<std::__cxx11::basic_string<char> >&, 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<std::__cxx11::basic_string<char> >&, 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<FileBuf*>&, EList<RefRecord>&, EList<unsigned int>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool, bool) [with TStr = SString<char>]' at ebwt.h:495:49,
inlined from 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, bool) [with TStr = SString<char>]' 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<std::__cxx11::basic_string<char> >&, const std::string&, bool) [with TStr = SString<char>]':
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="\"2025-03-18T15:28:07\"" -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<string>::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<char>::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<char>::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<char>::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<char>::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<char>::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<char>::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<char>::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<char>::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<char>::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<char>::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::__cxx11::basic_string<char>, std::map<int, std::map<int, jun_store_ij> > >&, 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<char>::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<char>::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)
