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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Rbowtie
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'Rbowtie' ...
** using staged installation
** libs
  running 'src/Makefile.win' ...
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  \"" -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2024-12-19T15:28:52\"" -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  
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  \"" -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2024-12-19T15:31:43\"" -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  
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++ `"F:/biocbuild/bbs-3.20-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp  -static-libgcc
g++ `"F:/biocbuild/bbs-3.20-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp -static-libgcc
g++ `"F:/biocbuild/bbs-3.20-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp -static-libgcc
g++ `"F:/biocbuild/bbs-3.20-bioc/R/bin/R" CMD config LDFLAGS` `"F:/biocbuild/bbs-3.20-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++ `"F:/biocbuild/bbs-3.20-bioc/R/bin/R" CMD config LDFLAGS` `"F:/biocbuild/bbs-3.20-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++ `"F:/biocbuild/bbs-3.20-bioc/R/bin/R" CMD config LDFLAGS` `"F:/biocbuild/bbs-3.20-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++ `"F:/biocbuild/bbs-3.20-bioc/R/bin/R" CMD config LDFLAGS` `"F:/biocbuild/bbs-3.20-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++ `"F:/biocbuild/bbs-3.20-bioc/R/bin/R" CMD config LDFLAGS` `"F:/biocbuild/bbs-3.20-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp -static-libgcc
g++ `"F:/biocbuild/bbs-3.20-bioc/R/bin/R" CMD config LDFLAGS` `"F:/biocbuild/bbs-3.20-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)