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###
### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rbowtie
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* 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<string>::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<char>::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<char>::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<char>::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<char>::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<char>::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<char>::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<char>::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<char>::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<char>::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<char>::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::__cxx11::basic_string<char>, std::map<int, std::map<int, jun_store_ij> > >&, 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<char>::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<char>::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