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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL Rbowtie
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘Rbowtie’ ...
** this is package ‘Rbowtie’ version ‘1.49.0’
** using staged installation
** libs
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -g -O2  -Wall -Werror=format-security  -g -O2  -Wall -Werror=format-security \"" -Wl,--hash-style=both -g -O2  -Wall -Werror=format-security  -g -O2  -Wall -Werror=format-security   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2025-10-23T20:20:35\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \
	 -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 \
	-L/usr/local/lib  -lz -lpthread 
In file included from ebwt_build.cpp:8:
In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’,
    inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’ at multikey_qsort.h:584:31:
ds.h:497:17: warning: ‘tmp2’ may be used uninitialized [-Wmaybe-uninitialized]
  497 |                 list_[cur_++] = el;
      |                 ^~~~~
In file included from diff_sample.h:14,
                 from blockwise_sa.h:17,
                 from ebwt.h:25,
                 from ebwt_build.cpp:10:
multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’:
multikey_qsort.h:583:36: note: ‘tmp2’ declared here
  583 |                         QSortRange tmp2;
      |                                    ^~~~
In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’,
    inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’ at multikey_qsort.h:593:31:
ds.h:497:17: warning: ‘tmp3’ may be used uninitialized [-Wmaybe-uninitialized]
  497 |                 list_[cur_++] = el;
      |                 ^~~~~
multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’:
multikey_qsort.h:592:36: note: ‘tmp3’ declared here
  592 |                         QSortRange tmp3;
      |                                    ^~~~
In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’,
    inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’ at multikey_qsort.h:601:31:
ds.h:497:17: warning: ‘tmp4’ may be used uninitialized [-Wmaybe-uninitialized]
  497 |                 list_[cur_++] = el;
      |                 ^~~~~
multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’:
multikey_qsort.h:600:36: note: ‘tmp4’ declared here
  600 |                         QSortRange tmp4;
      |                                    ^~~~
In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’,
    inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’ at multikey_qsort.h:584:31:
ds.h:497:17: warning: ‘tmp2’ may be used uninitialized [-Wmaybe-uninitialized]
  497 |                 list_[cur_++] = el;
      |                 ^~~~~
multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’:
multikey_qsort.h:583:36: note: ‘tmp2’ declared here
  583 |                         QSortRange tmp2;
      |                                    ^~~~
In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’,
    inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’ at multikey_qsort.h:593:31:
ds.h:497:17: warning: ‘tmp3’ may be used uninitialized [-Wmaybe-uninitialized]
  497 |                 list_[cur_++] = el;
      |                 ^~~~~
multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’:
multikey_qsort.h:592:36: note: ‘tmp3’ declared here
  592 |                         QSortRange tmp3;
      |                                    ^~~~
In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’,
    inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’ at multikey_qsort.h:601:31:
ds.h:497:17: warning: ‘tmp4’ may be used uninitialized [-Wmaybe-uninitialized]
  497 |                 list_[cur_++] = el;
      |                 ^~~~~
multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’:
multikey_qsort.h:600:36: note: ‘tmp4’ declared here
  600 |                         QSortRange tmp4;
      |                                    ^~~~
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -g -O2  -Wall -Werror=format-security  -g -O2  -Wall -Werror=format-security \"" -Wl,--hash-style=both -g -O2  -Wall -Werror=format-security  -g -O2  -Wall -Werror=format-security  \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2025-10-23T20:20:59\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \
	 -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 \
	-L/usr/local/lib  -lz -lpthread 
mkdir -p ../inst
cp bowtie-align-s ../inst/bowtie
cp bowtie-build-s ../inst/bowtie-build
cd SpliceMap; \
make -f Makefile; \
echo "MAKE of SpliceMap DONE"	
make[1]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rbowtie/src/SpliceMap'
`"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
`"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config LDFLAGS` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o
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 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 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 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 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;
      |         ^~~~~~~~~~~~
`"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config LDFLAGS` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o
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 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 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 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 unsigned int’} [-Wsign-compare]
  236 |                             if (nmloc2 == string::npos) {
      |                                 ~~~~~~~^~~~~~~~~~~~~~~
`"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config LDFLAGS` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o
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 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 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;
      |                               ^~~~~~~~~~
`"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config LDFLAGS` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp
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 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 unsigned int’} [-Wsign-compare]
   88 |     if(start_pos != string::npos && end_pos != string::npos)
      |                                     ~~~~~~~~^~~~~~~~~~~~~~~
`"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config LDFLAGS` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
`"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config LDFLAGS` `"/home/biocbuild/R/R-4.5.0/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o
make[1]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rbowtie/src/SpliceMap'
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)