##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rbowtie.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Rbowtie_1.30.0.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/Rbowtie.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rbowtie/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rbowtie' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Rbowtie' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 26.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
SpliceMap 0.03      0    5.69
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/Rbowtie.Rcheck/00check.log'
for details.

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##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rbowtie
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
* installing *source* package 'Rbowtie' ...
** using staged installation
** libs
  running 'src/Makefile.win' ...
c:/rtools40/mingw64/bin/g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY  \""  -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY    \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2   -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \
	 -isystem ./SeqAn-1.1 -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 tinythread.cpp  bowtie_build_main.cpp \
	  -lz  
In file included from blockwise_sa.h:19,
                 from ebwt.h:27,
                 from ebwt_build.cpp:11:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
In file included from ebwt.h:27,
                 from ebwt_build.cpp:11:
blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA()':
blockwise_sa.h:212:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
    ^~
blockwise_sa.h:212:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
                                ^~~
In file included from ebwt.h:31,
                 from ebwt_build.cpp:11:
hit.h: In member function 'void HitSink::maybeFlush(size_t)':
hit.h:580:26: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(ptCounts_[threadId] >= perThreadBufSize_) {
In file included from ebwt.h:39,
                 from ebwt_build.cpp:11:
reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
    uint64_t origBufOff = bufOff;
             ^~~~~~~~~~
In file included from ebwt_build.cpp:11:
ebwt.h: In destructor 'Ebwt<TStr>::~Ebwt()':
ebwt.h:843:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_fchr    != NULL) delete[] _fchr;    _fchr    = NULL;
    ^~
ebwt.h:843:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_fchr    != NULL) delete[] _fchr;    _fchr    = NULL;
                                            ^~~~~
ebwt.h:844:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_ftab    != NULL) delete[] _ftab;    _ftab    = NULL;
    ^~
ebwt.h:844:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_ftab    != NULL) delete[] _ftab;    _ftab    = NULL;
                                            ^~~~~
ebwt.h:845:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_eftab   != NULL) delete[] _eftab;   _eftab   = NULL;
    ^~
ebwt.h:845:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_eftab   != NULL) delete[] _eftab;   _eftab   = NULL;
                                            ^~~~~~
ebwt.h:851:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_isa     != NULL) delete[] _isa;     _isa     = NULL;
    ^~
ebwt.h:851:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_isa     != NULL) delete[] _isa;     _isa     = NULL;
                                            ^~~~
ebwt.h:852:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_plen    != NULL) delete[] _plen;    _plen    = NULL;
    ^~
ebwt.h:852:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_plen    != NULL) delete[] _plen;    _plen    = NULL;
                                            ^~~~~
ebwt.h:853:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
    ^~
ebwt.h:853:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
                                            ^~~~~~~~
In file included from ebwt.h:27,
                 from ebwt_build.cpp:11:
blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >; TIndexOffU = unsigned int]':
blockwise_sa.h:295:23:   required from here
blockwise_sa.h:305:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size<seqan::String<unsigned int, seqan::Alloc<void> > >::Type' {aka 'long long unsigned int'} [-Wsign-compare]
        for (int i = 0; i < length(_sampleSuffs) + 1; i++) {
                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TIndexOffU = unsigned int]':
blockwise_sa.h:295:23:   required from here
blockwise_sa.h:305:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size<seqan::String<unsigned int, seqan::Alloc<void> > >::Type' {aka 'long long unsigned int'} [-Wsign-compare]
c:/rtools40/mingw64/bin/g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY  \""  -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2   -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \
	 -isystem ./SeqAn-1.1 -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 tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
	  -lz  
In file included from blockwise_sa.h:19,
                 from ebwt.h:27,
                 from ebwt_search.cpp:21:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
In file included from ebwt.h:27,
                 from ebwt_search.cpp:21:
blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA()':
blockwise_sa.h:212:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
    ^~
blockwise_sa.h:212:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
                                ^~~
In file included from ebwt.h:31,
                 from ebwt_search.cpp:21:
hit.h: In member function 'void HitSink::maybeFlush(size_t)':
hit.h:580:26: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(ptCounts_[threadId] >= perThreadBufSize_) {
In file included from ebwt.h:39,
                 from ebwt_search.cpp:21:
reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
    uint64_t origBufOff = bufOff;
             ^~~~~~~~~~
In file included from ebwt_search.cpp:21:
ebwt.h: In destructor 'Ebwt<TStr>::~Ebwt()':
ebwt.h:843:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_fchr    != NULL) delete[] _fchr;    _fchr    = NULL;
    ^~
ebwt.h:843:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_fchr    != NULL) delete[] _fchr;    _fchr    = NULL;
                                            ^~~~~
ebwt.h:844:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_ftab    != NULL) delete[] _ftab;    _ftab    = NULL;
    ^~
ebwt.h:844:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_ftab    != NULL) delete[] _ftab;    _ftab    = NULL;
                                            ^~~~~
ebwt.h:845:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_eftab   != NULL) delete[] _eftab;   _eftab   = NULL;
    ^~
ebwt.h:845:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_eftab   != NULL) delete[] _eftab;   _eftab   = NULL;
                                            ^~~~~~
ebwt.h:851:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_isa     != NULL) delete[] _isa;     _isa     = NULL;
    ^~
ebwt.h:851:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_isa     != NULL) delete[] _isa;     _isa     = NULL;
                                            ^~~~
ebwt.h:852:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_plen    != NULL) delete[] _plen;    _plen    = NULL;
    ^~
ebwt.h:852:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_plen    != NULL) delete[] _plen;    _plen    = NULL;
                                            ^~~~~
ebwt.h:853:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
    ^~
ebwt.h:853:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
                                            ^~~~~~~~
pat.cpp: In member function 'std::pair<bool, bool> PatternSourcePerThread::nextReadPair()':
pat.cpp:109:36: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  bool this_is_last = buf_.cur_buf_ == last_batch_size_-1;
                      ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
pat.cpp: In member function 'virtual bool FastaPatternSource::parse(Read&, Read&, TReadId) const':
pat.cpp:711:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  for(size_t i = 0; i < seqoff - trim3; i++) {
                    ~~^~~~~~~~~~~~~~~~
pat.cpp: In member function 'virtual bool FastaContinuousPatternSource::parse(Read&, Read&, TReadId) const':
pat.cpp:889:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  for(size_t i = 0; i < seqoff; i++) {
                    ~~^~~~~~~~
In file included from ebwt_search_util.h:9,
                 from ebwt_search_util.cpp:1:
hit.h: In member function 'void HitSink::maybeFlush(size_t)':
hit.h:580:26: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(ptCounts_[threadId] >= perThreadBufSize_) {
In file included from sam.cpp:12:
hit.h: In member function 'void HitSink::maybeFlush(size_t)':
hit.h:580:26: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(ptCounts_[threadId] >= perThreadBufSize_) {
In file included from hit.cpp:1:
hit.h: In member function 'void HitSink::maybeFlush(size_t)':
hit.h:580:26: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(ptCounts_[threadId] >= perThreadBufSize_) {
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-3.12-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp  -static-libgcc
c:/rtools40/mingw64/bin/g++ `"C:/Users/biocbuild/bbs-3.12-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp -static-libgcc
c:/rtools40/mingw64/bin/g++ `"C:/Users/biocbuild/bbs-3.12-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp -static-libgcc
c:/rtools40/mingw64/bin/g++ `"C:/Users/biocbuild/bbs-3.12-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-3.12-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-3.12-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-3.12-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-3.12-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp -static-libgcc
c:/rtools40/mingw64/bin/g++ `"C:/Users/biocbuild/bbs-3.12-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