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###
### Running command:
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###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BitSeq
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'BitSeq' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ArgumentParser.cpp -o ArgumentParser.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FileHeader.cpp -o FileHeader.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GibbsParameters.cpp -o GibbsParameters.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GibbsSampler.cpp -o GibbsSampler.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MyTimer.cpp -o MyTimer.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:838: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  838 |       #pragma omp parallel for \
      | 
ReadDistribution.cpp:923: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  923 |    #pragma omp parallel for \
      | 
ReadDistribution.cpp:928: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
  928 |          #pragma omp critical
      | 
ReadDistribution.cpp: In function 'long int ns_rD::countDeletions(const bam1_t*)':
ReadDistribution.cpp:66:18: warning: comparison of integer expressions of different signedness: 'long int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare]
   66 |    for(long i=0;i<samA->core.n_cigar;i++){
      |                 ~^~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In function 'bool ns_rD::getCigarOp(const bam1_t*, long int, long int*, long int*)':
ReadDistribution.cpp:79:29: warning: comparison of integer expressions of different signedness: 'long int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare]
   79 |    if((cigarI<0) || (cigarI >= samA->core.n_cigar)) return false;
      |                      ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In member function 'bool ReadDistribution::observed(ns_rD::fragmentP)':
ReadDistribution.cpp:265:9: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
  265 |        (! frag->second->core.flag & BAM_FREVERSE))){
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In member function 'bool ReadDistribution::getP(ns_rD::fragmentP, double&, double&)':
ReadDistribution.cpp:687:14: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
  687 |             (! frag->second->core.flag & BAM_FREVERSE))){
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rhtslib_bam_plbuf.c -o Rhtslib_bam_plbuf.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rhtslib_sam.c -o Rhtslib_sam.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Sampler.cpp -o Sampler.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SimpleSparse.cpp -o SimpleSparse.o
SimpleSparse.cpp:35: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   35 |    #pragma omp parallel for reduction(+:count)
      | 
SimpleSparse.cpp:45: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   45 |    #pragma omp parallel for private(i,logRowSum)
      | 
SimpleSparse.cpp:57: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   57 |    #pragma omp parallel for private(i,logRowSum)
      | 
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TagAlignments.cpp -o TagAlignments.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TranscriptExpression.cpp -o TranscriptExpression.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TranscriptInfo.cpp -o TranscriptInfo.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TranscriptSequence.cpp -o TranscriptSequence.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c VariationalBayes.cpp -o VariationalBayes.o
VariationalBayes.cpp:86: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   86 |       #pragma omp parallel for
      | 
VariationalBayes.cpp:96: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   96 |    #pragma omp parallel for private(err) reduction(+:totalError)
      | 
VariationalBayes.cpp:103: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  103 |    #pragma omp parallel for
      | 
VariationalBayes.cpp:110: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  110 |    #pragma omp parallel for reduction(+:A,B)
      | 
VariationalBayes.cpp:119: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  119 |    #pragma omp parallel for reduction(+:C)
      | 
VariationalBayes.cpp:172: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  172 |       #pragma omp parallel for private(i,phiGradPhiSum_r,natGrad_i,gradGamma_i) reduction(+:squareNorm,valBeta,valBetaDiv)
      | 
VariationalBayes.cpp:219: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  219 |          #pragma omp parallel for
      | 
VariationalBayes.cpp:224: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  224 |          #pragma omp parallel for
      | 
VariationalBayes.cpp:238: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  238 |          #pragma omp parallel for
      | 
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c common.cpp -o common.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c estimateDE.cpp -o estimateDE.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:208: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  208 |       #pragma omp parallel for private(subCounter)
      | 
estimateExpression.cpp:244: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  244 |          #pragma omp parallel for private(subCounter)
      | 
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c estimateVBExpression.cpp -o estimateVBExpression.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getGeneExpression.cpp -o getGeneExpression.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getVariance.cpp -o getVariance.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c lowess.cpp -o lowess.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c misc.cpp -o misc.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c parseAlignment.cpp -o parseAlignment.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c transposeFiles.cpp -o transposeFiles.o
g++ -std=gnu++11 -shared -s -static-libgcc -o BitSeq.dll tmp.def ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o MyTimer.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Rhtslib_bam_plbuf.o Rhtslib_sam.o Sampler.o SimpleSparse.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o VariationalBayes.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o transposeFiles.o F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -lsbml-static -lwinmm -lwldap32 -lgdi32 -lbz2 -lcurl -lrtmp -lssl -lssh2 -lidn2 -lunistring -lcharset -lintl -liconv -lgcrypt -lcrypto -lgpg-error -lws2_32 -llzma -lz -lzstd -lmincore -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-BitSeq/00new/BitSeq/libs/x64
** 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 (BitSeq)