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###
### Running command:
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###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL BitSeq
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* installing to library 'F:/biocbuild/bbs-3.16-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++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.16-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++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.16-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++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.16-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++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.16-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++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.16-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++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.16-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++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.16-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++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.16-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++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'F:/biocbuild/bbs-3.16-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
In file included from ReadDistribution.cpp:7:
ReadDistribution.h:13:10: fatal error: bam.h: No such file or directory
   13 | #include "bam.h"
      |          ^~~~~~~
compilation terminated.
make: *** [F:/biocbuild/bbs-3.16-bioc/R/etc/x64/Makeconf:260: ReadDistribution.o] Error 1
ERROR: compilation failed for package 'BitSeq'
* removing 'F:/biocbuild/bbs-3.16-bioc/R/library/BitSeq'