BitSeq 1.2.2
Peter Glaus
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/BitSeq | | Last Changed Rev: 73009 / Revision: 74773 | | Last Changed Date: 2013-01-29 15:22:51 -0800 (Tue, 29 Jan 2013) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
install for i386
* installing *source* package 'BitSeq' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c ArgumentParser.cpp -o ArgumentParser.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c GibbsParameters.cpp -o GibbsParameters.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c GibbsSampler.cpp -o GibbsSampler.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:562:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ReadDistribution.cpp:571:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ReadDistribution.cpp:587:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ReadDistribution.cpp:618:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ReadDistribution.cpp:621:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c Sampler.cpp -o Sampler.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c TagAlignments.cpp -o TagAlignments.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c TranscriptExpression.cpp -o TranscriptExpression.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c TranscriptInfo.cpp -o TranscriptInfo.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c TranscriptSequence.cpp -o TranscriptSequence.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c common.cpp -o common.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c estimateDE.cpp -o estimateDE.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:171:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
estimateExpression.cpp:195:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c getGeneExpression.cpp -o getGeneExpression.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c getVariance.cpp -o getVariance.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c lowess.cpp -o lowess.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c parseAlignment.cpp -o parseAlignment.o
g++ -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c transposeFiles.cpp -o transposeFiles.o
g++ -m32 -shared -s -static-libgcc -o BitSeq.dll tmp.def ArgumentParser.o CollapsedSampler.o GibbsParameters.o GibbsSampler.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Sampler.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o parseAlignment.o transposeFiles.o D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -LD:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.11-bioc/meat/BitSeq.buildbin-libdir/BitSeq/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'BitSeq.Rnw'
** testing if installed package can be loaded
install for x64
* installing *source* package 'BitSeq' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c ArgumentParser.cpp -o ArgumentParser.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c GibbsParameters.cpp -o GibbsParameters.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c GibbsSampler.cpp -o GibbsSampler.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:562:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ReadDistribution.cpp:571:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ReadDistribution.cpp:587:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ReadDistribution.cpp:618:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ReadDistribution.cpp:621:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c Sampler.cpp -o Sampler.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c TagAlignments.cpp -o TagAlignments.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c TranscriptExpression.cpp -o TranscriptExpression.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c TranscriptInfo.cpp -o TranscriptInfo.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c TranscriptSequence.cpp -o TranscriptSequence.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c common.cpp -o common.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c estimateDE.cpp -o estimateDE.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:171:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
estimateExpression.cpp:195:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c getGeneExpression.cpp -o getGeneExpression.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c getVariance.cpp -o getVariance.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c lowess.cpp -o lowess.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c parseAlignment.cpp -o parseAlignment.o
g++ -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c transposeFiles.cpp -o transposeFiles.o
g++ -m64 -shared -s -static-libgcc -o BitSeq.dll tmp.def ArgumentParser.o CollapsedSampler.o GibbsParameters.o GibbsSampler.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Sampler.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o parseAlignment.o transposeFiles.o D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -LD:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.11-bioc/meat/BitSeq.buildbin-libdir/BitSeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BitSeq' as BitSeq_1.2.2.zip
* DONE (BitSeq)