BitSeq 1.0.1
Peter Glaus
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/BitSeq | | Last Changed Rev: 65606 / Revision: 69725 | | Last Changed Date: 2012-04-30 11:27:00 -0700 (Mon, 30 Apr 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] |
| petty | 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++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c argumentParser.cpp -o argumentParser.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c collapsedSampler.cpp -o collapsedSampler.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c common.cpp -o common.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c estimateDE.cpp -o estimateDE.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:182:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
estimateExpression.cpp:206:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c getGeneExpression.cpp -o getGeneExpression.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c getVariance.cpp -o getVariance.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c gibbsParameters.cpp -o gibbsParameters.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c gibbsSampler.cpp -o gibbsSampler.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c lowess.cpp -o lowess.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c parseAlignment.cpp -o parseAlignment.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c posteriorSamples.cpp -o posteriorSamples.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c readDistribution.cpp -o readDistribution.o
readDistribution.cpp:482:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
readDistribution.cpp:491:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
readDistribution.cpp:507:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
readDistribution.cpp:538:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
readDistribution.cpp:541:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c sampler.cpp -o sampler.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c transcriptExpression.cpp -o transcriptExpression.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c transcriptInfo.cpp -o transcriptInfo.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c transcriptSequence.cpp -o transcriptSequence.o
g++ -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -O2 -Wall -mtune=core2 -c transposeFiles.cpp -o transposeFiles.o
g++ -shared -s -static-libgcc -o BitSeq.dll tmp.def R_init_BitSeq.o argumentParser.o collapsedSampler.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o getGeneExpression.o getVariance.o getWithinGeneExpression.o gibbsParameters.o gibbsSampler.o lowess.o parseAlignment.o posteriorSamples.o readDistribution.o sampler.o transcriptExpression.o transcriptInfo.o transcriptSequence.o transposeFiles.o E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -LE:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LE:/biocbld/BBS-2~1.10-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:182:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
estimateExpression.cpp:206:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
g++ -m64 -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c readDistribution.cpp -o readDistribution.o
readDistribution.cpp:482:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
readDistribution.cpp:491:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
readDistribution.cpp:507:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
readDistribution.cpp:538:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
readDistribution.cpp:541:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
g++ -m64 -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"E:/biocbld/bbs-2.10-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 R_init_BitSeq.o argumentParser.o collapsedSampler.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o getGeneExpression.o getVariance.o getWithinGeneExpression.o gibbsParameters.o gibbsSampler.o lowess.o parseAlignment.o posteriorSamples.o readDistribution.o sampler.o transcriptExpression.o transcriptInfo.o transcriptSequence.o transposeFiles.o E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -LE:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2~1.10-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/BitSeq.buildbin-libdir/BitSeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BitSeq' as BitSeq_1.0.1.zip
* DONE (BitSeq)