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Package 79/609HostnameOS / ArchBUILDCHECKBUILD BIN
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 ]

Summary

Package: BitSeq
Version: 1.2.2
Command: rm -rf BitSeq.buildbin-libdir && mkdir BitSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BitSeq_1.2.2.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R BitSeq.buildbin-libdir
StartedAt: 2013-03-25 01:47:51 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:49:52 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 121.5 seconds
RetCode: 0
Status:  OK 
PackageFile: BitSeq_1.2.2.tgz
PackageFileSize: 1.386 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BitSeq.buildbin-libdir BitSeq_1.2.2.tar.gz'
>>>>>>> 

* installing *source* package 'BitSeq' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c ArgumentParser.cpp -o ArgumentParser.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c GibbsParameters.cpp -o GibbsParameters.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c GibbsSampler.cpp -o GibbsSampler.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:562: warning: ignoring #pragma omp critical
ReadDistribution.cpp:571: warning: ignoring #pragma omp critical
ReadDistribution.cpp:587: warning: ignoring #pragma omp parallel
ReadDistribution.cpp:618: warning: ignoring #pragma omp parallel
ReadDistribution.cpp:621: warning: ignoring #pragma omp critical
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c Sampler.cpp -o Sampler.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c TagAlignments.cpp -o TagAlignments.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c TranscriptExpression.cpp -o TranscriptExpression.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c TranscriptInfo.cpp -o TranscriptInfo.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c TranscriptSequence.cpp -o TranscriptSequence.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c common.cpp -o common.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c estimateDE.cpp -o estimateDE.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:171: warning: ignoring #pragma omp parallel
estimateExpression.cpp:195: warning: ignoring #pragma omp parallel
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c getGeneExpression.cpp -o getGeneExpression.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c getVariance.cpp -o getVariance.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c lowess.cpp -o lowess.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c parseAlignment.cpp -o parseAlignment.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c transposeFiles.cpp -o transposeFiles.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o BitSeq.so 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 /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/i386/libbam.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/i386/libbcf.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/i386/libtabix.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/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

* DONE (BitSeq)


>>>>>>> 
>>>>>>> FIXING LINKS FOR BitSeq.buildbin-libdir/BitSeq/libs/i386/BitSeq.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "BitSeq.buildbin-libdir/BitSeq/libs/i386/BitSeq.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "BitSeq.buildbin-libdir/BitSeq/libs/i386/BitSeq.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "BitSeq.buildbin-libdir/BitSeq/libs/i386/BitSeq.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "BitSeq.buildbin-libdir/BitSeq/libs/i386/BitSeq.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=BitSeq.buildbin-libdir --libs-only BitSeq_1.2.2.tar.gz'
>>>>>>> 

* installing *source* package 'BitSeq' ...
** libs
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c ArgumentParser.cpp -o ArgumentParser.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c GibbsParameters.cpp -o GibbsParameters.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c GibbsSampler.cpp -o GibbsSampler.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:562: warning: ignoring #pragma omp critical
ReadDistribution.cpp:571: warning: ignoring #pragma omp critical
ReadDistribution.cpp:587: warning: ignoring #pragma omp parallel
ReadDistribution.cpp:618: warning: ignoring #pragma omp parallel
ReadDistribution.cpp:621: warning: ignoring #pragma omp critical
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c Sampler.cpp -o Sampler.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c TagAlignments.cpp -o TagAlignments.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c TranscriptExpression.cpp -o TranscriptExpression.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c TranscriptInfo.cpp -o TranscriptInfo.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c TranscriptSequence.cpp -o TranscriptSequence.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c common.cpp -o common.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c estimateDE.cpp -o estimateDE.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:171: warning: ignoring #pragma omp parallel
estimateExpression.cpp:195: warning: ignoring #pragma omp parallel
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c getGeneExpression.cpp -o getGeneExpression.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c getVariance.cpp -o getVariance.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c lowess.cpp -o lowess.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c parseAlignment.cpp -o parseAlignment.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD  -I.  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/zlibbioc/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c transposeFiles.cpp -o transposeFiles.o
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o BitSeq.so 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 /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/x86_64/libbam.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/x86_64/libbcf.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/x86_64/libtabix.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/BitSeq.buildbin-libdir/BitSeq/libs/x86_64

* DONE (BitSeq)


>>>>>>> 
>>>>>>> FIXING LINKS FOR BitSeq.buildbin-libdir/BitSeq/libs/x86_64/BitSeq.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "BitSeq.buildbin-libdir/BitSeq/libs/x86_64/BitSeq.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "BitSeq.buildbin-libdir/BitSeq/libs/x86_64/BitSeq.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "BitSeq.buildbin-libdir/BitSeq/libs/x86_64/BitSeq.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "BitSeq.buildbin-libdir/BitSeq/libs/x86_64/BitSeq.so"