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Package 76/565HostnameOS / ArchBUILDCHECKBUILD BIN
BitSeq 1.1.1
Peter Glaus
Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BitSeq
Last Changed Rev: 65607 / Revision: 66885
Last Changed Date: 2012-04-30 11:28:08 -0700 (Mon, 30 Apr 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: BitSeq
Version: 1.1.1
Command: rm -rf BitSeq.buildbin-libdir && mkdir BitSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BitSeq_1.1.1.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R BitSeq.buildbin-libdir
StartedAt: 2012-06-21 04:37:05 -0700 (Thu, 21 Jun 2012)
EndedAt: 2012-06-21 04:41:23 -0700 (Thu, 21 Jun 2012)
EllapsedTime: 258.4 seconds
RetCode: 0
Status:  OK 
PackageFile: BitSeq_1.1.1.tgz
PackageFileSize: 1.629 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BitSeq.buildbin-libdir BitSeq_1.1.1.tar.gz'
>>>>>>> 

* installing *source* package 'BitSeq' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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:182: warning: ignoring #pragma omp parallel
estimateExpression.cpp:206: warning: ignoring #pragma omp parallel
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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:482: warning: ignoring #pragma omp critical
readDistribution.cpp:491: warning: ignoring #pragma omp critical
readDistribution.cpp:507: warning: ignoring #pragma omp parallel
readDistribution.cpp:538: warning: ignoring #pragma omp parallel
readDistribution.cpp:541: warning: ignoring #pragma omp critical
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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 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 /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 ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --no-multiarch --no-test-load --library=BitSeq.buildbin-libdir --libs-only BitSeq_1.1.1.tar.gz'
>>>>>>> 

* installing *source* package 'BitSeq' ...
** libs
*** arch - ppc
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c argumentParser.cpp -o argumentParser.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c collapsedSampler.cpp -o collapsedSampler.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c common.cpp -o common.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c estimateDE.cpp -o estimateDE.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c estimateExpression.cpp -o estimateExpression.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c getGeneExpression.cpp -o getGeneExpression.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c getVariance.cpp -o getVariance.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c gibbsParameters.cpp -o gibbsParameters.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c gibbsSampler.cpp -o gibbsSampler.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c lowess.cpp -o lowess.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c parseAlignment.cpp -o parseAlignment.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c posteriorSamples.cpp -o posteriorSamples.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c readDistribution.cpp -o readDistribution.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c sampler.cpp -o sampler.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c transcriptExpression.cpp -o transcriptExpression.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c transcriptInfo.cpp -o transcriptInfo.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c transcriptSequence.cpp -o transcriptSequence.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -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  -c transposeFiles.cpp -o transposeFiles.o
g++ -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o BitSeq.so 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 /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/ppc/libbam.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/ppc/libbcf.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/ppc/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/ppc

* DONE (BitSeq)


>>>>>>> 
>>>>>>> FIXING LINKS FOR BitSeq.buildbin-libdir/BitSeq/libs/ppc/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/ppc/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/ppc/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/ppc/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/ppc/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_1.1.1.tar.gz'
>>>>>>> 

* installing *source* package 'BitSeq' ...
** libs
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c argumentParser.cpp -o argumentParser.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c collapsedSampler.cpp -o collapsedSampler.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c common.cpp -o common.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c estimateDE.cpp -o estimateDE.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c estimateExpression.cpp -o estimateExpression.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c getGeneExpression.cpp -o getGeneExpression.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c getVariance.cpp -o getVariance.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c gibbsParameters.cpp -o gibbsParameters.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c gibbsSampler.cpp -o gibbsSampler.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c lowess.cpp -o lowess.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c parseAlignment.cpp -o parseAlignment.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c posteriorSamples.cpp -o posteriorSamples.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c readDistribution.cpp -o readDistribution.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c sampler.cpp -o sampler.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c transcriptExpression.cpp -o transcriptExpression.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c transcriptInfo.cpp -o transcriptInfo.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -c transcriptSequence.cpp -o transcriptSequence.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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  -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 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 /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"