>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BitSeq.buildbin-libdir BitSeq_1.6.1.tar.gz'
>>>>>>>
* installing *source* package ‘BitSeq’ ...
configure: Version def: -DBS_VERSION=\"1.6.1\"
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether llvm-g++-4.2 -arch x86_64 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to support OpenMP... -fopenmp
configure: SAM_INCLUDE: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usretc//Rsamtools.mk
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/Makevars.win
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c ArgumentParser.cpp -o ArgumentParser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c CollapsedSampler.cpp -o CollapsedSampler.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c FileHeader.cpp -o FileHeader.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c GibbsParameters.cpp -o GibbsParameters.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c GibbsSampler.cpp -o GibbsSampler.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c MyTimer.cpp -o MyTimer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c PosteriorSamples.cpp -o PosteriorSamples.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c R_init_BitSeq.cpp -o R_init_BitSeq.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c ReadDistribution.cpp -o ReadDistribution.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c Sampler.cpp -o Sampler.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c SimpleSparse.cpp -o SimpleSparse.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c TagAlignments.cpp -o TagAlignments.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c TranscriptExpression.cpp -o TranscriptExpression.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c TranscriptInfo.cpp -o TranscriptInfo.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c TranscriptSequence.cpp -o TranscriptSequence.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c VariationalBayes.cpp -o VariationalBayes.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c common.cpp -o common.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c estimateDE.cpp -o estimateDE.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c estimateExpression.cpp -o estimateExpression.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c estimateHyperPar.cpp -o estimateHyperPar.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c estimateVBExpression.cpp -o estimateVBExpression.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c getGeneExpression.cpp -o getGeneExpression.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c getVariance.cpp -o getVariance.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c lowess.cpp -o lowess.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c misc.cpp -o misc.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c parseAlignment.cpp -o parseAlignment.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.6.x\" -DPACKAGE_STRING=\"BitSeq\ 1.6.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.6.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fopenmp -fPIC -mtune=core2 -g -O2 -Wall -c transposeFiles.cpp -o transposeFiles.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o BitSeq.so ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o MyTimer.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Sampler.o SimpleSparse.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o VariationalBayes.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o transposeFiles.o -fopenmp /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/BitSeq.buildbin-libdir/BitSeq/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BitSeq)
>>>>>>>
>>>>>>> FIXING LINKS FOR BitSeq.buildbin-libdir/BitSeq/libs//BitSeq.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "BitSeq.buildbin-libdir/BitSeq/libs//BitSeq.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "BitSeq.buildbin-libdir/BitSeq/libs//BitSeq.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "BitSeq.buildbin-libdir/BitSeq/libs//BitSeq.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "BitSeq.buildbin-libdir/BitSeq/libs//BitSeq.so"