BitSeq 1.3.7
Peter Glaus
| Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BitSeq | | Last Changed Rev: 74691 / Revision: 74756 | | Last Changed Date: 2013-03-22 11:26:02 -0700 (Fri, 22 Mar 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / 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 |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] |
* installing *source* package 'BitSeq' ...
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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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=\"1.3.6\" -DPACKAGE_STRING=\"Bitseq\ 1.3.6\" -DPACKAGE_BUGREPORT=\"glaus@cs.man.ac.uk\" -DPACKAGE_URL=\"\" -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 -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 -o BitSeq.so ArgumentParser.o CollapsedSampler.o FileHeader.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 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-2.12-bioc/meat/BitSeq.buildbin-libdir/BitSeq/libs
** 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
packaged installation of 'BitSeq' as 'BitSeq_1.3.7.tgz'
* DONE (BitSeq)