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BioC 3.1: BUILD BIN report for BitSeq on petty

This page was generated on 2015-10-09 09:35:03 -0700 (Fri, 09 Oct 2015).

Package 111/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BitSeq 1.12.0
Antti Honkela , Panagiotis Papastamoulis
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/BitSeq
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BitSeq
Version: 1.12.0
Command: rm -rf BitSeq.buildbin-libdir && mkdir BitSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BitSeq_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R BitSeq.buildbin-libdir
StartedAt: 2015-10-09 03:01:24 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:02:29 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 65.5 seconds
RetCode: 0
Status:  OK 
PackageFile: BitSeq_1.12.0.tgz
PackageFileSize: 1.124 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf BitSeq.buildbin-libdir && mkdir BitSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BitSeq_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R BitSeq.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BitSeq.buildbin-libdir BitSeq_1.12.0.tar.gz'
>>>>>>> 

* installing *source* package ‘BitSeq’ ...
configure: Version def: -DBS_VERSION=\"1.12.0\"
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-g++-4.2 -arch x86_64 option to support OpenMP... -fopenmp
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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.12.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.2/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/Library/Frameworks/R.framework/Resources/lib -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 /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/BitSeq.buildbin-libdir/BitSeq/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* 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/3.2/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/3.2/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/3.2/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/3.2/Resources/lib/libreadline.dylib" "BitSeq.buildbin-libdir/BitSeq/libs//BitSeq.so"