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BioC 2.12: CHECK report for BitSeq on petty

This page was generated on 2013-10-09 09:40:10 -0700 (Wed, 09 Oct 2013).

Package 85/671HostnameOS / ArchBUILDCHECKBUILD BIN
BitSeq 1.4.3
Peter Glaus
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/BitSeq
Last Changed Rev: 78338 / Revision: 81334
Last Changed Date: 2013-07-11 09:05:10 -0700 (Thu, 11 Jul 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 Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: BitSeq
Version: 1.4.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BitSeq_1.4.3.tar.gz
StartedAt: 2013-10-08 21:45:28 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 21:49:34 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 246.0 seconds
RetCode: 0
Status:  OK 
CheckDir: BitSeq.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BitSeq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BitSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BitSeq' version '1.4.3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'BitSeq' can be installed ... [70s/71s] OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Components with restrictions not permitted:
  Artistic-2.0 + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [11s/11s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/BitSeq.Rcheck/00check.log'
for details.

BitSeq.Rcheck/00install.out:

* installing *source* package 'BitSeq' ...
configure: Version def: -DBS_VERSION=\"1.4.3\"
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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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 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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.3\" -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 -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 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.Rcheck/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)

BitSeq.Rcheck/BitSeq-Ex.timings:

nameusersystemelapsed
BitSeq-package0.3040.0090.315
estimateDE0.0110.0020.014
estimateExpression0.0120.0030.016
estimateHyperPar0.0070.0020.009
getDE0.0050.0020.007
getExpression0.0050.0010.007