BitSeq

Package: BitSeq
Type: Package
Depends: Rsamtools, zlibbioc
Imports: S4Vectors, IRanges
LinkingTo: Rsamtools (>= 1.19.38), zlibbioc
Suggests: edgeR, DESeq, BiocStyle
Title: Transcript expression inference and differential expression
analysis for RNA-seq data
Version: 1.16.0
Date: 2014-10-03
Author: Peter Glaus, Antti Honkela and Magnus Rattray
Maintainer: Antti Honkela <antti.honkela@hiit.fi>, Panagiotis Papastamoulis <panagiotis.papastamoulis@manchester.ac.uk>
Description: The BitSeq package is targeted for transcript expression
analysis and differential expression analysis of RNA-seq data
in two stage process. In the first stage it uses Bayesian
inference methodology to infer expression of individual
transcripts from individual RNA-seq experiments. The second
stage of BitSeq embraces the differential expression analysis
of transcript expression. Providing expression estimates from
replicates of multiple conditions, Log-Normal model of the
estimates is used for inferring the condition mean transcript
expression and ranking the transcripts based on the likelihood
of differential expression.
License: Artistic-2.0 + file LICENSE
Packaged: 2016-05-04 04:30:02 UTC; biocbuild
biocViews: GeneExpression, DifferentialExpression, Sequencing, RNASeq,
Bayesian, AlternativeSplicing, DifferentialSplicing,
Transcription
NeedsCompilation: yes

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'BitSeq' ...
configure: Version def: -DBS_VERSION="1.16.0"
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 g++ accepts -g... yes
checking for g++ option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/Makevars.win
** libs
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c ArgumentParser.cpp -o ArgumentParser.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c FileHeader.cpp -o FileHeader.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c GibbsParameters.cpp -o GibbsParameters.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c GibbsSampler.cpp -o GibbsSampler.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c MyTimer.cpp -o MyTimer.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c ReadDistribution.cpp -o ReadDistribution.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c Sampler.cpp -o Sampler.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c SimpleSparse.cpp -o SimpleSparse.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c TagAlignments.cpp -o TagAlignments.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c TranscriptExpression.cpp -o TranscriptExpression.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c TranscriptInfo.cpp -o TranscriptInfo.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c TranscriptSequence.cpp -o TranscriptSequence.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c VariationalBayes.cpp -o VariationalBayes.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c common.cpp -o common.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c estimateDE.cpp -o estimateDE.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c estimateExpression.cpp -o estimateExpression.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c estimateVBExpression.cpp -o estimateVBExpression.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c getGeneExpression.cpp -o getGeneExpression.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c getVariance.cpp -o getVariance.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c lowess.cpp -o lowess.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c misc.cpp -o misc.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c parseAlignment.cpp -o parseAlignment.o
g++ -I/home/ddbj/local/lib64/R/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="1.16.0" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"  -I. -fopenmp -fpic  -g -O2  -c transposeFiles.cpp -o transposeFiles.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -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 /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libbam.a /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libbcf.a /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -fopenmp -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/BitSeq/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'BitSeq'
    finding HTML links ... done
    BitSeq-package                          html  
    estimateDE                              html  
    estimateExpression                      html  
    estimateHyperPar                        html  
    estimateVBExpression                    html  
    getDE                                   html  
    getExpression                           html  
    getGeneExpression                       html  
    getMeanVariance                         html  
    loadSamples                             html  
    parseAlignment                          html  
    transcriptInfo                          html  
    transcriptInfoFile                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BitSeq)
Making 'packages.html' ... done