Antti Honkela
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/BitSeq |
| Branch: RELEASE_3_9 |
| Last Commit: 63856e9 |
| Last Changed Date: 2019-05-02 11:53:35 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:01:05 -0400 (Wed, 16 Oct 2019).
| Package 177/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BitSeq 1.28.0 Antti Honkela
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | [ OK ] | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: BitSeq |
| Version: 1.28.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BitSeq |
| StartedAt: 2019-10-15 18:54:24 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 18:56:01 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 97.3 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BitSeq
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘BitSeq’ ...
** using staged installation
configure: Version def: -DBS_VERSION=\"1.28.0\"
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++ -std=gnu++11 accepts -g... yes
checking for g++ -std=gnu++11 option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/Makevars.win
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c ArgumentParser.cpp -o ArgumentParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c FileHeader.cpp -o FileHeader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c GibbsParameters.cpp -o GibbsParameters.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c GibbsSampler.cpp -o GibbsSampler.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c MyTimer.cpp -o MyTimer.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp: In member function ‘bool ReadDistribution::observed(ns_rD::fragmentP)’:
ReadDistribution.cpp:265:9: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
(! frag->second->core.flag & BAM_FREVERSE))){
^~~~~~~~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In member function ‘bool ReadDistribution::getP(ns_rD::fragmentP, double&, double&)’:
ReadDistribution.cpp:687:14: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
(! frag->second->core.flag & BAM_FREVERSE))){
^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c Sampler.cpp -o Sampler.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c SimpleSparse.cpp -o SimpleSparse.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c TagAlignments.cpp -o TagAlignments.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c TranscriptExpression.cpp -o TranscriptExpression.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c TranscriptInfo.cpp -o TranscriptInfo.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c TranscriptSequence.cpp -o TranscriptSequence.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c VariationalBayes.cpp -o VariationalBayes.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c bam_plbuf.c -o bam_plbuf.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c common.cpp -o common.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c estimateDE.cpp -o estimateDE.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c estimateExpression.cpp -o estimateExpression.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c estimateVBExpression.cpp -o estimateVBExpression.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c getGeneExpression.cpp -o getGeneExpression.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c getVariance.cpp -o getVariance.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c lowess.cpp -o lowess.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c misc.cpp -o misc.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c parseAlignment.cpp -o parseAlignment.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c sam.c -o sam.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.28.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c transposeFiles.cpp -o transposeFiles.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/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 bam_plbuf.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o sam.o transposeFiles.o /home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/libhts.a -lz -lm -lbz2 -llzma -lpthread -fopenmp -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-BitSeq/00new/BitSeq/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BitSeq)