Back to Multiple platform build/check report for BioC 3.9 |
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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 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BitSeq ### ############################################################################## ############################################################################## * 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)