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INSTALL report for BitSeq on malbec1

This page was generated on 2020-08-10 11:36:03 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BitSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 184/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BitSeq 1.33.1
Antti Honkela , Panagiotis Papastamoulis
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/BitSeq
Branch: master
Last Commit: a27c864
Last Changed Date: 2020-07-14 16:10:37 -0400 (Tue, 14 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64 [ OK ] OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BitSeq
Version: 1.33.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BitSeq
StartedAt: 2020-08-09 16:50:21 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 16:51:43 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 81.6 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BitSeq
###
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##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BitSeq’ ...
** using staged installation
configure: Version def: -DBS_VERSION=\"1.33.1\"
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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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))){
              ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Rhtslib_bam_plbuf.c -o Rhtslib_bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Rhtslib_sam.c -o Rhtslib_sam.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c VariationalBayes.cpp -o VariationalBayes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c parseAlignment.cpp -o parseAlignment.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.33.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.12-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-3.12-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 Rhtslib_bam_plbuf.o Rhtslib_sam.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/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -fopenmp -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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)