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BioC 3.1: INSTALL report for seqbias on zin2

This page was generated on 2015-10-09 09:24:12 -0700 (Fri, 09 Oct 2015).

Package 888/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqbias 1.16.0
Daniel Jones
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/seqbias
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: seqbias
Version: 1.16.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD INSTALL seqbias
StartedAt: 2015-10-08 18:04:03 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 18:04:49 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 45.8 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD INSTALL seqbias
###
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* installing to library ‘/home/biocbuild/bbs-3.1-bioc/R/library’
* installing *source* package ‘seqbias’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c common.c -o common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c miscmath.c -o miscmath.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c pos_table.c -o pos_table.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c samtools_extra.c -o samtools_extra.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c kmer_matrix.cpp -o kmer_matrix.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c logger.cpp -o logger.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c motif.cpp -o motif.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c seqbias.cpp -o seqbias.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c sequencing_bias.cpp -o sequencing_bias.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c twobitseq.cpp -o twobitseq.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:2:0:
yaml-cpp/collectionstack.h:28:8: warning: unused parameter ‘type’ [-Wunused-parameter]
   void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
        ^
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++ -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o seqbias.so common.o miscmath.o pos_table.o samtools_extra.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o yaml-cpp/aliasmanager.o yaml-cpp/conversion.o yaml-cpp/directives.o yaml-cpp/emitfromevents.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/nodebuilder.o yaml-cpp/node.o yaml-cpp/nodeownership.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/regex.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/simplekey.o yaml-cpp/singledocparser.o yaml-cpp/stream.o yaml-cpp/tag.o /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/R/library/seqbias/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (seqbias)