Daniel Jones
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/seqbias |
| Branch: RELEASE_3_6 |
| Last Commit: 15c3c25 |
| Last Changed Date: 2017-10-30 12:39:32 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:09:21 -0400 (Thu, 12 Apr 2018).
| Package 1272/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| seqbias 1.26.0 Daniel Jones
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | [ OK ] | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: seqbias |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD INSTALL seqbias |
| StartedAt: 2018-04-11 18:03:54 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 18:04:31 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 36.7 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD INSTALL seqbias
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.6-bioc/R/library’
* installing *source* package ‘seqbias’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c common.c -o common.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c miscmath.c -o miscmath.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c pos_table.c -o pos_table.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c samtools_extra.c -o samtools_extra.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c kmer_matrix.cpp -o kmer_matrix.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c logger.cpp -o logger.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c motif.cpp -o motif.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c seqbias.cpp -o seqbias.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c sequencing_bias.cpp -o sequencing_bias.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c twobitseq.cpp -o twobitseq.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/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:28:48: warning: unused parameter ‘type’ [-Wunused-parameter]
void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
^
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++ -shared -L/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/R/library/seqbias/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (seqbias)