seqbias 1.2.0
Daniel Jones
| Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/seqbias | | Last Changed Rev: 59920 / Revision: 61898 | | Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | [ OK ] |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* installing *source* package 'seqbias' ...
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WARNING: this package has a configure script
It probably needs manual configuration
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** libs
gcc -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O3 -Wall -std=gnu99 -mtune=core2 -c common.c -o common.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O3 -Wall -std=gnu99 -mtune=core2 -c miscmath.c -o miscmath.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O3 -Wall -std=gnu99 -mtune=core2 -c pos_table.c -o pos_table.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O3 -Wall -std=gnu99 -mtune=core2 -c samtools_extra.c -o samtools_extra.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c kmer_matrix.cpp -o kmer_matrix.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c logger.cpp -o logger.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c motif.cpp -o motif.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c seqbias.cpp -o seqbias.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c sequencing_bias.cpp -o sequencing_bias.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c twobitseq.cpp -o twobitseq.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -I"E:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.9-bioc/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++ -shared -s -static-libgcc -o seqbias.dll tmp.def 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 E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -LE:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LE:/biocbld/bbs-2.9-bioc/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/seqbias.buildbin-libdir/seqbias/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'overview.Rnw'
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqbias' as seqbias_1.2.0.zip
* DONE (seqbias)