seqbias 1.7.0
Daniel Jones
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias | | Last Changed Rev: 70052 / Revision: 74774 | | Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
install for i386
* installing *source* package 'seqbias' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O3 -Wall -std=gnu99 -mtune=core2 -c common.c -o common.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O3 -Wall -std=gnu99 -mtune=core2 -c miscmath.c -o miscmath.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O3 -Wall -std=gnu99 -mtune=core2 -c pos_table.c -o pos_table.o
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O3 -Wall -std=gnu99 -mtune=core2 -c samtools_extra.c -o samtools_extra.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c kmer_matrix.cpp -o kmer_matrix.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c logger.cpp -o logger.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c motif.cpp -o motif.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c seqbias.cpp -o seqbias.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c sequencing_bias.cpp -o sequencing_bias.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c twobitseq.cpp -o twobitseq.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -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]
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++ -m32 -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-2.12-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LE:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/seqbias.buildbin-libdir/seqbias/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'overview.Rnw'
** testing if installed package can be loaded
install for x64
* installing *source* package 'seqbias' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mtune=core2 -c common.c -o common.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mtune=core2 -c miscmath.c -o miscmath.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mtune=core2 -c pos_table.c -o pos_table.o
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mtune=core2 -c samtools_extra.c -o samtools_extra.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c kmer_matrix.cpp -o kmer_matrix.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c logger.cpp -o logger.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c motif.cpp -o motif.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c seqbias.cpp -o seqbias.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c sequencing_bias.cpp -o sequencing_bias.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c twobitseq.cpp -o twobitseq.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -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]
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++ -m64 -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-2.12-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a E:/biocbld/bbs-2.12-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LE:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/seqbias.buildbin-libdir/seqbias/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqbias' as seqbias_1.7.0.zip
* DONE (seqbias)