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BioC 2.12: BUILD BIN report for seqbias on moscato2

This page was generated on 2013-10-09 09:38:52 -0700 (Wed, 09 Oct 2013).

Package 589/671HostnameOS / ArchBUILDCHECKBUILD BIN
seqbias 1.8.0
Daniel Jones
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/seqbias
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
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 Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: seqbias
Version: 1.8.0
Command: rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=seqbias.buildbin-libdir seqbias_1.8.0.tar.gz
StartedAt: 2013-10-09 05:28:52 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 05:32:16 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 204.1 seconds
RetCode: 0
Status:  OK  
PackageFile: seqbias_1.8.0.zip
PackageFileSize: 1.692 MiB

Command output


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
** 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_1.8.0.zip
* DONE (seqbias)