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Package 422/479HostnameOS / ArchBUILDCHECKBUILD BIN
seqbias 1.1.0
Daniel Jones
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias
Last Changed Rev: 54802 / Revision: 56603
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  ERROR  skipped  skipped 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  ERROR  skipped  skipped 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64 [ ERROR ] skipped  skipped 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: seqbias
Version: 1.1.0
Command: chmod a+r seqbias -R && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data seqbias
StartedAt: 2011-07-07 03:44:40 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 03:45:34 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 54.1 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

* checking for file 'seqbias/DESCRIPTION' ... OK
* preparing 'seqbias':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
      -----------------------------------
* installing *source* package 'seqbias' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c sequencing_bias.cpp -o sequencing_bias.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c kmers.cpp -o kmers.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c miscmath.cpp -o miscmath.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c common.cpp -o common.o
gcc  `echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'| "D:/biocbld/BBS-2˜1.9-B/R/bin/R" --vanilla --slave` -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -mtune=core2 -c table.c -o table.o
gcc  `echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'| "D:/biocbld/BBS-2˜1.9-B/R/bin/R" --vanilla --slave` -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -mtune=core2 -c logger.c -o logger.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c seqbias.cpp -o seqbias.o
In file included from D:/biocbld/BBS-2˜1.9-B/R/include/R.h:44:0,
                 from seqbias.cpp:10:
D:/biocbld/BBS-2˜1.9-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools213\mingw\bin\../lib/gcc/mingw32/4.5.0/../../../../include/wingdi.h:313:0: note: this is the location of the previous definition
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/aliascontent.cpp -o yaml-cpp/aliascontent.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/map.cpp -o yaml-cpp/map.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/parserstate.cpp -o yaml-cpp/parserstate.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/scalar.cpp -o yaml-cpp/scalar.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/sequence.cpp -o yaml-cpp/sequence.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -mtune=core2 -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
gcc  `echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'| "D:/biocbld/BBS-2˜1.9-B/R/bin/R" --vanilla --slave` -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -mtune=core2 -c gnulib/asprintf.c -o gnulib/asprintf.o
gnulib/asprintf.c: In function 'asprintf':
gnulib/asprintf.c:37:3: warning: implicit declaration of function 'vasprintf'
gcc  `echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'| "D:/biocbld/BBS-2˜1.9-B/R/bin/R" --vanilla --slave` -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -mtune=core2 -c gnulib/printf-args.c -o gnulib/printf-args.o
gcc  `echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'| "D:/biocbld/BBS-2˜1.9-B/R/bin/R" --vanilla --slave` -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -mtune=core2 -c gnulib/printf-parse.c -o gnulib/printf-parse.o
gcc  `echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'| "D:/biocbld/BBS-2˜1.9-B/R/bin/R" --vanilla --slave` -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -mtune=core2 -c gnulib/vasnprintf.c -o gnulib/vasnprintf.o
gcc  `echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'| "D:/biocbld/BBS-2˜1.9-B/R/bin/R" --vanilla --slave` -I"D:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"D:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -mtune=core2 -c gnulib/vasprintf.c -o gnulib/vasprintf.o
g++ -shared -s -static-libgcc -o seqbias.dll tmp.def sequencing_bias.o kmers.o miscmath.o common.o table.o logger.o seqbias.o yaml-cpp/aliascontent.o yaml-cpp/conversion.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/map.o yaml-cpp/node.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/parserstate.o yaml-cpp/regex.o yaml-cpp/scalar.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/sequence.o yaml-cpp/simplekey.o yaml-cpp/stream.o yaml-cpp/tag.o gnulib/asprintf.o gnulib/printf-args.o gnulib/printf-parse.o gnulib/vasnprintf.o gnulib/vasprintf.o -LD:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/usrlib/i386 -lbam -lbcf -ltabix -lws2_32 -L"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/libs/i386" -lzlib1bioc -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
c:/rtools213/mingw/bin/../lib/gcc/mingw32/4.5.0/../../../../mingw32/bin/ld.exe: cannot find -lzlib1bioc
collect2: ld returned 1 exit status
ERROR: compilation failed for package 'seqbias'
* removing 'D:/biocbld/bbs-2.9-bioc/tmpdir/RtmpQxKFnE/Rinst486a7297/seqbias'
      -----------------------------------
ERROR: package installation failed