seqbias 1.1.0
Daniel Jones
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias | | Last Changed Rev: 54802 / Revision: 55359 | | 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 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | [ OK ] |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* installing *source* package 'seqbias' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c sequencing_bias.cpp -o sequencing_bias.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c kmers.cpp -o kmers.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c miscmath.cpp -o miscmath.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c common.cpp -o common.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.9-bioc/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 -std=gnu99 -c table.c -o table.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.9-bioc/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 -std=gnu99 -c logger.c -o logger.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c seqbias.cpp -o seqbias.o
In file included from D:/biocbld/bbs-2.9-bioc/R/include/R.h:44:0,
from seqbias.cpp:10:
D:/biocbld/bbs-2.9-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:/rtools213/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/wingdi.h:63:0: note: this is the location of the previous definition
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/aliascontent.cpp -o yaml-cpp/aliascontent.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/map.cpp -o yaml-cpp/map.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/node.cpp -o yaml-cpp/node.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/null.cpp -o yaml-cpp/null.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/parserstate.cpp -o yaml-cpp/parserstate.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/scalar.cpp -o yaml-cpp/scalar.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
yaml-cpp/scanner.cpp: In member function 'YAML::Token::TYPE YAML::Scanner::GetStartTokenFor(YAML::Scanner::IndentMarker::INDENT_TYPE) const':
yaml-cpp/scanner.cpp:280:2: warning: control reaches end of non-void function
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/sequence.cpp -o yaml-cpp/sequence.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.9-bioc/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 -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
yaml-cpp/tag.cpp: In member function 'const std::string YAML::Tag::Translate(const YAML::ParserState&)':
yaml-cpp/tag.cpp:48:2: warning: control reaches end of non-void function
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.9-bioc/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 -std=gnu99 -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'
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.9-bioc/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 -std=gnu99 -c gnulib/printf-args.c -o gnulib/printf-args.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.9-bioc/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 -std=gnu99 -c gnulib/printf-parse.c -o gnulib/printf-parse.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.9-bioc/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 -std=gnu99 -c gnulib/vasnprintf.c -o gnulib/vasnprintf.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.9-bioc/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 -std=gnu99 -c gnulib/vasprintf.c -o gnulib/vasprintf.o
x86_64-w64-mingw32-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/x64 -lbam -lbcf -lRzlib -lws2_32 -LD:/biocbld/bbs-2.9-bioc/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/seqbias.buildbin-libdir/seqbias/libs/x64
** R
** inst
** preparing package for lazy loading
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
** 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_1.1.0.zip
* DONE (seqbias)