seqbias 1.24.0
Daniel Jones
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/seqbias | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/seqbias_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=seqbias.buildbin-libdir --merge-multiarch seqbias_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL seqbias_1.24.0.zip && rm seqbias_1.24.0.tar.gz seqbias_1.24.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* 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
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O3 -Wall -std=gnu99 -mtune=core2 -c common.c -o common.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O3 -Wall -std=gnu99 -mtune=core2 -c miscmath.c -o miscmath.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O3 -Wall -std=gnu99 -mtune=core2 -c pos_table.c -o pos_table.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O3 -Wall -std=gnu99 -mtune=core2 -c samtools_extra.c -o samtools_extra.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c kmer_matrix.cpp -o kmer_matrix.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c logger.cpp -o logger.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c motif.cpp -o motif.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c seqbias.cpp -o seqbias.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c sequencing_bias.cpp -o sequencing_bias.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c twobitseq.cpp -o twobitseq.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/node.cpp -o yaml-cpp/node.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/null.cpp -o yaml-cpp/null.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/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:28:48: warning: unused parameter 'type' [-Wunused-parameter]
void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
C:/Rtools/mingw_32/bin/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 C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-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
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mtune=core2 -c common.c -o common.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mtune=core2 -c miscmath.c -o miscmath.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mtune=core2 -c pos_table.c -o pos_table.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mtune=core2 -c samtools_extra.c -o samtools_extra.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c kmer_matrix.cpp -o kmer_matrix.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c logger.cpp -o logger.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c motif.cpp -o motif.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c seqbias.cpp -o seqbias.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c sequencing_bias.cpp -o sequencing_bias.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c twobitseq.cpp -o twobitseq.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/node.cpp -o yaml-cpp/node.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/null.cpp -o yaml-cpp/null.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/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:28:48: warning: unused parameter 'type' [-Wunused-parameter]
void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/local323/include" -Wall -Wextra -I. -O2 -Wall -mtune=core2 -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
C:/Rtools/mingw_64/bin/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 C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/seqbias.buildbin-libdir/seqbias/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqbias' as seqbias_1.24.0.zip
* DONE (seqbias)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'seqbias' successfully unpacked and MD5 sums checked