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BioC 3.4: INSTALL report for seqbias on moscato1

This page was generated on 2016-09-21 03:43:17 -0700 (Wed, 21 Sep 2016).

Package 1096/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqbias 1.21.0
Daniel Jones
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: seqbias
Version: 1.21.0
Command: rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/seqbias_1.21.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=seqbias.buildbin-libdir --merge-multiarch seqbias_1.21.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL seqbias_1.21.0.zip && rm seqbias_1.21.0.tar.gz seqbias_1.21.0.zip
StartedAt: 2016-09-19 20:52:54 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 20:57:37 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 283.0 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/seqbias_1.21.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=seqbias.buildbin-libdir --merge-multiarch seqbias_1.21.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL seqbias_1.21.0.zip  && rm seqbias_1.21.0.tar.gz seqbias_1.21.0.zip
###
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100  586k  100  586k    0     0  26.8M      0 --:--:-- --:--:-- --:--:-- 31.8M

install for i386

* installing *source* package 'seqbias' ...

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


** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LD:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include"   -I"D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LD:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/seqbias.buildbin-libdir/seqbias/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqbias' as seqbias_1.21.0.zip
* DONE (seqbias)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'seqbias' successfully unpacked and MD5 sums checked