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BUILD BIN report for seqbias on tokay2

This page was generated on 2019-10-16 12:24:37 -0400 (Wed, 16 Oct 2019).

Package 1491/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqbias 1.32.0
Daniel Jones
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/seqbias
Branch: RELEASE_3_9
Last Commit: edc384f
Last Changed Date: 2019-05-02 11:53:21 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: seqbias
Version: 1.32.0
Command: rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqbias.buildbin-libdir seqbias_1.32.0.tar.gz
StartedAt: 2019-10-16 10:11:48 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 10:14:22 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 153.8 seconds
RetCode: 0
Status:  OK  
PackageFile: seqbias_1.32.0.zip
PackageFileSize: 1.984 MiB

Command output

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###
### Running command:
###
###   rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqbias.buildbin-libdir seqbias_1.32.0.tar.gz
###
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##############################################################################



install for i386

* installing *source* package 'seqbias' ...
** using staged installation

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


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=generic -c sam.c -o sam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=generic -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=generic -c bam_aux.c -o bam_aux.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=generic -c common.c -o common.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=generic -c miscmath.c -o miscmath.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=generic -c pos_table.c -o pos_table.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c kmer_matrix.cpp -o kmer_matrix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c logger.cpp -o logger.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c motif.cpp -o motif.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c seqbias.cpp -o seqbias.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c sequencing_bias.cpp -o sequencing_bias.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c twobitseq.cpp -o twobitseq.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/node.cpp -o yaml-cpp/node.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/null.cpp -o yaml-cpp/null.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -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/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -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 sam.o bam_plbuf.o bam_aux.o common.o miscmath.o pos_table.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 -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/i386 -lhts -lz -lm -lws2_32 -lpthread -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/seqbias.buildbin-libdir/00LOCK-seqbias/00new/seqbias/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'seqbias'
    finding HTML links ... done
    count_reads                             html  
    kmer_freq                               html  
    random_intervals                        html  
    seqbias-class                           html  
    seqbias-package                         html  
    seqbias_fit                             html  
    seqbias_load                            html  
    seqbias_predict                         html  
    seqbias_save                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

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/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -std=gnu99 -mtune=generic -c sam.c -o sam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -std=gnu99 -mtune=generic -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -std=gnu99 -mtune=generic -c bam_aux.c -o bam_aux.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -std=gnu99 -mtune=generic -c common.c -o common.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -std=gnu99 -mtune=generic -c miscmath.c -o miscmath.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -std=gnu99 -mtune=generic -c pos_table.c -o pos_table.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c kmer_matrix.cpp -o kmer_matrix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c logger.cpp -o logger.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c motif.cpp -o motif.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c seqbias.cpp -o seqbias.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c sequencing_bias.cpp -o sequencing_bias.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c twobitseq.cpp -o twobitseq.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/node.cpp -o yaml-cpp/node.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/null.cpp -o yaml-cpp/null.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -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/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=generic -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 sam.o bam_plbuf.o bam_aux.o common.o miscmath.o pos_table.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 -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/x64 -lhts -lz -lm -lws2_32 -lpthread -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/seqbias.buildbin-libdir/seqbias/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqbias' as seqbias_1.32.0.zip
* DONE (seqbias)