Package: seqbias

Version: 1.34.0

Command: rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqbias.buildbin-libdir seqbias_1.34.0.tar.gz

StartedAt: 2020-04-15 09:39:52 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 09:40:20 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 28.2 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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### Running command:
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###   rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqbias.buildbin-libdir seqbias_1.34.0.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-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=core2 -c sam.c -o sam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=core2 -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=core2 -c bam_aux.c -o bam_aux.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/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/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/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/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=core2 -c pos_table.c -o pos_table.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c kmer_matrix.cpp -o kmer_matrix.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c logger.cpp -o logger.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c motif.cpp -o motif.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c seqbias.cpp -o seqbias.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c sequencing_bias.cpp -o sequencing_bias.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c twobitseq.cpp -o twobitseq.o
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/aliasmanager.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/conversion.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/directives.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/emitfromevents.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/emitter.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/emitterstate.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/emitterutils.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/exp.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/iterator.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/nodebuilder.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/node.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/nodeownership.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/null.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/ostream.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/parser.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/regex.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/scanner.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/scanscalar.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/scantag.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/scantoken.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/simplekey.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/singledocparser.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/stream.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: yaml-cpp/tag.o: File format not recognized
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
yaml-cpp/aliasmanager.o: file not recognized: File format not recognized
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'seqbias'
* removing 'C:/Users/biocbuild/bbs-3.10-bioc/meat/seqbias.buildbin-libdir/seqbias'