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### Running command:
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### C:\cygwin\bin\curl.exe -O http://zin2/BBS/2.14/bioc/src/contrib/VariantAnnotation_1.10.5.tar.gz && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch VariantAnnotation_1.10.5.tar.gz && rm VariantAnnotation_1.10.5.tar.gz
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install for i386
* installing to library 'E:/biocbld/bbs-2.14-bioc/R/library'
* installing *source* package 'VariantAnnotation' ...
** libs
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dna_hash.c -o dna_hash.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rle.c -o rle.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c strhash.c -o strhash.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c vcffile.c -o vcffile.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c vcftype.c -o vcftype.o
gcc -m32 -shared -s -static-libgcc -o VariantAnnotation.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LE:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LE:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.14-bioc/R/library/VariantAnnotation/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'tabulate' in package 'VariantAnnotation'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing to library 'E:/biocbld/bbs-2.14-bioc/R/library'
* installing *source* package 'VariantAnnotation' ...
** libs
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c dna_hash.c -o dna_hash.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rle.c -o rle.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c strhash.c -o strhash.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c vcffile.c -o vcffile.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c vcftype.c -o vcftype.o
gcc -m64 -shared -s -static-libgcc -o VariantAnnotation.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a E:/biocbld/bbs-2.14-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LE:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LE:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.14-bioc/R/library/VariantAnnotation/libs/x64
** testing if installed package can be loaded
* DONE (VariantAnnotation)