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Package 538/553HostnameOS / ArchBUILDCHECKBUILD BIN
VariantAnnotation 1.2.11
Valerie Obenchain
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/VariantAnnotation
Last Changed Rev: 68868 / Revision: 69725
Last Changed Date: 2012-08-28 09:18:42 -0700 (Tue, 28 Aug 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ]
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: VariantAnnotation
Version: 1.2.11
Command: rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.2.11.tar.gz
StartedAt: 2012-09-24 03:31:32 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 03:32:54 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 81.7 seconds
RetCode: 0
Status:  OK  
PackageFile: VariantAnnotation_1.2.11.zip
PackageFileSize: 1.181 MiB

Command output


install for i386

* installing *source* package 'VariantAnnotation' ...
** libs
gcc  -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc  -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c dna_hash.c -o dna_hash.o
gcc  -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c rle.c -o rle.o
gcc  -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
gcc  -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c vcffile.c -o vcffile.o
gcc  -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c vcftype.c -o vcftype.o
gcc  -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c writevcf.c -o writevcf.o
gcc -shared -s -static-libgcc -o VariantAnnotation.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o dna_hash.o rle.o utilities.o vcffile.o vcftype.o writevcf.o E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -LE:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LE:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LE:/biocbld/BBS-2~1.10-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'VariantAnnotation.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'VariantAnnotation' ...
** libs
gcc -m64 -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-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-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-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-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-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-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-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-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-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-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-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-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-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-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-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 -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c writevcf.c -o writevcf.o
gcc -m64 -shared -s -static-libgcc -o VariantAnnotation.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o dna_hash.o rle.o utilities.o vcffile.o vcftype.o writevcf.o E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a E:/biocbld/bbs-2.10-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -LE:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LE:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2~1.10-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantAnnotation' as VariantAnnotation_1.2.11.zip

* DONE (VariantAnnotation)