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Package 592/609HostnameOS / ArchBUILDCHECKBUILD BIN
VariantAnnotation 1.4.12
Valerie Obenchain
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/VariantAnnotation
Last Changed Rev: 74127 / Revision: 74773
Last Changed Date: 2013-03-09 17:25:33 -0800 (Sat, 09 Mar 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ]
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: VariantAnnotation
Version: 1.4.12
Command: rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.4.12.tar.gz
StartedAt: 2013-03-25 04:27:17 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 04:28:45 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 87.6 seconds
RetCode: 0
Status:  OK  
PackageFile: VariantAnnotation_1.4.12.zip
PackageFileSize: 1.207 MiB

Command output


install for i386

* installing *source* package 'VariantAnnotation' ...
** libs
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c writevcf.c -o writevcf.o
gcc -m32 -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 D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -LD:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LD:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-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 D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a D:/biocbld/bbs-2.11-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -LD:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LD:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.11-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantAnnotation' as VariantAnnotation_1.4.12.zip

* DONE (VariantAnnotation)