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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 && /Users/biocbuild/BBS/utils/build-universal.sh VariantAnnotation_1.4.12.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R VariantAnnotation.buildbin-libdir
StartedAt: 2013-03-25 02:11:07 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:11:51 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 43.4 seconds
RetCode: 0
Status:  OK 
PackageFile: VariantAnnotation_1.4.12.tgz
PackageFileSize: 1.207 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.4.12.tar.gz'
>>>>>>> 

* installing *source* package 'VariantAnnotation' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c dna_hash.c -o dna_hash.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c rle.c -o rle.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c utilities.c -o utilities.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c vcffile.c -o vcffile.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c vcftype.c -o vcftype.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c writevcf.c -o writevcf.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o dna_hash.o rle.o utilities.o vcffile.o vcftype.o writevcf.o /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/i386/libbam.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/i386/libbcf.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/i386/libtabix.a -lz -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/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

* DONE (VariantAnnotation)


>>>>>>> 
>>>>>>> FIXING LINKS FOR VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/i386/VariantAnnotation.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/i386/VariantAnnotation.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/i386/VariantAnnotation.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/i386/VariantAnnotation.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/i386/VariantAnnotation.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=VariantAnnotation.buildbin-libdir --libs-only VariantAnnotation_1.4.12.tar.gz'
>>>>>>> 

* installing *source* package 'VariantAnnotation' ...
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c dna_hash.c -o dna_hash.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c rle.c -o rle.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c utilities.c -o utilities.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c vcffile.c -o vcffile.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c vcftype.c -o vcftype.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c writevcf.c -o writevcf.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o dna_hash.o rle.o utilities.o vcffile.o vcftype.o writevcf.o /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/x86_64/libbam.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/x86_64/libbcf.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/x86_64/libtabix.a -lz -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x86_64

* DONE (VariantAnnotation)


>>>>>>> 
>>>>>>> FIXING LINKS FOR VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x86_64/VariantAnnotation.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x86_64/VariantAnnotation.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x86_64/VariantAnnotation.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x86_64/VariantAnnotation.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x86_64/VariantAnnotation.so"