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BioC 2.14: INSTALL report for VariantAnnotation on petty

This page was generated on 2014-10-08 08:59:41 -0700 (Wed, 08 Oct 2014).

Package 803/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.10.5
Valerie Obenchain
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/VariantAnnotation
Last Changed Rev: 91895 / Revision: 95116
Last Changed Date: 2014-06-26 05:58:14 -0700 (Thu, 26 Jun 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64 [ OK ] OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: VariantAnnotation
Version: 1.10.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL VariantAnnotation
StartedAt: 2014-10-07 18:09:15 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 18:10:10 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 54.8 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL VariantAnnotation
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library’
* installing *source* package ‘VariantAnnotation’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Biostrings_stubs.c -o Biostrings_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c IRanges_stubs.c -o IRanges_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c XVector_stubs.c -o XVector_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c dna_hash.c -o dna_hash.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c rle.c -o rle.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c strhash.c -o strhash.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c utilities.c -o utilities.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c vcffile.c -o vcffile.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c vcftype.c -o vcftype.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o VariantAnnotation.so 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 /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.1/Resources/library/VariantAnnotation/libs
** 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
* DONE (VariantAnnotation)