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BioC 3.2: INSTALL report for VariantAnnotation on zin1

This page was generated on 2015-08-24 10:48:03 -0700 (Mon, 24 Aug 2015).

Package 1049/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.15.26
Valerie Obenchain
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VariantAnnotation
Last Changed Rev: 107383 / Revision: 107696
Last Changed Date: 2015-08-13 11:48:00 -0700 (Thu, 13 Aug 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: VariantAnnotation
Version: 1.15.26
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD INSTALL VariantAnnotation
StartedAt: 2015-08-23 17:08:21 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 17:08:42 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 21.5 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD INSTALL VariantAnnotation
###
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* installing to library ‘/home/biocbuild/bbs-3.2-bioc/R/library’
* installing *source* package ‘VariantAnnotation’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c dna_hash.c -o dna_hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c rle.c -o rle.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c strhash.c -o strhash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c utilities.c -o utilities.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c vcffile.c -o vcffile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c vcftype.c -o vcftype.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c writevcf.c -o writevcf.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/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 writevcf.o /home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/R/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)