Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U [V] W  X  Y  Z 

BioC 3.1: INSTALL report for VariantAnnotation on zin2

This page was generated on 2015-10-09 09:24:25 -0700 (Fri, 09 Oct 2015).

Package 1003/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.14.13
Valerie Obenchain
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/VariantAnnotation
Last Changed Rev: 107909 / Revision: 109384
Last Changed Date: 2015-08-28 13:56:52 -0700 (Fri, 28 Aug 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: VariantAnnotation
Version: 1.14.13
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD INSTALL VariantAnnotation
StartedAt: 2015-10-08 18:08:24 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 18:08:45 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 21.2 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD INSTALL VariantAnnotation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.1-bioc/R/library’
* installing *source* package ‘VariantAnnotation’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.1-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-3.1-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-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c dna_hash.c -o dna_hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c rle.c -o rle.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c strhash.c -o strhash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c utilities.c -o utilities.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c vcffile.c -o vcffile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c vcftype.c -o vcftype.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c writevcf.c -o writevcf.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/R/library/VariantAnnotation/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (VariantAnnotation)