Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

INSTALL report for VariantAnnotation on malbec1

This page was generated on 2021-05-06 12:29:36 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the VariantAnnotation package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1930/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.36.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/VariantAnnotation
Branch: RELEASE_3_12
Last Commit: 9918bd1
Last Changed Date: 2020-10-27 10:42:24 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: VariantAnnotation
Version: 1.36.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL VariantAnnotation
StartedAt: 2021-05-05 16:35:26 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 16:36:47 -0400 (Wed, 05 May 2021)
EllapsedTime: 81.0 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL VariantAnnotation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘VariantAnnotation’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c dna_hash.c -o dna_hash.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rle.c -o rle.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c strhash.c -o strhash.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utilities.c -o utilities.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c vcffile.c -o vcffile.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c vcftype.c -o vcftype.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c writevcf.c -o writevcf.o
gcc -shared -L/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs
** R
** inst
** byte-compile and prepare 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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (VariantAnnotation)