[Bioc-devel] Error installing GenomicRanges

James Diggans james at Veracyte.com
Sat Aug 24 01:48:49 CEST 2013

All - trying to install GenomicRanges on a RHEL 5.7 machine today and ran into the following error from line 78 in SummarizedExperiment-rowData-methods.R:

R> biocLite("GenomicRanges")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1.
Installing package(s) 'GenomicRanges'
trying URL 'http://bioconductor.org/packages/2.12/bioc/src/contrib/GenomicRanges_1.12.4.tar.gz'
Content type 'application/x-gzip' length 2576074 bytes (2.5 Mb)
opened URL
downloaded 2.5 Mb

* installing *source* package 'GenomicRanges' ...
** libs
gcc -std=gnu99 -I/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -std=gnu99 -I/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c cigar_utils.c -o cigar_utils.o
gcc -std=gnu99 -I/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c transcript_utils.c -o transcript_utils.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o cigar_utils.o transcript_utils.o -L/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/lib -lR
installing to /nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/library/GenomicRanges/libs
** R
** inst
** preparing package for lazy loading
Error in fmls[[generic at signature]] <- quote(rowData(x)) :
  object of type 'symbol' is not subsettable
Error : unable to load R code in package 'GenomicRanges'
ERROR: lazy loading failed for package 'GenomicRanges'
* removing '/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/library/GenomicRanges'

The downloaded source packages are in
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package 'GenomicRanges' had non-zero exit status
Calls: biocLite -> biocLiteInstall -> install.packages

Any help on possible causation greatly appreciated. 

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