[Bioc-devel] Error installing GenomicRanges

[James Diggans]

Thanks Martin - biocValid() returned true and updated.packages() saw nothing else from CRAN to update. In desperation, I pulled the:

	source("http://bioconductor.org/biocLite.R")
	pkgs <- rownames(installed.packages())
	biocLite(pkgs)

and then re-tried biocLite("GenomicRanges") which then worked fine. No idea what end up being fixed.
-j

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
Sent: Friday, August 23, 2013 5:07 PM
To: James Diggans
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Error installing GenomicRanges

On 08/23/2013 04:48 PM, James Diggans wrote:
> 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'

It's a weird error and I'd guess that one or more of your packages are out of date or is too new (e.g., installed from the devel branch, or built with R-devel rather than R-3.0.1). Maybe

   library(BiocInstaller)
   biocValid()

points to something?

Martin

> * removing '/nfs/RD/DataAnalysis/software/R/R-3.0.1/lib64/R/library/GenomicRanges'
>
> The downloaded source packages are in
>          '/tmp/Rtmp8JSjBM/downloaded_packages'
> 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.
> -j
>
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