[Bioc-sig-seq] edgeR package: install on Linux

[Steve Lianoglou]

Hi,

On Wed, Mar 9, 2011 at 9:55 AM, Jean-Paul Bouchet
<jean-paul.bouchet at avignon.inra.fr> wrote:
> Hello
>
> I would like to install EdgeR on a Linux Debian system with a rather old
> version of R (2.7.1)
> The preselected selection of Core Bioconductor has been installed today with
> biocLite().
>
> I have first tried as explained at
> http://www.bioconductor.org/help/bioc-views/release/bioc/html/edgeR.html
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("edgeR")
> Running biocinstall version 2.2.11 with R version 2.7.1
> Your version of R requires version 2.2 of BioConductor.
> Avis dans install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, :
> argument 'lib' is missing: using '/usr/local/lib/R/site-library'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
> :
> package ‘edgeR’ is not available
>
> Then I have downloaded edgeR_2.0.4.tar.gz and tried to install the package
> from the archive :
> install.packages(".../R/packages/edgeR_2.0.4.tar.gz", dependencies = TRUE,
> repos = NULL)
> Avis dans install.packages(".../R/packages/edgeR_2.0.4.tar.gz", :
> l'argument 'lib' manque : '/usr/local/lib/R/site-library' est utilisé
> * Installing *source* package 'edgeR' ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Error in .walkClassGraph(classDef, "subclasses", where) :
> the "subClass" list for class "LargeDataObject", includes an undefined class
> "RGList"
> Error: unable to load R code in package 'edgeR'
> Execution halted
>
> Could someone give me any advices to help me in this installation ?

Honestly, I think the best advice you'd get is to install the latest
version of R (2.12.2) and just use the "normal" bioconductor install
steps (using the `biocLite` function). The version of R you are
running is (very) old. Also, R is extremely easy to compile and
install yourself somewhere in your home directory if your sysadmin
isn't willing to install it for you via the *.deb packages the
r-project makes available.

Another note: the error you get is complaining about an undefined
class "RGList" -- this class is defined in the limma package, so
you'll at least need to install that first ...

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact