Hi, On Wed, Mar 9, 2011 at 9:55 AM, Jean-Paul Bouchet <jean-paul.bouc...@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 _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing