The --vanilla seemed to do the trick. It installed fine now. Thanks a lot. Lien Molecular Endocrinology Laboratory Department of Cellular and Molecular Medicine | KU Leuven Campus GHB O&N1 | Herestraat 49 box 901 | BE-3000 Leuven | Belgium Phone +3216330648 ________________________________________ Van: Dan Tenenbaum [dtenenba at fhcrc.org] Verzonden: zaterdag 15 december 2012 1:28 To: Lien Spans Cc: bioconductor at r-project.org Onderwerp: Re: [BioC] warning during installation of cummeRbund On Fri, Dec 14, 2012 at 5:16 AM, Lien Spans <lien.spans at="" med.kuleuven.be=""> wrote: > Dear all, > > I'm working on RNA-seq data that I would like to analyze with the cummeRbund package. > I have R and biocLite installed, however when I try installing the cummeRbund package, I receive an error. I googled to find out if other people had a similar problem, but didn't really find an answer. > I first tried > > biocLite('cummeRbund') > Using R version 2.15.2, biocinstall version 2.4.13. > Installing Bioconductor version 2.4 packages: > [1] "cummeRbund" > Please wait... > Installing package(s) into ?/home/lien/R/x86_64-pc-linux-gnu- library/2.15? > (as ?lib? is unspecified) > Warning message: > package ?cummeRbund? is not available (for R version 2.15.2) > > > I then tried > > biocLite(character()) but the cummeRbund package doesn't show up in the list of all available packages. > > I also tried > > install.packages("cummeRbund", repos="http://www.omegahat.org/R", type="source") > Installing package(s) into ?/home/lien/R/x86_64-pc-linux-gnu- library/2.15? > (as ?lib? is unspecified) > Warning message: > package ?cummeRbund? is not available (for R version 2.15.2) > > > I'm not very familiar with R, so I hope this question is not too basic, but I would appreciate an answer. > Looks like the BiocInstaller package is not properly installed. Try starting R like this: R --vanilla Then do this: source("http://bioconductor.org/biocLite.R") biocLite("cummeRbund") If that does not work, please email the output of the following commands: sessionInfo() biocinstallRepos() Dan > Many thanks in advance, > Lien Spans > Molecular Endocrinology Laboratory > Department of Cellular and Molecular Medicine | KU Leuven > Campus GHB O&N1 | Herestraat 49 box 901 | BE-3000 Leuven | Belgium > Phone +3216330648 > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor