Hello all. I was using R 2.4x with Mac OSX without problems, but when I upgraded to 2.5 I'm always having problems trying to update the libraries. When I write update.packages() I do not receive any news. When I know that there is a new version of a library, I'm trying to install it but I always have the message : unable to access index for repository http://www.bioconductor.org/ packages/2.0/omegahat/bin/macosx/universal/contrib/2.5 ?Do someone know where is the problem o where must I change something to avoid this? Thanks a lot Gonzalo -- ?Donde me he equivocado, soy el ?nico responsable; donde no, el m?rito es de los que me han ayudado? ================================================================ M. Gonzalo CLAROS claros at uma.es Dpt. Biolog?a Molecular y Bioqu?mica Facultad de Ciencias Fax: (+34) 95 213 2041 Universidad de M?laga Tel: (+34) 95 213 7284 E-29071 M?laga (Spain) http://www.bmbq.uma.es/fmp/

"M. Gonzalo Claros D?az" <claros at="" uma.es=""> writes: > Hello all. > > I was using R 2.4x with Mac OSX without problems, but when I upgraded > to 2.5 I'm always having problems trying to update the libraries. > > When I write update.packages() I do not receive any news. When I know > that there is a new version of a library, I'm trying to install it > but I always have the message If you are calling update.packages with no arguments, then you are relying on the repos option (getOptions("repos")). You haven't told us what you have set there, but I suspect that may be related to the message you are seeing. I would recommend the following procedure to update: 1. Make sure Biobase is up-to-date. You can check the version number against what is available on the website. The current release version is Bioconductor 1.14.0. 2. Do this: library("Biobase") update.packages(repos=biocReposList()) > : unable to access index for repository http://www.bioconductor.org/ > packages/2.0/omegahat/bin/macosx/universal/contrib/2.5 > > ?Do someone know where is the problem o where must I change something > to avoid this? We renamed our "omegahat" repository "extra" because it really was not a mirror of the omegahat project's repository, but consists of extra non-CRAN, non-BioC packages that are used by various BioC packages. biocLite() and biocReposList() know about the change, but any hard-coded URLs to the repositories would not (obviously) know abou the change. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org