Dear List, I tried to update my bioconductor packages under R2.8.1 and got following error message: "Error: Indexing out of bounds". The same error occured when I installed R2.9.0 and tried to install Bioconductor and when I try to install individual packages. However, on a different computer everything still works fine. I tried different CRAN mirrors with the same result. Does anyone has any suggestions? Thanks very much, Mike > sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETAR Y=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.8.1 -- Dr. Michael Walter The Microarray Facility University of Tuebingen Calwerstr. 7 72076 T?bingen/GERMANY Tel.: +49 (0) 7071 29 83210 Fax. + 49 (0) 7071 29 5228 Confidentiality Note:\ This message is intended only for...{{dropped:9}}

Hi Michael, On Jun 25, 2009, at 10:35 AM, Michael Walter wrote: > Dear List, > > I tried to update my bioconductor packages under R2.8.1 and got > following error message: "Error: Indexing out of bounds". The same > error occured when I installed R2.9.0 and tried to install > Bioconductor and when I try to install individual packages. However, > on a different computer everything still works fine. I tried > different CRAN mirrors with the same result. Does anyone has any > suggestions? This is weird, a few things: 1. Instead of just giving the sessionInfo() results, could you rather show what happens when you run: source('http://bioconductor.org/biocLite.R') biocLite('Biobase') (I only choose Biobase since it seems to have minimal dependencies and will show an error message rather quickly, but you can try any other package that you're trying to install as well) 2. Does this only happen when you install bioconductor packages? What if you install some other R package, like: install.packages('gplots') 3. You're talking about installing bioconductor packages, so what do CRAN mirrors have to do with it (these two are orthogonal, no? (unless your BioC package has some CRAN dependencies?)) 4. Is there perhaps some hidden .R* files that are being loaded when you fire up R that might be messing things up. Eg: check if there is an .RData or .Rhistory file in your current working directory and move them out (or cd into another directory) before firing up R. Alternatively do an `ls()` when you load R and see if there's something floating around in your workspace that you can subsequently remove [via: rm(list=ls())] before you do your bioconductor installs. Honestly I don't really know what's causing this, so just taking a few stabs in the dark. -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact