[BioC] Error message, when updating packages

[Steve Lianoglou]

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