[BioC] [R] Problem using GOstats package in R 2.2.1

James W. MacDonald jmacdon at med.umich.edu
Fri Mar 10 15:30:17 CET 2006

Olivier BUHARD wrote:
> Dear all,
> This message is a kind of 'to be continued...' for that send by /Yu-An 
> Dong,/ [BioC] problems with GO package data  
> <https://stat.ethz.ch/pipermail/bioconductor/2006-February/011760.html>,  
> last february.
> I've just installed R 2.2.1 on my computer (Windows based version) and 
> downloaded Bioconductor available for this version via the graphical 
> interface facility provided by R. Then installed GO 1.8.2 using the zip 
> package, all goes well...
> I just tried to take a look at the output of GOLOCUSID2GO like Yu-An 
> Dong have done it after loading GOstats (1.4.0) package :
> //
> GOLOCUSID2GO[["4121"]]
> //Then, after a while, R hangs up, windows tells my the program Rgui.exe 
> is to be close by windows. So here, I don't think impatience is the 
> explanaition of this problem :-(
> If anyone could give my a few hints, it would be great.

My first hint would be to use the Bioconductor listserv for BioC related 
questions rather than R-help. I have moved this post there for you.

I don't have any problems getting the output from this environment, so 
it is likely some problem with your local installation. As with most 
posts to BioC, you should include the output from a call to 
sessionInfo(). Another bit of information that might be helpful is the 
amount of RAM on your machine. It takes about 328 Mb of RAM on my WinXP 
box to do this same call. In this situation I don't know if Windows will 
use the swap file if you don't have enough memory or if it will exit 
ungracefully as you describe.



James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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