[BioC] justGCRMA memory problem

[James W. MacDonald]

Hi Jianping,

Jianping Jin wrote:
> Dear list:
> 
> My PC has 2 GB of RAM. I set the max memory size for R equal to 2000M. But 
> R stopped running when memory size reached 1 GM. Current version I use is 
> R.2.2.0. I do not run into the problem with R 2.1.0. Does anyone have the 
> same problem with new version of R?

I haven't noticed any differences in memory usage. However, there are 
certain aspects of Windows' memory usage that can cause problems. First, 
if a large block of memory has already been allocated (even if it is 
subsequently freed up), you may not be able to use it. Can you replicate 
the above problem if no other programs are running on your computer with 
a fresh instance of R?

Also, memory.size() will simply give you the amount of RAM that R is 
currently using. More informative would be memory.size(max = TRUE).

Additionally, there is a note in the R-FAQ for Windows that setting the 
memory size > 1.7Gb may be detrimental. I have never seen this problem 
myself, but you might try setting --max.memory.size = 1700M and try again.

HTH,

Jim



-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623