[BioC] justGCRMA memory problem

[Jianping Jin]

Hi Jim, thanks for your quick reply!

I tried --max-mem-size=17000M and run just R 2.2.0 without any other 
programs running at the time. The message I got listed as the following:

> data <- justGCRMA(filenames=files)
Computing affinities.Computing affinities.Done.
Done.
Adjusting for optical effect..Error: cannot allocate vector of size 424868 
Kb
> memory.size(max=TRUE)
[1] 1194139648
> memory.limit()
[1] 1782579200

Any ideas about it?

Thanks again!

Jianping

--On Thursday, February 09, 2006 10:21 AM -0500 "James W. MacDonald" 
<jmacdon at med.umich.edu> wrote:

> 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



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