[BioC] justGCRMA memory problem

[James W. MacDonald]

Jianping Jin wrote:
> 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?

Odd. How many chips and what type are they? Maybe I can try to replicate 
that here.

Jim


> 
> 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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-- 
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