[BioC] Error: Cannot allocate vector of size 279.1Mb

[Martin Morgan]

On 04/03/2012 09:51 AM, Desiree Wilson wrote:
> I am running R in 32 bit mode because I have Windows XP. I wasn't aware
> that Windows XP can run 64 bit mode. I should look into this.

If you're planning on RMA or GCRMA normalization then memory efficient 
implementations are available in affy (justRMA) or gcrma (justGCRMA).

You might also look into using the Bioconductor AMI 
http://bioconductor.org/help/bioconductor-cloud-ami/ which would be more 
cost-effective than buying more memory (I think the 'try-it-now' 
instance has 4 GB of memory and so wouldn't cost you anything for 2 
hours of processing time).

Martin

>
> On Tue, Apr 3, 2012 at 11:46 AM, Steve Lianoglou<
> mailinglist.honeypot at gmail.com>  wrote:
>
>> Hi,
>>
>> Are you running R in 32 or 64 bit mode?
>> What is the value of `.Machine$sizeof.pointer` when you punch that
>> into your R workspace?
>> Also, please provide output of sessionInfo()
>>
>> -steve
>>
>>
>> On Tue, Apr 3, 2012 at 12:42 PM, Desiree Wilson
>> <desiree.s.wilson at gmail.com>  wrote:
>>> Hello everyone. How are you all doing?
>>>
>>> My name is Desiree. I'm a 1st grad student experiencing problems reading
>> 27
>>> CEL files into R using the ReadAffy command. The total size of these
>> files
>>> are 350 Mb. Here are my commands:
>>>
>>>> library(affy) # loads the "Affy" package
>>>> library(limma) # loads the "Limma" package
>>>> setwd("path directory to the CEL files")
>>>> mydata<-ReadAffy( ) # reads all of the CEL files in my work directory
>>>
>>> But after I run the last command, I get the following error message:
>>> Error: cannot allocate vector of size 279.1 Mb
>>> In addition: Warning messages:
>>> 1: In `rownames<-`(`*tmp*`, value = c("1", "2", "3", "4", "5", "6",  :
>>>   Reached total allocation of 1535Mb: see help(memory.size)
>>> 2: In `rownames<-`(`*tmp*`, value = c("1", "2", "3", "4", "5", "6",  :
>>>   Reached total allocation of 1535Mb: see help(memory.size)
>>> 3: In `rownames<-`(`*tmp*`, value = c("1", "2", "3", "4", "5", "6",  :
>>>   Reached total allocation of 1535Mb: see help(memory.size)
>>> 4: In `rownames<-`(`*tmp*`, value = c("1", "2", "3", "4", "5", "6",  :
>>>   Reached total allocation of 1535Mb: see help(memory.size)
>>>
>>> I've done it before on the same computer (specs: Lenovo Think with Intel
>>> Core 2 Quad CPU Q9400 @2.66GHz, 3.00 of RAM, Microsoft Windows XP
>>> Professional Version 2002).
>>>
>>> I've read previous posts and I will admit that the solutions offered are
>>> very hard for me to understand (I am a beginner). I have tried using the
>>> "memory.limit(size=3000)" command and then run the "ReadAffy()" command
>>> again but I still get the same error message. Any suggestions would be
>>> greatly appreciated.
>>> --Desiree Wilson
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>>
>>
>>
>> --
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>>   | Memorial Sloan-Kettering Cancer Center
>>   | Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>
>
> 	[[alternative HTML version deleted]]
>
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