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

[Martin Morgan]

On 04/03/2012 12:33 PM, Martin Morgan wrote:
> 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).

I guess the 'try-it-now' instances are so-called 'micro-instances', with 
only 613MB of memory, so to use the AMI you'd have to actually go 
through the process of creating a larger instance as outlined on

http://bioconductor.org/help/bioconductor-cloud-ami/

Martin

>
> 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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>>>> Bioconductor at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>>
>>> --
>>> 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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>
>


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