[R] memory problem on Suse

[Martin Morgan]

Ask on the bioconductpr mailing list, where you will be diirected to  
several solutions for analyzing what I guess are 100's is cel files

http://bioconductor.org

-- 
Martin Morgan

On Dec 11, 2009, at 8:02 AM, Marc Schwartz <marc_schwartz at me.com> wrote:

> On Dec 11, 2009, at 6:24 AM, Ambrosi Alessandro wrote:
>
>>
>> Dear all, I am meeting some problems with  memory allocation. I  
>> know it is an old issue, I'm sorry.
>> I looked for a solution in the FAQs and manuals, mails, but without  
>> finding the working answer.
>> I really hope you can help me.
>> For instance, if I try to read micorarray data I get:
>>
>>> mab=ReadAffy(cdfname="hgu133plus2cdf")
>> Error: cannot allocate vector of size 858.0 Mb
>>>
>>
>> I get similar errors with smaller objects, smaller data sets or  
>> other procedures
>> ("Error: cannot allocate vector of size 123.0 Mb").
>> I'm running R with Suse 11.1 Linux OS, on two Xeon processors (8  
>> cores), 32 GB RAM.
>> I suppose I have enough resources to manage these objects and data  
>> files....
>>
>> Any suggestions or hints will be really appreciated!
>> Many thanks in advance.
>> Alessandro
>
> Well, you are running into a situation where there is not a  
> contiguous chunk of RAM available in the sizes referenced, for  
> allocation to the vector.
>
> Presuming that you are running a 64 bit version of SUSE (what does  
> 'uname -a' show in a system console), you should also check to be  
> sure that you are also running a 64 bit version of R. What does:
>
>  .Machine$sizeof.pointer
>
> show?
>
> If it returns 4, then you are running a 32 bit version of R, which  
> cannot take advantage of your 64 bit platform. You should install a  
> 64 bit version of R.
>
> HTH,
>
> Marc Schwartz
>
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