[BioC] query regarding memory allocation...please help

[James W. MacDonald]

Hi Urvesh,

Please don't send the same exact email with slightly different subject 
line (one minute apart!). I'm not sure what you expect to gain by doing 
so, but rest assured that you will simply irritate those who might help you.

On 2/28/2013 4:11 AM, urvesh patel [guest] wrote:
>> f1=list.celfiles(path="D://urvesh//3",full.names=TRUE)
>> memory.size()
> [1] 11.45
>> x1=ReadAffy(filenames=f1)
> Error: cannot allocate vector of size 806.3 Mb
> In addition: Warning messages:
> 1: In dimnames(x)<- dn :
>    Reached total allocation of 1535Mb: see help(memory.size)
> 2: In dimnames(x)<- dn :
>    Reached total allocation of 1535Mb: see help(memory.size)
> 3: In dimnames(x)<- dn :
>    Reached total allocation of 1535Mb: see help(memory.size)
> 4: In dimnames(x)<- dn :
>    Reached total allocation of 1535Mb: see help(memory.size)
>> help(memory.size)
> starting httpd help server ... done
>
> this is the error which i am getting...please try to help me out..and i even tried extending memory size to 4095 using memory.limit(size=4095) ..but still the problem remains.....

The obvious answer here is that you don't have enough memory, and 
depending on how many celfiles you have, 4 Gb may never be enough. You 
can try justRMA(), which uses less memory, or you can try the xps 
package, which will also use less memory, or you can try 
aroma.affymetrix, which isn't a BioC package, but which uses less memory 
as well.

Best,

Jim


>
>
>   -- output of sessionInfo():
>
>> f1=list.celfiles(path="D://urvesh//3",full.names=TRUE)
>> memory.size()
> [1] 11.45
>> x1=ReadAffy(filenames=f1)
> Error: cannot allocate vector of size 806.3 Mb
> In addition: Warning messages:
> 1: In dimnames(x)<- dn :
>    Reached total allocation of 1535Mb: see help(memory.size)
> 2: In dimnames(x)<- dn :
>    Reached total allocation of 1535Mb: see help(memory.size)
> 3: In dimnames(x)<- dn :
>    Reached total allocation of 1535Mb: see help(memory.size)
> 4: In dimnames(x)<- dn :
>    Reached total allocation of 1535Mb: see help(memory.size)
>> help(memory.size)
> starting httpd help server ... done
>
> this is the error which i am getting...please try to help me out..and i even tried extending memory size to 4095 using memory.limit(size=4095) ..but still the problem remains.....
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099