[BioC] memory exhausted for readAligned

[Lana Schaffer]

Patrick,
Yes, I am on a 32-bit machine.
length=35bp
298,610kb  50% PF and 12% Align
 R version 2.9.0 Under development (unstable) (2009-02-12 r47905) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base   
Thanks,
Lana

-----Original Message-----
From: Patrick Aboyoun [mailto:paboyoun at fhcrc.org] 
Sent: Thursday, February 12, 2009 4:20 PM
To: Lana Schaffer
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] memory exhausted for readAligned

Lana,
Could you provide your session information for you R session as well as
the number of alignments you are trying to read in? My first guess is
that you are running on a 32-bit architecture, but without more
information we on the list can't help you very much.


Patrick



Lana Schaffer wrote:
> Hi,
> I am trying to read the alignment in a lane of Solexa data and ran out

> of memory.
> I have 3.2G memory on my desktop computer.
> Is there a setting I can use to have enough memory for the readAligned

> command?
> How much memory do i need?
>
> Lana Schaffer
> Biostatistics/Informatics
> The Scripps Research Institute
> DNA Array Core Facility
> La Jolla, CA 92037
> (858) 784-2263
> (858) 784-2994
> schaffer at scripps.edu
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: 
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>