[BioC] memory limit

[Steve Lianoglou]

Hi,

On Wed, Oct 6, 2010 at 6:13 PM, Noemi Andor <Noemi.Andor at campus.lmu.de> wrote:
> Hi,
>
> I have a problem with the R memory limits.
> First, I use R on a 64 bit system under windows 7.
> I start R with the following options:
> --min-vsize=10M --max-vsize=3G --min-nsize=500k --max-nsize=900M

Although your system is 64bit, it looks as if the version of R you are
running is only 32 bit. Look at the output of your sessionInfo() you
pasted below:

sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32

> Yet somewhere within the program I use, I get the error report:
>
> "can not allocate vector of size 370.8 MB".

As someone in R-help once put it, this 370.8 MB is the straw that
broke the camel's back. R has been chewing up memory while your
process is running, and now wanted to get 370MB more memory, but there
wasn't that much (contiguous) memory left.

> It is also worth mentioning, that I used RAE before, on ca 3/4 of the same data I'm using now, and it worked.

On the same machine? With the same setup?

> I would be very greatfull for a solution to my problem.

You can try running a 64bit version of R to see if you can access more
memory (how much RAM does your machine have, anyway?).

It seems that R-2.11 was the first R version that had a 64bit capable
version available for windows:

http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-use-R-on-64_002dbit-Windows_003f

-- 
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