[BioC] how to set R memory limit

[Sean Davis]

On Tue, Jan 10, 2012 at 9:15 AM, wang peter <wng.peter at gmail.com> wrote:
> thank u to all of your replies
> sorry to miss the sessionInfo()
> R version 2.13.2 (2011-09-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
>
> but i think how to set R memory is nothing related with R version.

Memory use is related to R version, architecture, and operating
system.  These three details are returned by sessionInfo().

> i got many news to set it but donot know which one is correct
>
> i tried
> R --max-vsize=20G
> options(java.parameters = "-Xmx8192m")

--max-vsize of 20G will limit memory to approximately 20G; I thought
you said that you had 64G of memory.  Does this make sense?

Java parameters do not affect R directly, only JVMs started by the
rare R package that runs java, so this will not solve your original
problem.

> and also restarted the computer to clean the memory
>
> but i still have no ideas with R memory management
>

See help('Memory-limits').  However, on 64-bit linux, the original
error message you reported is related to not having enough memory to
complete the operation; there is generally no need to manually
increase memory.  As Steve suggested, run 'top' in another window to
watch R memory use.  Use gc() regularly and be sure to clean up your R
workspace.  If you still cannot do what you need, let us know what you
are trying to do by including code, errors, and the output of
sessionInfo().  Perhaps there is a way to do things with less memory
use.  In the end, you may need more memory, though.

Sean


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