[Bioc-devel] Bioc-devel Digest, Vol 26, Issue 12

Mirjam van Vroonhoven m.vroonhoven at erasmusmc.nl
Mon May 15 14:53:20 CEST 2006

Hello all,

> From: Seth Falcon <sfalcon at fhcrc.org>
> Subject: Re: [Bioc-devel] Memory problem in affy package of BioC 1.7
> 	and	BioC 1.8
> Mirjam van Vroonhoven <m.vroonhoven at erasmusmc.nl> writes:
> > We have an SGI Origin computation server (32 cpu, 64 Gb RAM) running irix
> > 6.5.27. 
> We don't have such a system which makes reproducing/debugging this
> issue rather difficult.  If anyone else on the list has such a system,
> it would be great to attempt to reproduce this (I'm not holding my
> breath :-)

> affy and vsn aside, with R 2.3.0 can you address a reasonable amount
> of your RAM?  For example, you can test by allocating many large
> sequence vectors:  v <- seq(1, 2^29)

Good question. Tested it. No. So it's not a problem in Bioconductor, but
a problem in R. In R 2.0.0 I can allocate 8 Gb of RAM without any
problem by running
v1 <- seq(1,2^29)
v2 <- seq(1,2^29)
v3 <- seq(1,2^29)
v4 <- seq(1,2^29)

but in R 2.3.0 I cannot allocate even one vector of 2 Gb. I can go to
almost 1300 Mb, but no more....

I'll contact the R developers on this problem, Thanks for helping out
and diagnosing the problem!

						With kind regards,

Dr. Mirjam van Vroonhoven
	system administrator/programmer, dept. of Bioinformatics
	Erasmus Medical Center, Rotterdam, The Netherlands
	Room Number Ee 15.32, phone +31-10-463 81 11
Web: 	http://www.erasmusmc.nl/bioinformatics/
E-mail: m.vroonhoven at erasmusmc.nl

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