[BioC] memory error on unix
bcarvalh at jhsph.edu
Mon Jun 11 20:11:18 CEST 2007
R is using all the memory you have available.
How many array are you working with?
I'm finishing a version of snprma which requires less RAM, so maybe
by the beginning of next week, if you're willing to try the devel-
vesion of oligo, I think you'll be able to move forward.
On Jun 11, 2007, at 2:03 PM, Beth Wilmot wrote:
> I am running R-2.5.0 and Bioconductor 2.0 and oligo 1.0.2-3 on a Sun
> OS 5.10 Generic_118855-19 i86pc i386 i86pc and Solaris 10 6/06
> s10x_u2wos_09a X86.
> I have seen the help messages concerning memory errors but cannot find
> a solution to unix memory errors. I thought R would be using all
> available memory?
> I have 8Gb RAM and 4Gb swap available.
> I am running one 500K test chip and when I try to create a SnpQSet in
> oligo I get the following error:
> Error: cannot allocate vector of size 1.8 Gb
> $ ulimit -a
> time(seconds) unlimited
> file(blocks) unlimited
> data(kbytes) unlimited
> stack(kbytes) unlimited
> coredump(blocks) unlimited
> nofiles(descriptors) 256
> memory(kbytes) unlimited
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