I updated my mapping files (nsp and sty) to 0.2.6 and oligo to version 1.1 and on a 4GB (32 bit) machine with increased swap to ridiculous amounts (30GB) and I still am unable to create a snpqset.  I can read a single cel in, but at snprma, I get stuck.
Can't wait for that dev version of oligo Benilton!  Please distribute the path when you get it done.  Many thanks for your hard work!
-B




The memory error just means that you ran out of memory, it does not  
mean that you have less than 1.8GB in total. If you are on a 32bit OS  
you will not be able to use all 8 GB of ram. That has nothing to do  
with R per se.

Kasper

On Jun 11, 2007, at 11:03 AM, Beth Wilmot wrote:

> Hello,
>  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
>
> Thanks,
> Beth


       
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