[BioC] memory error on unix

Beth Wilmot wilmotb at ohsu.edu
Mon Jun 11 20:03:07 CEST 2007

 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


More information about the Bioconductor mailing list