[BioC] memory problems on IRIX machine

drnevich@uiuc.edu drnevich at uiuc.edu
Fri Oct 7 22:07:45 CEST 2005

Hello all,

We are having a problem analyzing a large data set (30 Affy
soybean arrays, ~61K probesets). I moved from my PC to our
server running IRIX, but I'm still getting the same error
message of "unable to allocate vector size...". There are 12 G
of physical memory on the server plus another 17 G swap; the R
process doesn't even touch a fraction of this, so it's not a
memory limitation problem. I found a similar discussion of
this on the listserve back in January 2005, but the only fix
suggested was to make sure R > 2.0 and BioC >1.5. Our versions
are beyond this, so does anyone have any other ideas?


Session output:
> norm <- normalize(rawdata) 
Error: cannot allocate vector of size 317553 Kb
> sessionInfo()
R version 2.1.1, 2005-06-20, mips-sgi-irix6.5 

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics" 
"grDevices" "utils"    
[7] "datasets"  "base"     

other attached packages:
soybeancdf       affy reposTools    Biobase 
   "1.5.1"    "1.6.7"   "1.5.19"   "1.5.12" 
Jenny Drnevich, Ph.D.
Functional Genomics Bioinformatics Specialist
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801

ph: 217-244-7355
fax: 217-265-5066 
e-mail: drnevich at uiuc.edu

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