[BioC] gcrma memory problems in R1.8.1 and R1.9.0-devel

[Dick Beyer]

I have been having problems using gcrma.  I have two cases.  

1) gcrma on 34 HGU133A chips: in the initial stages memory usage is about 800MB and slowly grows to 1.7GB and then R is hung.

2) Start with 8 HGU133A chips, gcrma processing takes about 45 mins, followed by another 8 HGU133A chips another 45 minutes, then 8 more chips and the memory is up to 1.7GB and R is hung.

I am running R 1.8.1 and Bioconductor 1.3 on a 4GB, 2 Xeon Windows box running Windows 2000:

gcrma 1.0.0 
MASS 7.1-11 
reposTools 1.3.5 
Biobase 1.4.0 
eda 1.8.1 
affy 1.3.27 
methods 1.8.1 
ctest 1.8.1 
mva 1.8.1 
modreg 1.8.1 
nls 1.8.1 
ts 1.8.1 
base 1.8.1 

I also tried R1.9.0-development and Bioconductor development and got the same behavior.

I would greatly appreciate any suggestions or pointers or workarounds.

Thanks,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
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