R help - Feb 2008 - Memory problem with 64bit R using PLASQ500k

Dear all,

First I apologize for cross-posting, but I think that this could be of
interest to BioC users, too.

For DNA copy-number analysis I have downloaded PLASQ500K from: 
http://genome.dfci.harvard.edu/~tlaframb/PLASQ/

After creating sub-directories SND and STD containing 3 Sty Mapping arrays
each, I tried to compute parent-specific copy number:
> library(PLASQ500K)
> psCN <-
pscn(StyFolder="STD",normStyFolder="SND",betasSty=NULL,quantSty=NULL,betasSty
File="betasSty.Rdata",rawCNStyfile="rawCNSty.Rdata")

Using only six 250K Sty CEL-files it was impossible to finish this
calculation. 
On a 32GB RAM Linux server the job got killed, since function EMSNP() which
is called from function getBetas() used up all RAM. Starting the computation
on our 64GB RAM Linux server, function EMSNP() could be executed,
nevertheless, we had to kill the job, when it reached memory consumption of
74GB!!! at a later stage!

Interestingly, when running PLASQ500K on my local workstation, I could finish
the computation w/o any memory  problems.

So what is the difference:
1. Server (4 Dual-Core AMD Opteron Processors, 64GB RAM): Fedora Core 6 and
R-2.6.1 and packages compiled from source for 64-bit.
> sessionInfo()
R version 2.6.1 (2007-11-26) 
x86_64-unknown-linux-gnu 

locale:
C

attached base packages:
[1] tcltk     tools     stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] PLASQ500K_0.0.5      GLAD_1.12.0          aws_1.3-3.1         
[4] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1        
[7] Biobase_1.16.1      

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17

2. Workstation (HP xw6400, 2 Intel Xeon Processors, 4GB RAM): Fedora Core 6
and R-2.6.1 and packages compiled from source for
32-bit.
> sessionInfo()
R version 2.6.1 (2007-11-26) 
i686-pc-linux-gnu 

locale:
C

attached base packages:
[1] tcltk     tools     stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] PLASQ500K_0.0.5      GLAD_1.12.0          aws_1.3-3.1         
[4] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1        
[7] Biobase_1.16.1      

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17

Does anybody know what  might be the reason for this behavior?

Thank you in advance
Best regards
Christian

=============================================Christian Stratowa, PhD
Boehringer Ingelheim Austria
Dept NCE Lead Discovery - Bioinformatics
Dr. Boehringergasse 5-11
A-1121 Vienna, Austria
Tel.: ++43-1-80105-2470
Fax: ++43-1-80105-2782
email: christian.stratowa@vie.boehringer-ingelheim.com



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