[BioC] cannot allocate vector of size 762 Mo ! One more time !

[Germain Paimparay]

Hello,

My name is Germain and I'm Bioinformatician.

I have installed R (v 2.4) on RHEL5, and I try to read 93 CEL files  
with ReadAffy function.

Despite 8Go RAM, I obtain this error :

Error: cannot allocate vector of size 762 Mo ...

I read all topics about this error and try all proposed solutions, but  
it still doesn't work.


By unix "top" command, I can seen that % of use memory keep under 20%

Note that I tried with R 2.7 on the same computer but it s doesn't work too.


"ulimit" command return => unlimited


gc command (in R) return

(before ReadAffy)
> gc()
          used (Mb) gc trigger (Mb) max used (Mb)
Ncells 222874  6.0     407500 10.9   350000  9.4
Vcells  98794  0.8     786432  6.0   358096  2.8

(After ReadAffy)
> gc()
          used (Mb) gc trigger   (Mb)  max used   (Mb)
Ncells 464170 12.4     818163   21.9    597831   16.0
Vcells 215236  1.7  224490510 1712.8 280335642 2138.8



Session Info on Server with troubles
> sessionInfo()
R version 2.4.0 (2006-10-03)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_
MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_A
DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
     affy   affyio  Biobase
"1.12.2"  "1.2.0" "1.12.2"



I tried with an other server (RHEL4) with 10Go RAM and the same R  
version (2.4) and it's work...

Session Info on Server ok
> sessionInfo()
R version 2.4.1 (2006-10-03)
x86-64-unknow-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_
MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_A
DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
     affy   affyio  Biobase
"1.12.2"  "1.2.0" "1.12.2"



Any idea ? could you please help me ?

THANK YOU !