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

[cstrato]

If your 93 CEL files are Exon arrays, then 8 GB RAM are surely not enough!
Have a look at either my package "xps" available at BioC 2.2, or at 
package "aroma.affymetrix", both of which work with only 1 GB RAM.

Regards
Christian
_._._._._._._._._._._._._._._._
C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a
V.i.e.n.n.a       A.u.s.t.r.i.a
e.m.a.i.l:    cstrato at aon.at
_._._._._._._._._._._._._._._._


Germain Paimparay wrote:
> 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 !
>
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