[BioC] memory limit

[Noemi Andor]

Hi,

I have a problem with the R memory limits.
First, I use R on a 64 bit system under windows 7.
I start R with the following options:
--min-vsize=10M --max-vsize=3G --min-nsize=500k --max-nsize=900M

Yet somewhere within the program I use, I get the error report:

"can not allocate vector of size 370.8 MB".


Now, what I try to do while getting this message is to use RAE, a program for analysis of CGH data.
It is very time consuming, and I have to wait for ca. 2 hours till the message appears.
Also, it seems to appear earlier as I keep trying: at my second trial the error message appeared sooner then in the first trial.
It is also worth mentioning, that I used RAE before, on ca 3/4 of the same data I'm using now, and it worked.

I also tried to restart my pc, yet no improval.

********before RAE:
 memory.size(max=TRUE)
[1] 16.94
 memory.limit()
[1] 3583
 memory.size()
[1] 6.89
gc()
         used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 119268  3.2     500000 13.4    25200.0   500000 13.4
Vcells  78210  0.6    1310720 10.0    24576.1   426021  3.3
********


***********After error message within RAE:
memory.size(max=TRUE)
[1] 3583.88
memory.size()
[1] 511.92
memory.limit()
[1] 3583
gc()
           used  (Mb) gc trigger (Mb) limit (Mb)  max used   (Mb)
Ncells   285631   7.7     633250   17    25200.0    633250   17.0
Vcells 65059765 496.4  274195172 2092    24576.1 462143052 3525.9
************

sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252

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

other attached packages:
[1] DNAcopy_1.20.0

I would be very greatfull for a solution to my problem.

best,

Noemi