[R] Memory allocation

alex lam (RI) alex.lam at bbsrc.ac.uk
Thu Sep 7 16:20:25 CEST 2006

Dear list,

I have been trying to run the function "qvalue" under the package qvalue
on a vector with about 20 million values.

> asso_p.qvalue<-qvalue(asso_p.vector)
Error: cannot allocate vector of size 156513 Kb
> sessionInfo()
Version 2.3.1 (2006-06-01)

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

other attached packages:
> gc()
            used  (Mb) gc trigger   (Mb)  max used   (Mb)
Ncells    320188   8.6   23540643  628.7  20464901  546.5
Vcells 101232265 772.4  294421000 2246.3 291161136 2221.4

I have been told that the linux box has 4Gb of RAM, so it should be able
to do better than this.
I searched the FAQ and found some tips on increasing memory size, but
they seem to be windows specific, such as memory.size() and the
-max-mem-size flag. On my linux box R didn't recognise them.

I don't understand the meaning of max-vsize, max-nsize and max-ppsize.
Any help on how to increase the memory allocation on linux is much

Many thanks,

Alex Lam
PhD student
Department of Genetics and Genomics
Roslin Institute (Edinburgh)
Midlothian EH25 9PS

Phone +44 131 5274471
Web   http://www.roslin.ac.uk

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