[R] Memory allocation

[JFRI (Jesper Frickmann)]

Go download R version 1.8.1 (or later if available). They fixed
something with memory management from 1.8.0 to 1.8.1 which helped me out
of the exact same problem. I think it has to do with memory
fragmentation; R cannot find any chunk big enough for even a small
vector after some time.

Kind regards, 
Jesper Frickmann 
Statistician, Quality Control 
Novozymes North America Inc. 
Tel. +1 919 494 3266
Fax +1 919 494 3460

-----Original Message-----
From: Richards, Thomas [mailto:RichardsTJ2 at UPMC.EDU] 
Sent: Monday, December 22, 2003 3:11 PM
To: 'r-help at stat.math.ethz.ch'
Subject: [R] Memory allocation


Hello:

	I am trying to work with a couple of microarray data sets, using

platform i386-pc-mingw32
arch     i386           
os       mingw32        
system   i386, mingw32  
status                  
major    1              
minor    8.1            
year     2003           
month    11             
day      21             
language R              


In the shortcut for invoking R I have set --max-mem-size=1024M, so that
I get

> memory.limit()
[1] 1073741824

Below is an example of what keeps happening as I am working. Any
suggestions as to how I can stop running out of mermory?

> memory.size()
[1] 502904736
> log2.harvAD <- log2.harvAD[log2.harvAD$Probesets %in%
harvard.genes$probeset,]
Error: cannot allocate vector of size 49 Kb
> log2.harvAD <- log2.harvAD[,c(1,1+order(names(log2.harvAD)[-1]))]
Error: cannot allocate vector of size 49 Kb
> log2.harvAD.annot <- 
> unlist(lapply(strsplit(names(log2.harvAD),split=":"),
+   function(L) L[1]))[-1]
> log2.harvAD$probeset <- as.character(log2.harvAD$probeset)
Error: cannot allocate vector of size 49 Kb
> memory.size()
[1] 502912536
> gc()
           used  (Mb) gc trigger  (Mb)
Ncells  2586025  69.1    6812252 182.0
Vcells 20108076 153.5   41205530 314.4
> memory.size()
[1] 330645720
> memory.limit()/memory.size()
[1] 3.247408
> ##  Try again:
> log2.harvAD <- log2.harvAD[log2.harvAD$Probesets %in%
harvard.genes$probeset,]
Error: cannot allocate vector of size 49 Kb

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