[R] Memory allocation

[Prof Brian Ripley]

Not really much hope here, but

1) If you have fast discs, try increasing --max-mem-size to more than your 
RAM, and

2) Try compiling up R-devel (see the FAQ for where to get it) as it has
a potentially better memory allocator.

I supect though that your problem is too big for R on 32-bit Windows.

BDR

On Mon, 22 Dec 2003, Richards, Thomas wrote:

> 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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> 
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> 
> 

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595