[R] Memory allocation
Prof Brian Ripley
ripley at stats.ox.ac.uk
Mon Dec 22 21:38:06 CET 2003
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
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>
>
--
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
More information about the R-help
mailing list