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]] > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > > -- Brian D. Ripley, [EMAIL PROTECTED] 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 ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help