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:[EMAIL PROTECTED] Sent: Monday, December 22, 2003 3:11 PM To: '[EMAIL PROTECTED]' 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 [[alternative HTML version deleted]] ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help