[R] Memory limits using read.table on Windows XP Pro

From: Latchezar Dimitrov <ldimitro_at_wfubmc.edu>
Date: Sat 25 Jun 2005 - 01:38:58 EST


When I try:

<-read.table("2500.geno.tab",header=TRUE,sep="\t",na.strings=".",quote=" ",comment.char="",colClasses=c("factor"),nrows=2501)

I get, after hour(s) of work:

Error: cannot allocate vector of size 9 Kb

I have:

Rgui.exe --max-mem-size=3Gb


multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft Windows XP Professional" /fastdetect /NoExecute=OptIn /PAE /3GB

in boot.ini

2500.geno.tab is a tab-delimited text table with 2500 x 125000 = 312,500,000 3-level (two alphabet characters) factors (x 4 bites = 1,250,000,000 (1.25GB). Even if we double it (as per read.table help) it's still 2.5GB < 3Gb. And actually Windows Task Manager shows peak mem use for Rgui 2,056,992K (~2.057GB) and total memory used 2.62GB. And the total physical memory is 4GB (of which windows recognizes above 3GB)

Any help or suggestions?


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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sat Jun 25 01:44:39 2005

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