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

[Latchezar Dimitrov]

Hello,

When I try:

 geno
<-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

and

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?

Thanks,
Latchezar