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

[Prof Brian Ripley]

On Fri, 24 Jun 2005, Latchezar Dimitrov wrote:

> 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?

Do check the rw-FAQ.  If you modified R to address more than 2GB, you 
omitted to tell us a vital fact, so I guess you did not.

I think you need to check the actual meaning of G and K, although they are 
much misused. 1,250,000,000 is 1.16GB in the units you are using for 3GB.

-- 
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