Dear Community,

I am very new to the world of Linux and R and I have stumbled upon a problem that I cannot seem to resolve on my own. Here is the relevant background:

I am working on a 64-bit Linux Fedora Core 6 OS. I using R version 2.5.1. I have 3.8 Gb of RAM and 1.9 Gb of swap. As I see it, there are no restraints on the amount of memory that R can use imposed by this particular OS build. When I type in the 'ulimit' command at the command line the response is 'unlimited'.

Here is the problem:

I have uploaded and normalized 48 ATH1 microarray slides using the justRMA function.

>library("affy")

>setwd("/Data/cel")

>Data<-justRMA()

The next step in my analysis is to calculate a distance matrix for my dataset using bioDist package. This is where I get my error.

>library("bioDist")

>x<-cor.dist(exprs(Data))

Error: cannot allocate vector of size 3.9 Gb

I used the following function to examine my memory limitations:

> mem.limits()

nsize vsize 

NA NA 

I believe this means there isn't any specified limit to the amount of memory R can allocate to my task. I realize I only have 3.8 Gb of RAM but I would expect that R would use my 1.9 Gb of swap. 

Does R not use my swap space? Can I explicitly tell R to use my swap space for large tasks such as this? 

I was not able to find any information regarding this particular issue in the R Linux manual, Linux FAQ, or on previous listserv threads. Many of the users who had similar questions resolved their problems in a different manner.

Thanks to anyone who thinks they can provide assistance!

Max 

Graduate Student

Molecular Plant Sciences

Washington State University


	[[alternative HTML version deleted]]

