[BioC] Error: Cannot allocate vector of size 279.1Mb

[Steve Lianoglou]

Hi,

Are you running R in 32 or 64 bit mode?
What is the value of `.Machine$sizeof.pointer` when you punch that
into your R workspace?
Also, please provide output of sessionInfo()

-steve


On Tue, Apr 3, 2012 at 12:42 PM, Desiree Wilson
<desiree.s.wilson at gmail.com> wrote:
> Hello everyone. How are you all doing?
>
> My name is Desiree. I'm a 1st grad student experiencing problems reading 27
> CEL files into R using the ReadAffy command. The total size of these files
> are 350 Mb. Here are my commands:
>
>> library(affy) # loads the "Affy" package
>> library(limma) # loads the "Limma" package
>> setwd("path directory to the CEL files")
>>mydata<-ReadAffy( ) # reads all of the CEL files in my work directory
>
> But after I run the last command, I get the following error message:
> Error: cannot allocate vector of size 279.1 Mb
> In addition: Warning messages:
> 1: In `rownames<-`(`*tmp*`, value = c("1", "2", "3", "4", "5", "6",  :
>  Reached total allocation of 1535Mb: see help(memory.size)
> 2: In `rownames<-`(`*tmp*`, value = c("1", "2", "3", "4", "5", "6",  :
>  Reached total allocation of 1535Mb: see help(memory.size)
> 3: In `rownames<-`(`*tmp*`, value = c("1", "2", "3", "4", "5", "6",  :
>  Reached total allocation of 1535Mb: see help(memory.size)
> 4: In `rownames<-`(`*tmp*`, value = c("1", "2", "3", "4", "5", "6",  :
>  Reached total allocation of 1535Mb: see help(memory.size)
>
> I've done it before on the same computer (specs: Lenovo Think with Intel
> Core 2 Quad CPU Q9400 @2.66GHz, 3.00 of RAM, Microsoft Windows XP
> Professional Version 2002).
>
> I've read previous posts and I will admit that the solutions offered are
> very hard for me to understand (I am a beginner). I have tried using the
> "memory.limit(size=3000)" command and then run the "ReadAffy()" command
> again but I still get the same error message. Any suggestions would be
> greatly appreciated.
> --Desiree Wilson
>
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>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact