[BioC] Error: cannot allocate vector of size 649.8 Mb

[Martin Morgan]

On 08/20/2010 08:19 AM, Marco Ortiz wrote:
> * Hi All, ** ** I am new to the world of R and Bioconductor and I had
> the** following error when I try to read a fastaq file of 2 Gb****
> First I try to run it in Linux, but there i had an error that tell me
> *
> 
> * <**
> 
> Error: (dirPath, pattern, ...) cannot open file
> 
> *
> 
> * Then i try to run it in Windows and there i had this error*
> 
> *
> *
> 
> *
> *
> 
> * > library(ShortRead)*
> 
> *** > plantula <- readFastq("s6_plantula.fq", qualityType="SFastqQuality")*
> 
> *** Error: cannot allocate vector of size 649.8 Mb*

This is likely limited memory problem; R is saying 'I allocated some
memory, and now I'm trying to allocate 649.8Mb more, and that additional
memory allocation fails'. Memory limits on 32-bit windows systems are
hard to get around; you're better using a 64-bit Windows or Linux
system. Your Linux problem seems really  straight-forward -- you haven't
specified the file path correctly. Your R likely has command completion, so

  readFastq("~/

and then use the tab key to complete the path.

Please include sessionInfo() when you're posting to the list; it makes
clear what software and hardware you're using.

Martin
> 
> *
> *
> 
> * *
> 
> * Then i **set memory.size() at 3000 as well as memory.limit() but i'm
> already having the problem*
> 
> * i has a processor of 32 bits, a virtual memory of 3754 Mb*
> 
> *  ** Can someone tell me if this is due to an improper configuration,
> lack** of sufficient memory, etc?*
> 
> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793