[R] vector allocation error

[Martin Morgan]

On 08/21/2010 12:19 AM, josquint wrote:
> 
> I am running and analysis of sequencing data uisng the EdgeR package. I have
> received the following error:
> 
> Using grid search to estimate tagwise dispersion. Error: cannot allocate
> vector of size 307.3 Mb
> 
> indicating the memory allocation is too small. How would I change this
> confiuration in R so that the script can run with the files I have?
> 
> Help appreciated, Josquin

Hi Josquin

edgeR is a Bioconductor package so please ask on that list.

  http://bioconductor.org/help/mailing-list/

You must be a subscriber to post.

Adjusting memory allocation on Windows is an R FAQ


http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-be-a-limit-on-the-memory-it-uses_0021

Often the end answer is 'use a 64-bit Windows or Linux machine with more
physical memory'.

While the error says that you are running out of memory, my guess is
that the function is being invoked incorrectly. To help diagnose the
problem, please include the output of

  sessionInfo()

and a code snippet (preferably directly reproducible by others) showing
exactly what you are doing. The output of traceback() after the error
occurs can be informative.

Martin
-- 
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