[R] Error: cannot allocate vector of size X.0 Mb

[Martin Morgan]

On 09/14/2010 08:02 AM, Marc Schwartz wrote:
> On Sep 14, 2010, at 9:47 AM, John1983 wrote:
> 
>> 
>> Yes I see. So I typed as you mentioned and I get an 8 (therefore
>> this is a 64-bit R).
>> 
>> Is there anything else I need to check to remove this error?
> 
> 
> 1. Add more RAM.
> 
> 2. Depending upon what you are doing relative to data
> management/analysis, you might want to see if there are more
> efficient approaches.
> 
> 3. Free up RAM that may be in use by other processes, etc.
> 
> 4. Look at R packages such as biglm, ff/bit, biganalytics, etc.
> 
> 5. Consider using a backend data base application (eg. MySQL,
> Postgres, etc.) to manage the data sets and use R only for analyses,
> as may be appropriate relative to splitting the tasks.
> 
> 
> You did not indicate just how much RAM you have on the machine in
> question, but if it is within your budget/capability, adding more RAM
> would be the most transparent approach.

Before spending the big bucks you might try asking on the Bioconductor
mailing list

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

home of the Biostrings package and BStringSet, andwhere for instance the
ShortRead package readFastq would be a natural way of parsing your FASTQ
file, and most operations you'd likely perform on a fastq file (given
sufficient memory) would take more than a few (tens of, at the most)
seconds.

Martin

> HTH,
> 
> Marc Schwartz
> 
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