[BioC] startup options

[Nicolas Delhomme]

Hej Kasper, Benilton!

This is from a previous post from Martin (titled SummarizedExperiments from September 5 2012):

As a miscellaneous 'tip', when working with large data I find it useful to start R with --min-vsize=2048M --min-nsize=20M. These are documented in RShowDoc("R-intro") as 'for expert use only' and influence how much memory R allocates for vectors ('vsize'; vsize can be very large) and for S-expressions ('nsize' 50000000) and help get up to large memory allocations without innumerable garbage collections. Of course having big memory is of primary importance.

These are not OS specific as far as I know. 

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
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On Mar 13, 2013, at 3:35 PM, Benilton Carvalho wrote:

> --max-mem-size and --max-vsize are the only items that I can
> remember... but, AFAIR, they're Windows-exclusive...
> 
> 2013/3/13 Kasper Daniel Hansen <kasperdanielhansen at gmail.com>:
>> When we load say IRanges, it takes a while.  I seem to recall it has
>> something to do with memory allocation or something, and that there is
>> (or used to be) a startup option to R where you could increase the
>> relevant memory and thereby decrease startup time (including loading
>> of "standard" packages).  I seem to recall Martin Morgan posting about
>> it.
>> 
>> Does this ring any bells?
>> 
>> Best,
>> Kasper
>> 
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