[R] Error: cannot allocate vector of size 1.2 Gb

[joris meys]

Dear Roman,

could you give us the trace given by traceback() ? I suspect the error
is resulting from the permutations and/or jackknife procedure in the
underlying functions specaccum and specpool.

You can take a look at the package R.huge, but that one is deprecated
already. There are other packages around too, but I have no experience
with them. You find some more tips here :
http://www.matthewckeller.com/html/memory.html

This should give you a place to start looking.
Kind regards
Joris

On Mon, Oct 12, 2009 at 11:39 AM, romunov <romunov at gmail.com> wrote:
> Dear List,
>
> today I turn to you with a next problem. I'm trying to compare species
> richness between various datasets (locations) using species accumulation
> curves (Chapter 4, page 54 in Tree diversity
> analysis<http://www.worldagroforestry.org/treesandmarkets/tree_diversity_analysis.asp>by
> Kindt & Coe). To accomplish this I'm using package
> BiodiversityR. My data is comprised of species community (PoCom) (10
> locations with 83 species) and environmental factors (PoEnv) (10 locations
> with 17 factors).
> In attempt to calculate the function (accumcomp) I receive the following
> error. I can not imagine how a 10x83+10x17 matrix can grow to a GB or more.
> Unless I'm missing something? How can I combat this?
>
>> poacc2 <- accumcomp(PoCom, y=PoEnv, factor1="HM_sprem", method="exact")
> Error: cannot allocate vector of size 1.2 Gb
> In addition: Warning messages:
> 1: In vector("integer", length) :
>  Reached total allocation of 1023Mb: see help(memory.size)
> 2: In vector("integer", length) :
>  Reached total allocation of 1023Mb: see help(memory.size)
> 3: In vector("integer", length) :
>  Reached total allocation of 1023Mb: see help(memory.size)
> 4: In vector("integer", length) :
>  Reached total allocation of 1023Mb: see help(memory.size)
>
>
> Cheers,
> Roman
>
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>
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