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

joris meys jorismeys at gmail.com
Mon Oct 12 13:56:33 CEST 2009


Hi Roman,

that throws a different light on the problem. It goes wrong from the
start, so it has little to do with the bootstrap or jackknife
procedures. R.huge won't help you either.

Likely your error comes from the fact that "factor1" is not an
argument of the function accumcomp. the argument is "factor". As R
doesn't find this, it'll try to tabulate the complete environmental
dataset, and this gives the memory overflow.

Try :

poacc2 <- accumcomp(PoCom, y=PoEnv, factor="HM_sprem", method="exact")

That should work. I can't try it out without dataset off course. If it
doesn't work, post the traceback again, I'll take another look.

Kind regards
Joris

On Mon, Oct 12, 2009 at 1:07 PM, romunov <romunov at gmail.com> wrote:
> Hello joris,
>
> this is the traceback() output. Hopefully you can make some sense out of it.
> Thank you for the tips as well (R.huge looks promising)!
>
>> traceback()
> 7: vector("integer", length)
> 6: integer(nbins)
> 5: tabulate(bin, pd)
> 4: as.vector(data)
> 3: array(tabulate(bin, pd), dims, dimnames = dn)
> 2: table(y[, factor])
> 1: accumcomp(PoCom, y = PoEnv, factor1 = "HM_sprem", method = "exact")
>
> Cheers,
> Roman
>
>
>
> On Mon, Oct 12, 2009 at 12:52 PM, joris meys <jorismeys at gmail.com> wrote:
>>
>> 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
>> >
>> >        [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-help at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> > http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>> >
>
>




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