[Biomod-commits] cannot allocate vector size

[Wilfried Thuiller]

Hi Pep,

(same thing with the boucing problem).

Memory problem is indeed a serious problem in R. First make sure you 
have enough RAM on your computer (at least 2G is minimum now). Increase 
your virtual memory at maximum.

If you use Tinn-R and open R from Tinn-R with the convenient icone, 
there is a very simple way to correct the problem. Go in "Options", then 
"Applications". Then in the R icone, type the following
--max-mem--size=5000000000000
in the parameters text window.
 

If you do not use Tinn-R, edit an R-profile file and put some text.
Some years ago, I made this little doc file (attached) to explain how to 
do that (do not look at the files and so on as it was for the ancestor 
of the biomod library). There are certainly better way to set the memory 
now.

Hope it helps,
Wilfried


  

mailman-bounces at r-forge.wu-wien.ac.at a écrit :
> The attached message was received as a bounce, but either the bounce
> format was not recognized, or no member addresses could be extracted
> from it.  This mailing list has been configured to send all
> unrecognized bounce messages to the list administrator(s).
>
> For more information see:
> https://lists.r-forge.r-project.org/cgi-bin/mailman/admin/biomod-commits/bounce
>
>
>   
>
> ------------------------------------------------------------------------
>
> Sujet:
> cannot allocate vector size
> Expéditeur:
> Pep Serra <josep.serra at uab.cat>
> Date:
> Tue, 15 Sep 2009 15:05:12 +0200
> Destinataire:
> biomod-commits-bounces at lists.r-forge.r-project.org
>
> Destinataire:
> biomod-commits-bounces at lists.r-forge.r-project.org
>
>
> Dear BIOMODers,
>
> I am using BIOMOD and I encountered this problem:
>
> <<
> #####              pseudo-absence run 1                 #####
> Model=Artificial Neural Network
>          2 Fold Cross Validation + 3 Repetitions
> Calibration and evaluation phase: Nb of cross-validations:  3
> Evaluating Predictor Contributions in  ANN ...
> Model=Classification tree
>          50 Fold Cross-Validation
> Evaluating Predictor Contributions in  CTA ...
> Model=GAM spline
>          3  Degrees of smoothing
> Evaluating Predictor Contributions in  GAM ...
> Model=Generalised Boosting Regression
>          2000 maximum different trees and lambda Fold Cross-Validation
> Evaluating Predictor Contributions in  GBM ...
> Model=GLM polynomial + quadratic         Stepwise procedure using AIC 
> criteria
> Evaluating Predictor Contributions in  GLM ...
> Model=Multiple Adaptive Regression Splines
> Evaluating Predictor Contributions in  MARS ...
> Model=Mixture Discriminant Analysis
> Evaluating Predictor Contributions in  MDA ...
> Model=Breiman and Cutler's random forests for classification and 
> regression
> *Error: no se puede ubicar un vector de tamaño  137.3 Mb
>
> in English : cannot allocate vector size 137.3 Mb
> >>
>
> *I checked some solutions using memory.size, memory.limit,  [ memory 
> limit (2000) ]... but I cannot find the solution...
> Did you have the same problem so far? How did you solve it?
> I thought my data frame was not that large.... 'data.frame':   41386 
> obs. of  8 variables: "
>
> Thank you very much,
> Enjoy your modeling
>
> Pep
>
>

-- 
--
Wilfried Thuiller
Laboratoire d'Ecologie Alpine, UMR-CNRS 5553
Université J. Fourier
BP 53, 38041 Grenoble Cedex 9, France
Tel: +33 (0)4 76 63 54 53
Fax: +33 (0)4 76 51 42 79

Email: wilfried.thuiller at ujf-grenoble.fr
Home page: http://www.will.chez-alice.fr
Website: http://www-leca.ujf-grenoble.fr/equipes/tde.htm

FP6 European MACIS project: http://www.macis-project.net
FP6 European EcoChange project: http://www.ecochange-project.eu

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.r-forge.r-project.org/pipermail/biomod-commits/attachments/20090915/5cf30e2c/attachment-0001.htm 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: moz-screenshot-1.jpg
Type: image/jpeg
Size: 35936 bytes
Desc: not available
Url : http://lists.r-forge.r-project.org/pipermail/biomod-commits/attachments/20090915/5cf30e2c/attachment-0001.jpg