This may be a long shot.  You might try shutting down R and running your 
script from a command ("DOS") window using the RTERM.EXE utility. 
Things do seem to run a little better that way as a rule. 

David 




"ONKELINX, Thierry" <Thierry.ONKELINX@inbo.be> 
Sent by: r-sig-ecology-bounces@r-project.org
10/10/2008 10:12 AM

To
"hadley wickham" <h.wickham@gmail.com>
cc
r-sig-ecology@r-project.org
Subject
Re: [R-sig-eco] Clustering large data






Hi Hadley,

R ran out of memory. I got the "can't allocate vector of xxx mb" type of
error.

I did something like this.

Dataset #reading a two column (species, location) dataframe from a
database. 1154024 rows, 1381 species and 6354 locations.
Dataset$value <- 1
library(reshape)
cast(data = Dataset, formula = species ~ location) #this gave the error

Thierry

------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium 
tel. + 32 54/436 185
Thierry.Onkelinx@inbo.be 
www.inbo.be 

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: hadley wickham [mailto:h.wickham@gmail.com] 
Verzonden: vrijdag 10 oktober 2008 14:40
Aan: ONKELINX, Thierry
CC: Peter Solymos; r-sig-ecology@r-project.org
Onderwerp: Re: [R-sig-eco] Clustering large data

> Thanks for your responses. The biggest problem seems to be cast() for
> the reshape package which could not handle the dataset. Peter's
solution
> using the mefa package worked fine. I found an other solution: table()
> which works fine to crosstabulate presence-only data.

Exactly what error did you get?  Or did it just take a very long time
and then you gave up?  I have an experimental rewrite of the reshape
package that is more memory efficient and much faster (10 - 20x) -
however, it's still some time from being ready for production use.

Hadley


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