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" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 10/10/2008 10:12 AM To "hadley wickham" <[EMAIL PROTECTED]> 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 [EMAIL PROTECTED] 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:[EMAIL PROTECTED] 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 -- http://had.co.nz/ Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology