I grep for "n, n)" in all the R code of the package (current version), and the only place that happens is in creating proximity. Can you do a traceback() and see where it happens?
You should seriously consider upgrading R and the packages... Andy > -----Original Message----- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Czerminski, Ryszard > Sent: Thursday, January 20, 2011 1:08 PM > To: r-h...@stat.math.ethz.ch > Subject: [R] randomForest: too many elements specified? > > I getting "Error in matrix(0, n, n) : too many elements specified" > while building randomForest model, which looks like memory allocation > error. > Software versions are: randomForest 4.5-25, R version 2.7.1 > > Dataset is big (~90K rows, ~200 columns), but this is on a > big machine ( > ~120G RAM) > and I call randomForest like this: randomForest(x,y) > i.e. in supervised mode and not requesting proximity matrix, therefore > answer from Andy Liaw to an email reporting the same problems in 2005 > (see below) > is probably not directly applicable, still it looks like it is too big > data set for this dataset/machine combination. > > How does memory usage in randomForest scale with dataset size? > Is there a way to build global rf model with dataset of this size? > > Best regards, > Ryszard > > Ryszard Czerminski > AstraZeneca Pharmaceuticals LP > 35 Gatehouse Drive > Waltham, MA 02451 > USA > 781-839-4304 > ryszard.czermin...@astrazeneca.com > > RE: [R] randomForest: too many element specified? > Liaw, Andy > Mon, 17 Jan 2005 05:56:28 -0800 > > From: luk > > > > When I run randonForest with a 169453x5 matrix, I got the > > following message. > > > > Error in matrix(0, n, n) : matrix: too many elements specified > > > > Can you please advise me how to solve this problem? > > > > Thanks, > > > > Lu > > 1. When asking new questions, please don't reply to other posts. > > 2. When asking questions like these, please do show the commands you > used. > > My guess is that you asked for the proximity matrix, or is running > unsupervised randomForest (by not providing a response vector). This > will > requires a couple of n by n matrices to be created (on top of other > things), > n being 169453 in this case. To store a 169453 x 169453 matrix in > double > precision, you need 169453^2 * 8 bytes, or or nearly 214 GB of memory. > Even > if you have that kind of hardware, I doubt you'll be able to make much > sense > out of the result. > > Andy > > > > -------------------------------------------------------------- > ------------ > Confidentiality Notice: This message is private and may > ...{{dropped:11}} > > ______________________________________________ > R-help@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. > Notice: This e-mail message, together with any attachme...{{dropped:11}} ______________________________________________ R-help@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.