It's trying to allocate about 850 MB. And that's just the "object that broke the camel's back". You probably really are out of memory. You could increase swap space and cross your fingers, but probably daisy creates the 10481 x 10481 distance matrix, which would be about 800 MB since each entry is 8 bytes. It may even create multiple copies.
You might try increasing RAM to 4 GB or a clustering routine that doesn't need a distance matrix, like k-means (which is based on Euclinean distance as well). Reid Huntsinger -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Betty Gilbert Sent: Tuesday, February 22, 2005 5:57 PM To: [email protected] Subject: [R] Memory error in Mac OS X Aqua GUI v1.01 with cluster package functions I'm sorry if the answer to my problem is buried in the archives. I have limited experience with R and I couldn't find a solution to my particular problem. I am running Mac OS X Aqua GUI v1.01 on a new G5 running os 10.3.8 with a 1.8Ghz processor and 1GB of sdram. I just downloaded bioconducter a week ago and I'm trying to cluster a matrix I created with a simulation with dimensions dim(nca35) [1] 10481 12 with size > object.size(nca352) [1] 1426204 I checked my ulimits variable on the unix terminal and it says it's unlimited as does > mem.limits() nsize vsize NA NA But I'm still getting errors like the following with funtions in the cluster package > daisy(nca352, metric= "euclidean", stand=FALSE)->dnca35 Error: cannot allocate vector of size 858213 Kb *** malloc: vm_allocate(size=878813184) failed (error code=3) *** malloc[599]: error: Can't allocate region if it helps i also checked > gc() used (Mb) gc trigger (Mb) Ncells 448662 12.0 741108 19.8 Vcells 847630 6.5 135357901 1032.7 I tried the suggested unix command in the memory help doc but that doesn't work in the Aqua GUI. Can someone tell me how to change the Vcells? Although to the best of my understanding (which is limited) I shouldn't have to do that. Any suggestions would be greatly appreciated. thanks, betty -- Betty Gilbert [EMAIL PROTECTED] Taylor Lab Plant and Microbial Biology 321 Koshland Hall U.C. Berkeley Berkeley, Ca 94720 ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
