Some suggestions: The line:
pearson.dist <- as.dist(1-cor(t(todos.norm), method="pearson")) includes several data manipulations in "one go". Each manipulation creates at least one extra copy of your data in memory. When you do it this, you make it harder for the R garbage collector to clean out such memory. The following should use less memory: todos.norm <- t(todos.norm); gc(); # Explicit garbage collect; cleans out the 1st 'todos.norm' object. rho <- cor(todos.norm, method="pearson"); rm(todos.norm); # Not needed anymore gc(); # Explicit garbage collect; cleans out the 2nd 'todos.norm' object. rho <- 1-rho; gc(); # Explicit garbage collect; cleans out the 1st 'rho' object. pearson.dist <- as.dist(rho); Not sure if it helps in your case/with your data, but this is how you are a user can help R at bit on the way. You should of course also clean out all other stray objects you don't use anymore, before doing the above. My $.02 /Henrik On Sat, Feb 20, 2010 at 1:13 PM, Marcelo Laia <marcelol...@gmail.com> wrote: > Hi, I am trying to run a script on R and it died before finish. > > I already read the list archives, and memory help pages > (http://tinyurl.com/yaxco6w), but I am unable to solve the issue. > > My Debian shows: > > marc...@laia:~$ ulimit > unlimited > marc...@laia:~$ > > On system monitor (gnome) I see that R reaches 1.9 Gb, before die. > > The R code is: > >> ls() ## only todos.norm object are listed > [1] "todos.norm" >> dim(todos.norm) > [1] 9600 15 >> >> library("cluster") >> pearson.dist <- as.dist(1-cor(t(todos.norm), method="pearson")) > Died > > What I could do to solve my problem? > >> sessionInfo() ## after restart R > R version 2.10.1 (2009-12-14) > i486-pc-linux-gnu > > locale: > [1] LC_CTYPE=pt_BR.UTF-8 LC_NUMERIC=C > [3] LC_TIME=pt_BR.UTF-8 LC_COLLATE=pt_BR.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=pt_BR.UTF-8 > [7] LC_PAPER=pt_BR.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=pt_BR.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base >> > > My system: > > Linux laia 2.6.32-trunk-686 #1 SMP Sun Jan 10 06:32:16 UTC 2010 i686 GNU/Linux > > Than you very much! > > -- > Marcelo Luiz de Laia > Brazil > Linux user number 487797 > > ______________________________________________ > 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. > ______________________________________________ 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.
