It seems like the objects are reasonable size and the memory size also seems reasonable. That is what I usually go by to see if there are large objects in my memory. If it was showing that R had 1.2GB of memory allocated to it, I wonder if there might be a memory leak somewhere.
On Fri, Aug 1, 2008 at 1:36 PM, Tom La Bone <[EMAIL PROTECTED]> wrote: > > Same problem. The Windows Task Manager indicated that Rgui.exe was using > 1,249,722 K of memory when the error occurred. This is R 2.7.1 by the way. > >> library(boot) >> setwd("C:/Documents and Settings/Tom/Desktop") >> >> data.in <- read.csv("inputdata.csv",header=T,as.is=T) >> >> per95 <- function( annual.data, b.index) { > + sample.data <- annual.data[b.index,] > + return(quantile(sample.data$Result,probs=c(0.95))) } >> >> m <- 10000 >> for (i in 1:39) { > + annual.data <- data.in[data.in$Year == (i+1949),] > + B <- boot(data=annual.data,statistic=per95,R=m) > + gc() > + print(i) > + print(object.size(B)) > + print(memory.size()) > + } > [1] 1 > [1] 90352 > [1] 12.35335 > [1] 2 > [1] 111032 > [1] 12.39024 > [1] 3 > [1] 155544 > [1] 12.48451 > [1] 4 > [1] 159064 > [1] 11.10526 > [1] 5 > [1] 243456 > [1] 11.23505 > [1] 6 > [1] 280592 > [1] 12.74642 > [1] 7 > [1] 302416 > [1] 11.33087 > [1] 8 > [1] 319752 > [1] 12.84377 > [1] 9 > [1] 351448 > [1] 11.42264 > Error: cannot allocate vector of size 284.4 Mb >> >> > > > > jholtman wrote: >> >> Use gc() in the loop to possibly free up any fragmented memory. You >> might also print out the size of B (object.size(B)) since that appears >> to be the only variable in your loop that might be growing. >> >> On Fri, Aug 1, 2008 at 12:09 PM, Tom La Bone <[EMAIL PROTECTED]> >> wrote: >>> >>> >>> I have a data file called inputdata.csv that looks something like this" >>> >>> ID Year Result Month Date >>> 1 7174 1954 10 3 540301 >>> 2 7174 1954 4 3 540322 >>> 3 20924 1967 4 2 670223 >>> 4 20924 1967 -7 5 670518 >>> 5 20924 1967 -3 7 670706 >>> ... >>> 67209 ... >>> >>> i.e., it goes on for 67209 rows (~2 Mb file). When I run the following >>> bootstrap session I get the indicated error: >>> >>>> >>>> library(boot) >>>> setwd("C:/Documents and Settings/Tom/Desktop") >>>> >>>> data.in <- read.csv("inputdata.csv",header=T,as.is=T) >>>> >>>> per95 <- function( annual.data, b.index) { >>> + sample.data <- annual.data[b.index,] >>> + return(quantile(sample.data$Result,probs=c(0.95))) } >>>> >>>> m <- 10000 >>>> for (i in 1:39) { >>> + annual.data <- data.in[data.in$Year == (i+1949),] >>> + B <- boot(data=annual.data,statistic=per95,R=m) >>> + print(i) >>> + print(memory.size()) >>> + } >>> [1] 1 >>> [1] 20.26163 >>> [1] 2 >>> [1] 61.6352 >>> [1] 3 >>> [1] 134.4187 >>> [1] 4 >>> [1] 149.4704 >>> [1] 5 >>> [1] 290.3090 >>> [1] 6 >>> [1] 376.7017 >>> [1] 7 >>> [1] 435.7683 >>> [1] 8 >>> [1] 463.7404 >>> [1] 9 >>> [1] 497.7946 >>> Error: cannot allocate vector of size 568.8 Mb >>>> >>> >>> I am running this on a Windows XP Pro machine with 4 Gb of memory. The >>> same >>> problem occurs when the code is executed on the same box running Ubuntu >>> 8.04. Does anyone see any obvious reason why this should run out of >>> memory? >>> I would be happy to email the data file to anyone who cares to try it on >>> their computer. >>> >>> Tom >>> >>> >>> >>> >>> >>> -- >>> View this message in context: >>> http://www.nabble.com/Memory-Problems-with-a-Simple-Bootstrap-tp18777897p18777897.html >>> Sent from the R help mailing list archive at Nabble.com. >>> >>> ______________________________________________ >>> 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. >>> >> >> >> >> -- >> Jim Holtman >> Cincinnati, OH >> +1 513 646 9390 >> >> What is the problem that you are trying to solve? >> >> ______________________________________________ >> 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. >> >> > > -- > View this message in context: > http://www.nabble.com/Memory-Problems-with-a-Simple-Bootstrap-tp18777897p18779433.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > 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. > -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? ______________________________________________ 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.