similar to: memory limit in aov

I''m using acts_as_ferret and when I call Object.find_by_contents("A & B"), Ruby dies with the following message: ^Cruby(5014,0xa000cf60) malloc: *** vm_allocate(size=1069056) failed (error code=3) ruby(5014,0xa000cf60) malloc: *** error: can''t allocate region ruby(5014,0xa000cf60) malloc: *** set a breakpoint in szone_error to debug ruby(5014,0xa000cf60) malloc:

Hi, I'm Sorry for any cross-posting. I've reviewed the archives and could not find an exact answer to my question below. I'm trying to generate very large sparse matrices (< 1% non-zero entries per row). I have a sparse matrix function below which works well until the row/col count exceeds 10,000. This is being run on a machine with 32G memory: sparse_matrix <-

Full_Name: Hans Kestler Version: 2.2.0 OS: 10.4.3 Submission from: (NULL) (84.156.184.101) > sam1.out<-sam(raw1[,2:23],raw1.cl,B=0,rand=124) We're doing 319770 complete permutations Error: cannot allocate vector of size 575586 Kb R(572,0xa000ed68) malloc: *** vm_allocate(size=589402112) failed (error code=3) R(572,0xa000ed68) malloc: *** error: can't allocate region

Dear R Experts, I am using R.app (the Mac OS X binary) for neuroimage analysis, so I am loading in some large image files. I get the following error in the middle of my script: > source("3dLME.R") Read 1 record Read 1 record Read 1 record Read 1 record Read 1 record Error: cannot allocate vector of size 3.1 Gb R(2081,0xa000d000) malloc: *** vm_allocate(size=3321675776) failed (error

Dear all, I am having a memory problem when analyzing a rather large data set with nested factors in R. The model is of the form X~A*B*(C/D/F) A,B,C,D,F being the independent variables some of which are nested. The problem occurs when using aov but also when using glm or lme. In particular I get the following response, Error: cannot allocate vector of size 1.6 Gb R(311,0xa000d000) malloc: ***

I am using the Openbase adapter and have had a similar glitch here and there, but after I go into production I consistently get an error on one page. ActionView::TemplateError (NoMemoryError: failed to allocate memory: SELECT * FROM ... I cannot track down the exact location of the error, but the production log says it was around:

Hello, all, First thanks in advance for helping me. I am now handling a data frame, dimension 11095400 rows and 4 columns. It seems work perfect in my MAC R (Mac Pro, Intel Chip with 4G RAM) until I was trying to write this file out using the command: write.table(all,file="~/Desktop/alex.lgen",sep=" ",row.names=F,na="0",quote=F,col.names=F) I got the error

Does anyone know how to make one legend above the plots drawn using par(mfrow=c(1,2)), ie in the margin? All I've managed is to put a legend inside the plot region of one graph. Although I could write text in the margin I don't know how to draw lines in the margin if I were to construct the legend from scratch. Thanks for any help. Lucy Crooks Theoretical Biology

Full_Name: Eric Libby Version: 2.1.1 OS: OS Tiger Submission from: (NULL) (65.93.158.117) I am trying to analyze microarray data of 42 human arrays. I typed in the following instructions: library(affy) Data <-ReadAffy() eset <- expresso(Data, normalize.method="invariantset", bg.correct=FALSE, pmcorrect.method="pmonly",summary.method="liwong") And I get some

Hi, I'm tying to fit a glm using quasi with variance=mu(1-mu) (to try and get "well behaved" residuals). I get an error message: "cannot find valid starting values, please specify some". I have tried using start= and specifying coefficients from a previous fit (with different error structure) but get the same message. What would be valid starting values? I am using a

Hi all, I am having memory allocation problem with my R 2.2.1 for Mac OS. The following is the error message that I get. I do not get this message if I break down the large dataset in to sub datasets. I think breaking up the dataset is not a sustainable solution in the long run. The data that I am analysing is essentially big, and it would be reasonable to do the analyis on the whole dataset

Hi All, I want to print a square matrix of 7000 x 7000 into a text file. But I got a error after few hours of computation... -------- > write.table(MyDistMxDF, file = "temp.csv", sep=",", quote=F) *** malloc: vm_allocate(size=8421376) failed (error code=3) *** malloc[2889]: error: Can't allocate region Error: vector memory exhausted (limit reached?) *** malloc:

I''m using ferret (0.9.4) in rails, but outside of the "acts_as_ferret" plugin. Whenever I use a QueryFilter (even a very simple one), the server will crash after one, two, or three reloads of a page (same page, same query, same filter). It''s very non-deterministic and I can''t seem to reproduce it outside of my application environment (I can''t get it

Hi, FreeBSD-9 works fine on this Lenovo T400 - except that suspending with no USB devices plugged in result in no ports working after resume. If I have a device plugged in during suspend - on any port - then all the ports work fine after resume. I've attached usbconfig and acpidump output. here's what is logged in the kernel buffer during suspend and resume: Her'es the suspend:

On Jul 10, 2007, at 15:39, Chris Lattner wrote: > On Tue, 10 Jul 2007, Sandro Magi wrote: > >>> used. Your choices are to either override malloc/free for both >>> the JIT and the program or for neither of them. >> >> I want to 'intercept' ALL allocations actually, including the >> stack if possible, so the above suits me just fine. > >

Hello. I am not sure if this is a bug. I loaded into R a very large matrix, around 600,000 X 30 integers. My machine has 2G ram. After trying to write.table a modification of this matrix, R generated some sort of malloc error. Then, Error: vector memory exhausted (limit reached?) > q() Save workspace image? [y/n/c]: n *** malloc: vm_allocate(size=8421376) failed (error code=3) ***

Hi, I am trying to get bootstrap confidence intervals on variance components and related statistics. To calculate the variance components I use the package lme4. > off.fun <- function(data, i){ d <- data[i,] lme1<- lmer(y ~ trt + (trt-1|group), d) VarCorr(lme1)@reSumry$group[2,1] #just as an example } > off.boot <- boot(data=data.sim, statistic=off.fun, R=100) If

On Sun, Aug 8, 2010 at 9:20 PM, Reid Kleckner <reid.kleckner at gmail.com>wrote: > On Sun, Aug 8, 2010 at 8:20 PM, Jakob Stoklund Olesen <stoklund at 2pi.dk> > wrote: > > > > On Aug 7, 2010, at 7:05 PM, Steven Noonan wrote: > >> I've been doing work on memory reduction in Unladen Swallow, and > >> during testing, LiveRanges seemed to be

Hi there, What''s the current status of the Windows port? I may be in a position to lend a hand over the next couple of weeks - where should I start looking? And what''s the best way to get SVN HEAD? This happens: $ svn checkout svn://www.davebalmain.com/ferret/trunk ferret svn: Can''t connect to host ''www.davebalmain.com'': Connection refused --

Dear list, I am using R.2.0.1 on a G5 biprocessor 2.5GHz with 2Go RAM (Mac OS X 10.3.8). I'm trying to calculate an object of type "dist". I am getting the following memory error : *** malloc: vm_allocate(size=1295929344) failed (error code=3) *** malloc[25960]: error: Can't allocate region Error: cannot allocate vector of size 1265554 Kb When I do a top on the terminal, I