similar to: malloc: vm_allocate(size=381886464) failed (error code=3)

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 <-

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 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:

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

Hi list, I have been trying to pileup dataframes with different column names using rbind. I am getting the following error message. I was wondering if there is a way to go around this minor problem? Error in match.names(clabs, names(xi)) : names don't match previous names: G Thanks indeed for your information Regards Mahdi -- ----------------------------------- Mahdi Osman (PhD)

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 want to do an unbalanced anova on 272,992 observations with 405 factors including 2-way interactions between 1 of these factors and the other 404. After fitting only 11 factors and their interactions I get error messages like: Error: cannot allocate vector of size 1433066 Kb R(365,0xa000ed68) malloc: *** vm_allocate(size=1467461632) failed (error code=3) R(365,0xa000ed68) malloc: ***

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 list, I am doing cluster analysis using the cluster package. I created a dendrogram using the function plot(agnes(myData)). When I try to change the sise of labels, it does not work. I tried cex = 1.5, etc. Nothing worked. Can anyone give me a hint on how to change the sise of the labels, as well as the sise of axes labels. Thanks Mahdi -- ----------------------------------- Mahdi Osman

Dear list, This is a simple question but I spent an hour on it without success. So I sorry to bother you. I fit a linear model "lm" and then did "anova". My idea is to run multiple pairwise comparision for several factor variables (f1, f2, f3, f4 each with its own levels, say "0", "1", "3" etc )at the same time and get statistics for each

Hi list, I am fitting microarray data (intensity) model using the lme package in R environment. I have 5 fixed variables in the model. One of the fixed variables is genes. I am trying to get p-values for different genes. But I am getting only one p-value for all genes together. I can get a list of p-value when I run lm. Why can't this work in lme? I was wondering if some one can help me

Dear list, I have been trying to resolve the following problem for a couple of hours, but couldn't get around. I updated my R pacages from CRAN which went somoothly. However, updating HTML is not going well. I got the following error message: 1: Package R2HTML is in use and will not be installed. 2: Number of rows of results is not a multiple of vector length (arg 1) in cbind (pkgs, lib).

Hi, list, I have got a dataset on soil and plant. I would like to fit a "glm" to my data. My response variable is percentage data. That is percent of plant root length colonized by Arbuscular micorrhiza fungi. Because of the nature of my data, I am not quite sure whether gamma or gaussian distribution is suitable for this type of data. If I use gamma distribution, which link function is

Hi, list, Sorry if I am bothering you. I am interested in using xgrid with R for distributed computing. I am using MacOS X and my R 2.1. 1 is already installed and running. The client computers are all of the same type and the same version of R has been installed on them. We have also set up xgrid on my system and client computers as well. I am wondering if any one can give me some clues

Hi list, I am fitting microarray data (intensity) model using the lme package in R environment. I have 5 fixed variables in the model. One of the fixed variables is genes. I am trying to get p-values for different genes. But I am getting only one p-value for all genes together. I can get a list of p-value when I run lm. Why can't this work in lme? My aim is to do multiple comaprison of all

Hi, dear list members, I've been using R under windows XP and I am now changing my system to SUSE LINUX 9.3. I could figure out that there is no precompiled version of R for LINUX. To get me going, I would like your help regarding what I need to setup R under my SUSE LINUX. Which compiler do I need to be able to compile the source and I was wondering if I could get GNU compiler?

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

Hi all, I am running R 2.0.1 under Windows XP in German. I configured my path as follows: C:\Programme\R\rw2001\bin;C:\Programme\xemacs-packages\lib-src\;C:\Programme\XEmacs-21.4.13\i586-pc-win32 I can not start R proccess or ESS from within XEmacs. What is going wrong? I can not start S. M-x S gives "no matching" How can I configure XEmacs for STATA 8? Thanks for your help. M

Hi list, I am analysing a large dataset using random coefficient (using nlme) and fixed effects (using lm function) models. I have problem with my R version 2. 2. 1 due to memory allocation difficulties. When I try to expand the memory I get the following error message. > R --min-vsize=10000000 --max-vsize=1000000000 --min-nsize=500 --max-nsize=10000000 Error: target of assignment expands