similar to: R would not quit (bug?) (PR#6600)

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:

Simply gooling for "writing ARFF file in R" gave the following as first hit, which is right on the WEKA page: Miscellaneous code [...] Function for reading ARFF files into the R statistical package (kindly provided by Dr Craig Struble). Function for writing ARFF files from the R statistical package (kindly provided by Nigel Sim).

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 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

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

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: ***

The call to system() probably is an internal call used to delete the session's tempdir(). This sort of failure means that a potentially large amount of disk space is not being recovered when R is done. Perhaps R_CleanTempDir() could call R_unlink() instead of having a subprocess call 'rm -rf ...'. Then it could also issue a specific warning if it was impossible to delete all of

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 <-

On 11/24/20 11:27 AM, Jan Gorecki wrote: > Thanks Bill for checking that. > It was my impression that warnings are raised from some internal > system calls made when quitting R. At that point I don't have much > control over checking the return status of those. > Your suggestion looks good to me. > > Tomas, do you think this could help? could this be implemented? I think

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

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. > >

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

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

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

On Tue, 24 Nov 2020, Jan Gorecki wrote: > As for other calls to system. I avoid calling system. In the past I > had some (to get memory stats from OS), but they were failing with > exactly the same issue. So yes, if I would add call to system before > calling quit, I believe it would fail with the same error. > At the same time I think (although I am not sure) that new allocations

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

Hello. I have a dataset with about 500,000 observations, most of which are not unique. The first 10 observations look like 901000000000100000010100101011002 901101101110100000010100101011002 901000000000100000010100000001002 901000000000100000010101001011002 901000000000100000010101010011002 901000000000100000010100110101002 901000000000100000010100101011002 900000000000100000010010101011002