similar to: Huge workspace cannot be opened

Dear all, I don't get it: First of all, the help doesn't say what are the memory limits of R. Say, what's the max heap size for instance ???? Secondly, I invoke R with the following commands each time: rgui --vsize 30M --nsize 1000K rgui --vsize 30M --nsize 2000K rgui --vsize 30M --nsize 3000K rgui --vsize 30M --nsize 4000K I try to open a matrix 8000x8000 by issuing

Dear sir, I am using R in windows. I want to extend R Memory size. I use the following command, but unfortunately it doesn't work. -- vsize=15M --nsize=1000K Your help is appreciated. Thanks, Esmail Amiri. __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! Mail. http://personal.mail.yahoo.com/

Hello- Since my data bank in SPSS has > 40 variables, I think that R crashes because of the memory limit. In Maindonald?s UsingR text, on pg 3, there?s a footnote that reads: "If you want larger memory space than the default you may want a target akin to <path to binary>\rw091\bin\rgui.exe --visize 30M --nsize 1000K [The default is --vsize 6M --nsize 250K

Hi, I have a few questions about how to handle large data sets in R. What is the size of the largest matrix that R can comfortably deal with? Is this size limit imposed by R's software, or is it a question of the machine that one runs on? How does one go about choosing reasonable values of vsize and nsize? I have a data set with about 1,000,000 rows, and 30

I'm sure this question is answered in the help file, but likely I'm not reading it corrected. Running windows version 1.00.0, loading a table (35K rows by 10 columns) from Excel using the read.table command I receive the following message. Error: cons memory (350000 cells) exhausted See "help(Memory)" on how to increase the number of cons cells. >From reading the

Sorry, but I lost this thread, so I sending this as a new message. This is really a follow-up to a post from a couple days ago saying that fisher.test from the ctest library crashed on the following data set: > T [,1] [,2] [1,] 2 1 [2,] 2 1 [3,] 4 0 [4,] 8 0 [5,] 6 0 [6,] 0 0 [7,] 1 0 [8,] 1 1 [9,] 7 1 [10,] 8 2 [11,]

Martin M has suggested I widen this discussion to R-devel, and > I agree that we should increase them, > but I'm not sure at all about the amount. > > The default could even depend on the architecture (via "./configure").. Views, please. ------------- Begin Forwarded Message ------------- Is is not time we increased the defaults a bit? As the base gets bigger I hit

Hi, I have recently installed R-1.2.2 for windows (16MB RAM, P-166) and I getting the following message after processing my data (6 variables and 1200 observations): >Error: cannot allocate vector of size 4 Kb >In addition: Warning message: >Reached total allocation of 15Mb: see help(memory.size) Then, the program close. With the last version, 1.1.1 (I think) I didn't have this

My group is working with datasets between 100 Mb and 1 GB in size, using multiple log ins. From the documentation, it appears that vsize is limited to 2^30-1, which tends to prove too restrictive for our use. When we drop that restriction (set vsize = NA) we end up hanging the server, which requires a restart. Is there any way to increase the memory limits on R while keeping our jobs from

I am trying to use R to cluster 7129 samples, my data set is a 7129 x 38 matrix, when I trying to get the distance matrix using function dist( ), the memory exhausted, and I tried to set the memory when I run R by R --vsize=250M --nsize=1000k no matter what I set for vsize the result is the same, it says: Error: heap memory (256000kb) exhausted [need 198498Kb more]

Let me begin stating that I read all help files and faq's on the subject matter (there aren't more than about a dozen) but either did not find solutions or found them not to work. Here is the issue. I am trying to run a spatial regression on a medium-sized dataset. Part of the functions in the spdep package I use require me to allocate a vector of 1.1 Gb (mine is not a spatial SIG

Hello R-community, It's been a week now that I am struggling with the implementation of a cox model in R. I have 80 cancer patients, so 80 time measurements and 80 relapse or no measurements (respective to censor, 1 if relapsed over the examined period, 0 if not). My microarray data contain around 18000 genes. So I have the expressions of 18000 genes in each of the 80 tumors (matrix

Dear R-users, I am trying to run some simulations in batch mode. In an older version of the program, I used rterm --vsize=100M --nsize=5000K --restore --save <input file> output file, however, in the new version R 2.2.0 , the parameters vsize and nsize are ignored. I can use the command memory.limit to increase memory, but I am not sure if this corresponds to vsize and nsize.

Dear R-ers, somehow it is not possible to increase nsize to more than 20000k. When I specify e.g. > R --vsize=10M --nsize=21000K the result is: free total (Mb) Ncells 99658 350000 6.7 Vcells 1219173 1310720 10.0 Maybe I have overlooked s.th.... Marcus -- +------------------------------------------------------- | Marcus Eger | E-Mail: eger.m at gmx.de (NEW) |

Hi, Is the following command used to increase the memory or any other command when a background R job is run? R --min-vsize=vl --max-vsize=vu --min-nsize=nl --max-nsize=nu --max-ppsize=N source: http://stat.ethz.ch/R-manual/R-patched/library/base/html/Memory.html Thx Carol [[alternative HTML version deleted]]

I am running R version ??? under Redhat 5.2. It seems as though the --nsize object has no effct on the size of the allocated Ncells as determined using gc(). Yes, I have that much data.... That is if I envoke R with R --vsize 100 --nsize 5000000 then type gc() I get free total Ncells 92202 200000 Vcells 12928414 13107200 Thanks Tony Long Ecology and Evolutionary Biology Steinhaus

Dear Group I'm still trying to bring many data into R (see older postings). After solving some troubles with the database I do most of the work in MySQL. But still I could be nice to work on some data using R. Therefore I can use a dedicated Server with Gentoo Linux as OS hosting only R. This Server is a nice machine with two CPU and 4GB RAM which should do the job: Dual Intel XEON 3.06 GHz

I am trying to upload into R 143 Affymetrix chips onto using R on the NIH Nimbus server. I can load 10 chips without a problem, however, when I try to load 143 I receive a error message: cannot create a vector of 523263 KB. I have expanded the memory of R as follows: R --min-vsize=10M --max-vsize=2500M --min-nsize=10M -max-nsize=50M (as specified in help in R). After running this command the

Dear R-helpers, I am running R version 2.9.1 on a Mac Quad with 32Gb of RAM running Mac OS X version 10.5.6. With over 20Gb of RAM "free" (according to the Activity Monitor) the following happens. > x <- matrix(rep(0, 6600^2), ncol = 6600) # So far so good. But I need 3 matrices of this size. > y <- matrix(rep(0, 6600^2), ncol = 6600) R(3219) malloc: ***

Dear R users, I have noticed that my R startup is extremely slow. It takes almost 3 minutes from "double-click" to R prompt. I have been running R-0.64.1 till recently and it took about 30 sec. I still have access to R-0.64.1. When I started it up, it took about 25 sec. Can anyone tell me if this is a bug in R or a problem with my machine? Note: This is after bootup with R being the