similar to: setting a large value of --max-vsize

  R-devel, I am migrating from R.2.13.2 to R.2.15.1 and just realize that R command line options --max-nsize and --max-vsize are no longer supported along with the defunct of mem.limits(). To me, the function and options along with other two, --min-nsize and --min-vsize, are useful in allowing some explicit control of R memory usage. One benefit is that the setting of maximum boundary could

Hi, somtimes i have trivial recodings like this: > dim(tt) [1] 252382 98 system.time(for(i in 2:length(tt)){ tt[,i][is.na(tt[,i])] <- 0 }) ...and a win2000(XP2000+,1GB) machine makes it in several minutes, but my linux notebook (XP2.6GHZ,512MB) don't get success after some hours. I recognize that the cpu load is most time relative small, but the hardisk

Hi, In both R 2.13 and the SVN trunk, I observe odd behaviour with the --max-vsize command-line argument: 1. passing a largeish value (about 260M or greater) makes mem.limits() report NA for the vsize limit; gc() continues to report a value... 2. ...but that value (and the actual limit) is wrong by a factor of 8. I attach a patch for issue 2, lightly tested. I believe that fixing issue 1

Full_Name: Markus Neteler Version: 1.0.0 OS: Linux 2.2.10/i686 Submission from: (NULL) (130.75.72.37) Hi, I wanted to "check" the R.GRASS GIS interface from Roger Bivand: http://www.geog.uni-hannover.de/grass/statsgrasslist.html using R CMD check --vsize=10M GRASS but: [error message shortened] > G <- gmeta() Error: heap memory (6144 Kb) exhausted [needed 1024 Kb more]

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

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

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

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]

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

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

The R memory docs say that the --*-vsize option takes an integer argument and then 'G', 'M', 'K', or 'k'. When I start R using R --max-vsize=10G I receive the warning: WARNING: --max-vsize=10G=10'M': too large and ignored The system that I'm working on is a 64-bit Sun server with 40G of memory. What is the correct syntax for this command? Daniel

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

Hi everyone, I have a problem that some people may have already encountered but i did not find the solution yet. As I use R to simulate several arrays of data, my workspace is now 35Mb big and I cannot launch R with it. An "xdr real data read error occured" and R tells me to delete .RData or increase memory. I WON'T delete this file and changing the max-nsize to 40600k did not

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

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.

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

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

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]]

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

Hi, I am not on this mailing list, but here is a terrible bug that has stopped me in my tracks. I am unable to remove observations from a data matrix. temp is the original matrix. Notice that there are 288 entries with a 104 in the first column. I attempt to remove these entries, but R does not do it. brad ACTUAL COMMANDS: > dim(temp) [1] 30528 11 > table(temp[,1]) 1 3 4