[R] Memory problem

Gang Chen gangchen at mail.nih.gov
Thu Aug 9 16:36:25 CEST 2007

I got a long list of error message repeating with the following 3  
lines when running the loop at the end of this mail:

R(580,0xa000ed88) malloc: *** vm_allocate(size=327680) failed (error  
R(580,0xa000ed88) malloc: *** error: can't allocate region
R(580,0xa000ed88) malloc: *** set a breakpoint in szone_error to debug

There are 2 big arrays, IData (54x64x50x504) and Stat (4x64x50x9), in  
the code. They would only use about 0.8GB of memory. However when I  
check the memory usage during the looping, the memory usage keeps  
growing and finally reaches the memory limit of my computer, 4GB, and  
spills the above error message.

Is there something in the loop about lme that is causing memory  
leaking? How can I clean up the memory usage in the loop?

Thank you very much for your help,


tag <- 0; dimx<-54; dimy<-64; dimz<-50; NoF<-8; NoFile<-504;

IData <- array(data=NA, dim=c(dimx, dimy, dimz, NoFile));
Stat <- array(data=NA, dim=c(dimx, dimy, dimz, NoF));

for (i in 1:NoFile) {
    IData[,,,i] <- fill in the data for array IData here;

for (i in 1:dimx) {
for (j in 1:dimy) {
for (k in 1:dimz) {
    for (m in 1:NoFile) {
		Model$Beta[m] <- IData[i, j, k, m];
    try(fit.lme <- lme(Beta ~ group*session*difficulty+FTND, random =  
~1|Subj, Model), tag <- 1);
    if (tag != 1) {
	   Stat[i, j, k,] <- anova(fit.lme)$F[-1];	
    else {
        Stat[i, j, k,] <- rep(0, NoF-1);
    tag <- 0;

More information about the R-help mailing list