[R] Problem extracting labels from a large dendrogram

Oleksandr Moskalenko om at hpc.ufl.edu
Fri Jan 4 02:45:13 CET 2013


I have an issue with extracting labels from a ~30k member dendrogram using a 64-bit R/2.15.1 build. Inevitably, the following error pops up when using labels(dendrogram_object) - "Error in match.fun(FUN) : node stack overflow". I though the issue was the stack size, so I rebuilt R with a much larger max-ppsize limit and kept raising it on the command line with --max-ppsize, but it didn't work even with R running with a 500 million --max-ppsize. I notice that the process consistently grows up to about 39-40Gb of RAM before the error happens. I've been trying to find a way around it, but using dendrapply didn't work out either. Same error happened.

Here is an example:

> attributes(h)
[1] 27109

[1] 2.609272

[1] 6322.5

[1] "dendrogram"

> local({
       getLab <<- function(n) {
         if(is.leaf(n)) {
           a <- attributes(n)
           i <<- i+1
           lbl <- attr(n, "label")
    i <- 0
> n2 <- dendrapply(h, getLab)
Error in `[[.dendrogram`(X, 1L) : node stack overflow



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