caught segfault - 'memory not mapped' error in R

Question

I have a problem running some R scripts on our cluster. The problems appeared suddenly (all the scripts were working just fine but one day they started giving a caught seg

Answer 1

It's not really an explanation of the problem or a satisfactory answer but I examined the codes more closely and figured out that in the first example, the problem appears when using acast from the reshape2 package. I deleted it in this case because I realized it's not actually needed there but it can be replaced with reshape from the reshape package (as shown in another question): reshape(input, idvar="x", timevar="y", direction="wide")[-1].

As for the second example, it's not easy to find the exact cause of the problem but as a workaround in my case helped to set a smaller number of cores used for parallel computation - the cluster has 48, I was using only 15 since even before this issue R was running out of memory if the code was run using all 48 cores. When I reduced the number of cores to 10 it suddenly started working like before.