[R] --mem-vsize in R

kparamas kparamas at asu.edu
Fri Apr 29 22:14:29 CEST 2011


I am calculation pairwise correlation coefficient for a matrix of 234 X
I am getting the following error,
Error in cbind(as.vector(row(cl)), as.vector(col(cl)), as.vector(cl)) : 
  allocMatrix: too many elements specified
In addition: There were 50 or more warnings (use warnings() to see the first

The function used is,
corGraphPearson = function(cData, COR) #COR is threshold 0.5,0.7, etc

    cl = unname(cor(cData, use="pairwise.complete.obs", method="pearson"))

        result = cbind(as.vector(row(cl)),as.vector(col(cl)),as.vector(cl))
        result = result[result[,1] != result[,2],]

        corm = result

# remove low cor pairs
        corm =corm[abs(corm[,3]) >= COR, ]
# the network
        net <- network(corm, directed = F)

I am running this in a cluster with 4 machines with 24 GB memory each.

How should I start R so that I make max use of the memory availbale?
Or how to overcome this issue?

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