creating a matrix of "objects"

Problem: I need to get a "matrix" of "datapoints".
         Each datapoint has to contain tree attributes.

Have you tried:

m <- matrix(list(), nrbases, nrbases)

?  You would then index it using m[[i,j]].    A list is a basic
vector, so you can make a matrix with it, just as you can with a
vector of numbers.

Hadley