Fix in calcDissimilarityMatrix: indeces have been changed to unsigned long int to allow for bigger dissimilarity matrices to be handled. Also, added option onlyLS in calcDissimilarityMatrix to restrict the function calcOptimalClustering to do the calculations for the optimal partition by least squares only (not using PAM). When onlyLS=TRUE the dissimilarity matrix is not copied from C++ to R (and therefore avoids memory problems).
Fixed a couple of things to pass --check cleanly.