Dear all, I have an ontology which I would like to load in R to then compute the minimum distance between elements. Since this ontology is not only DAG, the problem is non trivial and therefore decided to use R with the powerful e1071 library (allShortestPaths) to do that. That method requires to provide a distance matrix between the various objects. My ontology contains 32768 objects and therefore I have to load a matrix of 32768x32768. Values in the matrix are set to 1 for those pair of terms that have a link (semantic or hyper/hypo-nimic). I am trying to reproduce at least part of the infrastructure described in the following work |--------------------------------------------------------------------------------| | 1. Sugato Basu, Raymond J. Mooney, Krupakar V. Pasupuleti and Joydeep Ghosh | | Evaluating the Novelty of Text-Mined Rules using Lexical Knowledge | | Submitted to the Seventh ACM SIGKDD International Conference on Knowledge | | Discovery and Data Mining (KDD-2001), 2001 | |--------------------------------------------------------------------------------| Unfortunately, when I try to do that I get into the reported problem (cannot allocate vector of length 1073741824). I am operating on an Irix Origin 2000 with 24 processors and 16 GB of shared memory. My process has no limits set to the amount of memory it can use. I have noticed in the mailing as well as in the FAQ that since version >1.2 the memory management has been changed and I got the information that somebody already successfully managed in loading a 2GB dataset in previous versions. I would be delighted to learn your opinion and instructions on how to proceed. Regards and compliments Dr. Luca Toldo Bioinformatician at Merck KGaA, Darmstadt -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
[R-1.4.0] minimum spanning tree of large ontology
1 message · Luca.Toldo@merck.de