Dear all, I am in trouble with pamr.knnimpute (library pamr) When I use this function in a "for" loop with matrix of 4 samples at each loop, R does a segmentation fault which ends with a fatal error (R close itself) I used this function previously with 8 samples and 1327 genes and it worked. I try my script using Windows and on server using Linux, still error remains (so this mustn't be a ressource error, I think) He breaks on knnimp function The dimensions of my tables are 1337*4 and 1327*4 and I use a k=10 for the number of neighbors. My main problem is that the error is not permanent, sometimes (but not generally) it may work, and when I have the error it could be either on the first or on the second table . Thanks for helping. Alice. -- Alice Le Bars INSERM U533 - IFR 26 1 Rue Gaston Veil- BP 53508 44 035 NANTES FRANCE Tel : (33) 2 40 41 29 86 Fax : (33) 2 40 41 29 50 http://cardioserve.nantes.inserm.fr/ptf-puce

Hi Alice, Alice Le Bars <alice.le-bars@nantes.inserm.fr> writes: > I am in trouble with pamr.knnimpute (library pamr) When I use this > function in a "for" loop with matrix of 4 samples at each loop, R > does a segmentation fault which ends with a fatal error (R close > itself) I used this function previously with 8 samples and 1327 > genes and it worked. In order for us to try and help, please tell us: - Your version of R and version of pamr - Show us the code that is breaking (the for loop), if possible - Tell us about the resources available on the machines you've tried this on (how much memory is the important thing). The segfaulting you are reporting sounds like out of memory behavior, but could also be a bug in pamr. But you'll need to help of with much more detail... + seth