"Joshi, Nina (NIH/NCI)" <[EMAIL PROTECTED]> writes: > I am trying to upload into R 143 Affymetrix chips onto using R on the NIH > Nimbus server. I can load 10 chips without a problem, however, when I try > to load 143 I receive a error message: cannot create a vector of 523263 KB. > I have expanded the memory of R as follows: R --min-vsize=10M > --max-vsize=2500M --min-nsize=10M -max-nsize=50M (as specified in help in > R). After running this command the memory in R is as follows: > > > > Used (Mb) gc trigger (Mb) limit > (Mb) > > Ncells 513502 13.8 10485760 280.0 1400 > > Vcells 142525 1.1 162625696 1240.8 2500 > > > > However, I am still getting the error cannot create a vector of 523263 KB. > Any suggestions/ideas?
Well, it basically means that you're running out of memory. The 523263 KB is just the last request that R tries to honour when it fails, but it is in fact a whole half gigabyte. I forget what the memory usage per Affy chip is (and it depends on the chip, I suppose), but how much did the 10 chips take? Do you have space for 14 times that amount? It is not unlikely that you're running into the limits of the 32bit address space, in which case there is little to do but to move to a 64bit platform (with plenty of swap space). (Note that you may get replies from more specifically experienced people on the Bioconductor lists.) -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
