Hi, I had the same opportunity and ran into the same problem. The error occurred when trying to read >25 CEL-files with the ReadAffy-package and happened in R1.9 as well as R2.0. The problem seemed to be due to an error in the Tcl/Tk package and might relate to the installation of Tcl/Tk on our Irix machine. We did not completely tracked it down, as we than discovered that we were using Bioconductor 1.4 (which actually worked on a second Irix machine with R1.9). Upgrading this to version 1.5 solved all our problems. Bottomline: make sure you use R2.0, Bioconductor 1.5 and install the most recent packages available. Regards, Roel Verhaak > Tae-Hoon Chung <thchung@tgen.org> writes: > >> Hi, all; >> >> I know there has been a lot of discussions on memory usage in R. >> However, I have some odd situation here. Basically, I have a rare >> opportunity to run R in a system with 64GB memory without any limit on >> memory usage for any person or process. However, I encountered the >> memory >> problem error message like this: >> >> Error: cannot allocate vector of size 594075 Kb > .... >> Although I have no idea of memory allocation in R, apparently >> something's >> wrong with this. The memory problem must have nothing to do with >> physical >> memory. My question is this. Is this memory problem due to some >> non-optimal >> configuration of memory usage? If so, then what will be the optimal >> configuration for this? If not, then there must be problems on actual >> implementations of functions I used here, right? The reason I am asking >> this >> is that, according to the reference manual, the error message I got can >> be >> brought up by roughly three reasons. First, when the system is unable to >> provide the R requested memory. Second, when the requested memory size >> exceeds the address-space limit for a process. Finally, when the length >> of a >> vector is larger than 2^31-1. > > Hmm, the length issue should not kick in before the length exceeds 2 > billion or so and you are not beyond 75 or 150 million (counting 8 or > 4 bytes per elements). > >> I wonder the problem has anything to do with >> the third case. (If so, then I think I am hopeless unless the internal >> implementations change...) > > Well, revolutionaries often find themselves just below the cutting > edge... > > Just a sanity check: this is using a 64-bit compiled R on a 64-bit > operating system, right? > > -- > O__ ---- Peter Dalgaard Blegdamsvej 3 > c/ /'_ --- Dept. of Biostatistics 2200 Cph. N > (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 > ~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk) FAX: (+45) 35327907 > > >

"R.G.W. Verhaak" <r.verhaak@erasmusmc.nl> writes: > Hi, > > I had the same opportunity and ran into the same problem. The error > occurred when trying to read >25 CEL-files with the ReadAffy-package and > happened in R1.9 as well as R2.0. The problem seemed to be due to an error > in the Tcl/Tk package and might relate to the installation of Tcl/Tk on > our Irix machine. We did not completely tracked it down, as we than > discovered that we were using Bioconductor 1.4 (which actually worked on a > second Irix machine with R1.9). Upgrading this to version 1.5 solved all > our problems. > Bottomline: make sure you use R2.0, Bioconductor 1.5 and install the most > recent packages available. It's not very likely to be the same issue as someone expecting to get a 64bit address space with a 32bit version of R! And please trim the list of recipients to those who might be interested (hint: r-help readers would probably join the bioconductor list if they were interested in BioC, Cel files, and Affy). -pd -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk) FAX: (+45) 35327907