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Betty Gilbert
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50
@betty-gilbert-1120
Last seen 10.2 years ago
I'm sorry if the answer to my problem is buried in the archives. I
have limited experience with R and I couldn't find a solution to my
particular problem. I am running Mac OS X Aqua GUI v1.01 on a new G5
running os 10.3.8 with a 1.8Ghz processor and 1GB of sdram. I just
downloaded bioconducter a week ago and I'm trying to cluster a matrix
I created with a simulation with dimensions
dim(nca35)
[1] 10481 12
with size
> object.size(nca352)
[1] 1426204
I checked my ulimits variable on the unix terminal and it says it's
unlimited as does
> mem.limits()
nsize vsize
NA NA
But I'm still getting errors like the following with funtions in the
cluster package
> daisy(nca352, metric= "euclidean", stand=FALSE)->dnca35
Error: cannot allocate vector of size 858213 Kb
*** malloc: vm_allocate(size=878813184) failed (error code=3)
*** malloc[599]: error: Can't allocate region
if it helps i also checked
> gc()
used (Mb) gc trigger (Mb)
Ncells 448662 12.0 741108 19.8
Vcells 847630 6.5 135357901 1032.7
I tried the suggested unix command in the memory help doc but that
doesn't work in the Aqua GUI. Can someone tell me how to change the
Vcells? Although to the best of my understanding (which is limited) I
shouldn't have to do that. Any suggestions would be greatly
appreciated.
thanks,
betty
--
Betty Gilbert
lgilbert@berkeley.edu
Taylor Lab
Plant and Microbial Biology
321 Koshland Hall
U.C. Berkeley
Berkeley, Ca 94720