[R] Memory error in Mac OS X Aqua GUI v1.01 with cluster package functions

Betty Gilbert lgilbert at berkeley.edu
Tue Feb 22 23:57:06 CET 2005

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
[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 
Betty Gilbert
lgilbert at berkeley.edu
Taylor Lab
Plant and Microbial Biology
321 Koshland Hall
U.C. Berkeley
Berkeley, Ca 94720

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