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

[Huntsinger, Reid]

It's trying to allocate about 850 MB. And that's just the "object that broke
the camel's back". You probably really are out of memory. You could increase
swap space and cross your fingers, but probably daisy creates the 10481 x
10481 distance matrix, which would be about 800 MB since each entry is 8
bytes. It may even create multiple copies.

You might try increasing RAM to 4 GB or a clustering routine that doesn't
need a distance matrix, like k-means (which is based on Euclinean distance
as well).

Reid Huntsinger

-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Betty Gilbert
Sent: Tuesday, February 22, 2005 5:57 PM
To: r-help at stat.math.ethz.ch
Subject: [R] Memory error in Mac OS X Aqua GUI v1.01 with cluster package
functions


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

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