Error: cannot allocate vector of size 1.8 Gb

I hope the following info will help, thanks again!

sessionInfo()

R version 2.7.1 (2008-06-23) 
x86_64-redhat-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

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dim(data)

[1] 22283    19

dm=dist(data, method = "euclidean", diag = FALSE, upper = FALSE, p = 2)

Error: cannot allocate vector of size 1.8 Gb

That would be an object of size 1.8Gb.

See ?"Memory-limits"

Hi Guys, thank you in advance for helping. :-D

Recently I ran into the "cannot allocate vector of size 1.8GB" error.  I am
pretty sure this is not a hardware limitation because it happens no matter I
ran the R code in a 2.0Ghz Core Duo 2GB ram Mac or on a Intel Xeon 2x2.0Ghz
quard-core 8GB ram Linux server.

Why? Both will have a 3GB address space limits unless the Xeon box is 
64-bit.  And this works on my 64-bit Linux boxes.

I also tried to clear the workspace before running the code too, but it
didn't seem to help...

Weird thing though is that once in a while it will work, but next when I run
clustering on the above result

hc=hclust(dm, method = "complete", members=NULL)

it give me the same error...

See ?"Memory-limits" for the first part.

I searched around already, but the memory.limit, memory.size method does not
seem to help.  May I know what can i do to resolve this problem?

What are you going to do with an agglomerative hierarchical clustering of 
22283 objects?  It will not be interpretible.

Thank you so much for your help.

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

What are you going to do with an agglomerative hierarchical clustering of

22283 objects?  It will not be interpretible.

As a matter of fact I was ask to do a clustering analysis on gene
expression. Something 
http://www.ncbi.nlm.nih.gov/projects/geo/gds/analyze/analyze.cgi?datadir=UCorrelationUPGMA&ID=GDS3254&myType=0
Like this

Why? Both will have a 3GB address space limits unless the Xeon box is

64-bit.  And this works on my 64-bit Linux boxes.

I am pretty sure the linux server is 64bit.



Sorry I am just a beginner in R.  I read the "memory-limit" help you
suggested, but I still cannot find a solution to my problem...  May I know
if there is any work around for this issue?

Thank you so much again!

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