Error: cannot allocate vector of size 1.8 Gb
On Mon, 22 Dec 2008, iamsilvermember wrote:
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