[R] tree in tree package - Error: cannot allocate vector of size 2.0 Gb

Steve Lianoglou lianoglou.steve at gene.com
Fri May 31 23:58:32 CEST 2013


On Fri, May 31, 2013 at 5:38 PM, Stephen Sefick <sas0025 at auburn.edu> wrote:
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-redhat-linux-gnu (64-bit)
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>  [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
>  [7] LC_PAPER=C                LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 6GB RAM, intel core2 quad, Scientific Linux 6.4
> I am using tree in the tree package.  and I get the following error:
> Error: cannot allocate vector of size 2.0 Gb
> shouldn't I be able to allocate more memory than 2GB?  I am sure that I am
> missing something.  Any help would be greatly appreciated.

I don't remember who on the R list had previously put it this way, but
it puts it best, I think:

The 2gb is the straw that broke the camel's back.

R has likely been allocating more and more memory for whatever it's
trying to do and at some point it asked the OS for another 2gb more,
and *bam* ... toasted.

If you look at top (or htop) and monitor the R process as it's
running, I reckon that's what you'll see, too.



Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology

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