[R-sig-phylo] Infinite Recursion Error with write, tree() on an stree()

Klaus Schliep klaus.schliep at gmail.com
Thu Sep 16 08:44:21 CEST 2010


Hi David,

increase as the error message indicates the number of nested expressions:
options("expressions"=20000)
This should work for trees with 1700 taxa.

Cheers,
Klaus

On 9/15/10, David Bapst <dwbapst at uchicago.edu> wrote:
> Hello all,
>
> I am having trouble with write.tree() in ape, when used on a tree
> produced with stree() with type="left", at a certain number of tip
> taxa.
>
> You can reproduce the error with:
>
>  x<-stree(1000,type="left")
> write.tree(x,file.choose())
>
> produces the following:
>
> Error: evaluation nested too deeply: infinite recursion /
> options(expressions=)?
>
> Any idea what produces this error and if there is any way around it? I
> have no difficulty with rtree(), "star" type trees produced with
> stree(), nor when I reduce the number of tips to 100 (which doesn't
> work for my purposes: I need to produce "left" type trees with over
> 1700 tip taxa). I have also had problems with plot() on such trees,
> but most functions seem to work fine on such trees.
>
> Thanks for the help,
> -Dave Bapst, UChicago
>
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-- 
Klaus Schliep
Université Paris 6 (Pierre et Marie Curie)
9, Quai Saint-Bernard, 75005 Paris



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