[Phylobase-devl] conversion from ade4 to phylog format: problem

[Peter Cowan]

Peter,

I've also noticed some problems with 2.12 and phylobase.  Unfortunately, I've been busy putting the final touches on a dissertation and haven't had time to attend to them.  I can take a look at it next week, unless someone else can get to it sooner.

I've looked over the 2.12 release notes, and I'm not sure what change has caused these problems.  Are you and your colleague using the same version of ape?

If you could send me a private email with the full code to reproduce the problem it would make things faster/easier to debug.

A quick grepping didn't reveal where these warnings might be coming from.  Does anyone know why there is a global assignment to STRING happening?

Thanks for the report,

Peter
---
Peter Cowan


On Oct 25, 2010, at 5:14 AM, Peter B. Pearman wrote:

> Hello phylobase users and developers,
> 
> I've got a little problem that seems strange.  Perhaps one of you can enlighten me?
> 
> It seems that with updating to R-version 2.12.0 (2010-10-15) the following code no longer works:
> 
> >  tree <- drop.tip(tree,name.check(tree,data.names=names.final)$Tree.not.data)
> > tree$node.label <- paste("node_",as.character(c(410:807)),sep="")
> > phylo4.tree <- as(tree,"phylo4")
> > tree.phylog <- as(phylo4.tree,"phylog")
> There were 50 or more warnings (use warnings() to see the first 50)
> 
> > warnings()
> Warning messages:
> 1: In STRING[k] <<- x :
>  number of items to replace is not a multiple of replacement length
> 2: In STRING[k] <<- x :
>  number of items to replace is not a multiple of replacement length
> 
> (continues ad nauseum)
> 
> The node names are all mixed up and there seem to be other problems as well:
> 
> > tree.phylog$nodes
>    node_410   node_410_1   node_410_2   node_410_3   node_410_4   node_410_5
>   16.252392     8.929608    24.678913     9.461009     5.245589    32.854018
>  node_410_6   node_410_7   node_410_8   node_410_9  node_410_10  node_410_11
>   17.960096    15.064738    21.827794     2.024337    49.192003    42.923378
> node_410_12  node_410_13  node_410_14  node_410_15  node_410_16  node_410_17
> 
> I re-installed phylobase from source on my MacOS (snow-L 10.6.4), but that did not fix the problem.  All phylogenetics and statistical packages have been updated.
> 
> My office mate ran the same code on his Mac, with R-version:
> 2.11.1 (2010-5-31)
> and a previous binary installation of phylobase.  Everything worked fine for him.
> 
> I can supply the relevant objects if someone needs to try this on your machine.
> 
> Any help greatly appreciated.
> 
> Best,
> 
> Peter
> 
> 
> -- 
> Peter B. Pearman
> 
> 
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