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

[Peter B. Pearman]

Dear All,

Thank you for your responses.  I have been asked to post the offending 
code and objects to the list.  Here they are, attached.

I've been working with a tree with 400 tips.  I made a tree with rtree, 
added some tip and node names and ran the same code on it, and obtained 
the same results.

I guess that this means that, at least on my machine, this problem is 
likely replicable with any tree.

Please remember, I'm running this with a Mac, R updated to 2.12.0

Thanks in advance

Peter

> 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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