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

[Ben Bolker]

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   Could you send the reproducible code to the whole list (or at least
to me as well) please?  So it's archived for posterity, and so that if
someone else has a chance (perhaps me, who knows) they can get to it sooner?

  thanks
    Ben Bolker

On 10-10-25 02:32 PM, Peter Cowan wrote:
> 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
>> 
>> 
>> _______________________________________________ Phylobase-devl
>> mailing list Phylobase-devl at lists.r-forge.r-project.org 
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl
>
>> 
> _______________________________________________ Phylobase-devl
> mailing list Phylobase-devl at lists.r-forge.r-project.org 
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