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

[Peter B. Pearman]

Just an addendum,

My colleague, for whom the tree conversion works correctly, has Ape 
version 2.5-3, as well as R version 2.11.1

Best,

Peter



On 25.10.10 20:32, 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
>>
>>
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>


-- 
Peter B. Pearman, Ph.D.
Land Use Dynamics
Federal Research Institute WSL
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pearman at wsl.ch
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