Thanks for that, Klaus!
Regards
Agus

2018-02-13 22:51 GMT-02:00 Klaus Schliep <klaus.schl...@gmail.com>:

> Dear Agustín,
>
> the nexus file on dropbox does not contain any trees.
> If you open it in an editor you see this:
>
>
> #NEXUS
>
> [Tree distribution from: The global diversity of birds in space and time;
> W. Jetz, G. H. Thomas, J. B. Joy, K. Hartmann, A. O. Mooers
> doi:10.1038/nature11631]
> [Subsampled and pruned from birdtree.org on 2018-02-13T21:49:59Z ]
> [Data: "Hackett All Species" (see Jetz et al. 2012 supplement for details)]
>
> BEGIN TREES;
>     TREE tree_4104 =
>     TREE tree_9438 =
> ...
>     TREE tree_1868 =
>     TREE tree_0011 =
> END;
>
>
> Looks like your download did not work and the error message from
> read.nexus could improve.
>
> Cheers,
> Klaus
>
>
> On Tue, Feb 13, 2018 at 5:11 PM, Agus Camacho <agus.cama...@gmail.com>
> wrote:
>
>> Dear list,
>>
>> I am puzzled with this error when importing a bird tree subset from
>> https://birdtree.org/subsets/ .
>>
>> The subset is supposed to be in nexus format. However,
>>
>> trees<-read.nexus("output.nex")
>>
>> Error in if (tp[3] != "") obj$node.label <- tp[3] :
>>
>> missing value where TRUE/FALSE needed
>>
>>
>> read.tree gives the same error
>> read.newick gets stuck, it never ends reading in the tree
>>
>> I tried scanning the file and then several notes appear before the actual
>> trees Thus, I tried read.annotated.nexus from OutbreakTools.
>> But it gives another error:
>>
>> Error in read.annotated.nexus("C:/Users/agusc/Dropbox/output.nex") :
>> .annotated.clado.build is not yet implemented.
>>
>>
>> I tried with several different subsets from different backbones and none
>> worked.
>> Here is one: https://www.dropbox.com/s/037u6pjr4006o6r/output.nex?dl=0
>>
>> Somebody has reported this error previously in the internet, but it still
>> seems to be unsolved.
>>
>> Thanks in advance and best regards.
>> Agus
>>
>>
>> --
>> Agustín Camacho Guerrero.
>> http://www.agustincamacho.com
>> Doutor em Zoologia.
>> Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
>> Biociências, USP.
>> Rua do Matão, trav. 14, nº 321, Cidade Universitária,
>> São Paulo - SP, CEP: 05508-090, Brasil.
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>>
>
>
>
> --
> Klaus Schliep
> Postdoctoral Fellow
> Revell Lab, University of Massachusetts Boston
> http://www.phangorn.org/
>
>


-- 
Agustín Camacho Guerrero.
http://www.agustincamacho.com
Doutor em Zoologia.
Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
Biociências, USP.
Rua do Matão, trav. 14, nº 321, Cidade Universitária,
São Paulo - SP, CEP: 05508-090, Brasil.

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