[R-sig-eco] [R-sig-phylo] ape prop.part error malloc(): memory corruption

[Mario José Marques-Azevedo]

Dear Klaus,

Thank you for your answer and good news that ape/phangorn will load tree
with singletons! Can I send the tree to your email?

My problem with collapse.singles is, for instance, when I have only one
genus/specie. I want the node name with genus and a tip name with species.
When I collapse, genus node name is removed. For instance:

This tree:

((((A_1,A_2,)A,(B1,B2,B3)B)C,((((D1))),(E1,E2)E)D),(F1)F)R;

when 'collapsed' will be:

((((A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),F1)R;

​Note that I lost node name 'F'.

I don't know why, but month ago I ran extract.clade of my tree without
problem. Maybe some update that I did, but I'm not sure.

Thank you again!

Best regards,

Mario


​....................................................................
Mario José Marques-Azevedo
Ph.D. Candidate in Ecology
Department of Plant Biology, Institute of Biology
University of Campinas, Campinas, São Paulo, Brazil
https://github.com/mariojose​




On 1 June 2017 at 11:17, Klaus Schliep <klaus.schliep at gmail.com> wrote:

> Dear Mario,
> Emmanuel and I are working to allow singletons in ape / phangorn. In the
> next version will read the tree in with read.tree().
> Can you send me your larger tree for testing purposes, as it is one which
> would fail at the moment?
> Regards,
> Klaus
>
>
>
>
>
>
> On Thu, Jun 1, 2017 at 8:51 AM, Klaus Schliep <klaus.schliep at gmail.com>
> wrote:
>
>> Hi Mario,
>>
>> the problem with your tree is that it contains singleton (nodes of degree
>> 2). Try collapse.singles() before using extract.clade().
>>
>> Cheers,
>> Klaus
>>
>>
>>
>>
>> On Thu, Jun 1, 2017 at 1:31 AM, Mario José Marques-Azevedo <
>> mariojmaaz at gmail.com> wrote:
>>
>>> Dears,
>>>
>>> I'm using extract.clade from ape package and get some issues. I'm using
>>> phytools package to load tree with single clade like above:
>>>
>>> library(phytools)
>>>
>>> t1 <- read.newick(text='(((((A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)
>>> E)D),(F1)F)G)R;')
>>>
>>> t2 <- read.newick(text='((((A_1,A_2,)A,(B1,B2,B3)B)C,((((D1))),(
>>> E1,E2)E)D),(F1)F)R;
>>>
>>> When I extract 'F' clade, for instance:
>>>
>>> c1 <- extract.clade(t1, 'F')
>>>
>>> or
>>>
>>> c2 <- extract.clade(t2, 'F')
>>>
>>> I have this error:
>>>
>>> Error in prop.part(phy) : attempt to set index 8/8 in SET_VECTOR_ELT
>>>
>>> I have one tree with mode than 300 tips. When I try extract any clade, I
>>> have the same error. If I repeat the command I have this one:
>>>
>>> *** Error in `/usr/lib/rstudio/bin/rsession': malloc(): memory
>>> corruption:
>>> 0x000000000a3aaa40 ***
>>>
>>> My configurations was:
>>>
>>> platform       x86_64-pc-linux-gnu
>>> arch           x86_64
>>> os             linux-gnu
>>> system         x86_64, linux-gnu
>>> language       R
>>> version.string R version 3.3.3 (2017-03-06)
>>>
>>> phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10)
>>>
>>> I try update R to 3.4 and recompile all my packages, but I get the same
>>> error.
>>>
>>> My new configurations:
>>>
>>> platform       x86_64-pc-linux-gnu
>>> arch           x86_64
>>> os             linux-gnu
>>> system         x86_64, linux-gnu
>>> language       R
>>> version.string R version 3.4.0 (2017-04-21)
>>>
>>> phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10)
>>>
>>> I don't know why I have this error if I can extract with the same
>>> commands
>>> some time ago.
>>>
>>> I have the same error if I run in RStudio or in terminal. When I use
>>> RStudio, it abort after the error.
>>>
>>> I try Google, but I don't found nothing that can help me.
>>>
>>> Thank you and best regards,
>>>
>>> Mario
>>>
>>>
>>> ....................................................................
>>> Mario José Marques-Azevedo
>>> Ph.D. Candidate in Ecology
>>> Department of Plant Biology, Institute of Biology
>>> University of Campinas, Campinas, São Paulo, Brazil
>>> https://github.com/mariojose <http://www.github.com/mariojose>
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-phylo mailing list - R-sig-phylo at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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>>> sig-phylo at r-project.org/
>>
>>
>>
>>
>> --
>> Klaus Schliep
>> Postdoctoral Fellow
>> Revell Lab, University of Massachusetts Boston
>> http://www.phangorn.org/
>>
>>
>
>
> --
> Klaus Schliep
> Postdoctoral Fellow
> Revell Lab, University of Massachusetts Boston
> http://www.phangorn.org/
>
>

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