Dear Emmanuel,

Thank you for the quick response! I have confirmed that it works perfectly
in my environment: R 3.4.3 on macOS Sierra.

Cheers,
Watal

On Tue, Feb 20, 2018 at 1:51 AM, Emmanuel Paradis <emmanuel.para...@ird.fr>
wrote:
>
> Dear Watal,
>
> Thank you. This is now in ape.
>
> I've just uploaded a new testing version (5.0-5) with the last changes
and fixes on ape's site:
>
> http://ape-package.ird.fr/ape_installation.html#versions
>
> A Windows version is available. The list of changes are listed there:
>
> http://ape-package.ird.fr/NEWS
>
> Best,
>
> Emmanuel
>
>
> Le 14/02/2018 à 08:30, Watal M. Iwasaki a écrit :
>>
>> Dear developer team,
>>
>> Thank you for providing an excellent package. But I have encountered a
>> small problem with as.igraph.phylo().
>>
>> Error in graph.edgelist(x$edge, directed = directed, ...) :
>>    could not find function "graph.edgelist"
>> Calls: as.igraph.phylo
>>
>> The workaround for a user is to do `library(igraph)` explicitly because
it
>> exports `graph.edgelist()`. But I think the ape package should call this
>> function with explicit namespace like `igraph::graph.edgelist()`. Also it
>> would be better to add igraph to Suggests section in DESCRIPTION so that
>> `utils::globalVariables("graph.edgelist")` can be removed. Also note that
>> `graph.edgelist()` is deprecated (it still works, though) and replaced by
>> `graph_from_edgelist()` in the current version of igraph.
>>
>> In summary, I suggest the following modification:
>> - replace line 143 in as.phylo.R with
`igraph::graph_from_edgelist(x$edge,
>> directed = directed)`
>> - remove line 131 in as.phylo.R:
`utils::globalVariables("graph.edgelist")`
>> - add igraph to Suggests in DESCRIPTION
>>
>> Best regards,
>> Watal
>>



--
Watal M. Iwasaki / 岩嵜 航
SOKENDAI, The Graduate University for Advanced Studies,
Hayama, Kanagawa 240-0193, Japan
+81-46-858-1576
https://heavywatal.github.io/

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