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
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