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 <[email protected]> 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/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
