[R-sig-phylo] Suggestion for update of as.igraph.phylo

[Watal M. Iwasaki]

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
[phone]
https://heavywatal.github.io/

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[Emmanuel Paradis]

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

Post by Watal M. Iwasaki
Dear developer team,
Thank you for providing an excellent package. But I have encountered a
small problem with as.igraph.phylo().
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.
- 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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[Watal M. Iwasaki]

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

Post by Emmanuel Paradis
Dear Watal,
Thank you. This is now in ape.
I've just uploaded a new testing version (5.0-5) with the last changes
http://ape-package.ird.fr/ape_installation.html#versions
http://ape-package.ird.fr/NEWS
Best,
Emmanuel

Post by Watal M. Iwasaki
Dear developer team,
Thank you for providing an excellent package. But I have encountered a
small problem with as.igraph.phylo().
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.
- replace line 143 in as.phylo.R with

`igraph::graph_from_edgelist(x$edge,

Post by Emmanuel Paradis

Post by Watal M. Iwasaki
directed = directed)`

`utils::globalVariables("graph.edgelist")`

Post by Emmanuel Paradis

Post by Watal M. Iwasaki
- 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
[phone]
https://heavywatal.github.io/

[[alternative HTML version deleted]]

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https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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