That doesn't sound correct. I just created a simple package with
DESCRIPTION
Package: PkgA
Title: What the Package Does (one line, title case)
Version: 0.0.0.9000
Authors@R: person("First", "Last", email = "first.l...@example.com", role =
c("aut", "cre"))
Description: What the package does (one paragraph).
Depends: R (>= 3.5.1)
Imports: phylobase, methods
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
NAMESPACE
import(methods)
importMethodsFrom(phylobase, "nNodes")
exportMethods("nNodes")
and R/cls.R
.A = setClass("A", slots = c(x="numeric"))
setMethod("nNodes", "A", function(x) "I'm an 'A'")
This package builds and checks OK (complaining about documentation, but...) and
nNodes can be used.
Do you have more information on the problem that you are seeing? Is it a
problem with roxygen2?
Martin
On 10/19/18, 12:18 PM, "Bioc-devel on behalf of Elizabeth Purdom"
<bioc-devel-boun...@r-project.org on behalf of epur...@stat.berkeley.edu> wrote:
Sorry, I copied the wrong code from phylobase (I copied the setMethod
code). Their setGeneric calls are in the following format:
setGeneric("nNodes", function(x) {
standardGeneric("nNodes")
})
> On Oct 19, 2018, at 9:07 AM, Elizabeth Purdom <epur...@stat.berkeley.edu>
wrote:
>
> Hello,
>
> In my package (`clusterExperiment`) I want to extend a S4 method from a
package `phylobase` for my class. However, in the phylobase package, all of the
`setGeneric` calls are in the form of
>
> setMethod("nTips", signature(x="phylo"),
> function(x) {
> Ntip(x)
> })
>
> Namely, they use braces in their function definitions, which I have just
learned creates a `nonstandardGenericFunction` rather than a `standardGeneric`.
Because of this I can’t just do `importMethodFrom` and then just extend the
method. And if I try to create my own `standardGeneric` (e.g.
https://stat.ethz.ch/R-manual/R-devel/library/methods/html/Methods_for_Nongenerics.html
<https://stat.ethz.ch/R-manual/R-devel/library/methods/html/Methods_for_Nongenerics.html>)
I can no longer call the function in the original `phylobase` package, i.e.
for the original class for which it is applied.
>
> My only solution appears to be if I put `phylobase` in the `Depends`
section, at which point I can then extend their generics. But this gives my
package the significant warning:
>
> " Warning: replacing previous import ‘phylobase::plot’ by
‘graphics::plot’ when loading ‘clusterExperiment’”
>
> My question is whether there is anything I can do on my end to either 1)
extend phylobase generics without a depends statement or 2) to get rid of the
warning about the imports (I have made sure to use `graphics::plot` in all of
my functions’ calls to plot to make sure there is no problem with the import
conflict)?
>
> Or is my only hope to have the developers of the package fix their calls?
Personally, I was going to strip my setGeneric calls of braces after this
experience, since I also have braces in my call but not for any good reason. Is
there a good reason that setGenerics might have the braces in their calls?
(Hadley’s Advanced R seems to say no, perhaps for this reason
https://adv-r.hadley.nz/s4.html#generics-and-methods
<https://adv-r.hadley.nz/s4.html#generics-and-methods>). Does using braces keep
you from colliding with future developers or other packages?
>
> Thanks,
> Elizabeth
>
>
>
>
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