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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