[Bioc-devel] How to extend nonstandardGenericFunction

[Elizabeth Purdom]

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 <epurdom using 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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