[Bioc-devel] How to extend nonstandardGenericFunction

Martin Morgan mtmorg@n@bioc @ending from gm@il@com
Fri Oct 19 21:03:36 CEST 2018

That doesn't sound correct. I just created a simple package with 


Package: PkgA
Title: What the Package Does (one line, title case)
Authors using R: person("First", "Last", email = "first.last using 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


importMethodsFrom(phylobase, "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?


On 10/19/18, 12:18 PM, "Bioc-devel on behalf of Elizabeth Purdom" <bioc-devel-bounces using r-project.org on behalf of epurdom using 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) {
    > 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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