[Bioc-devel] How to extend nonstandardGenericFunction

[Elizabeth Purdom]

No, sorry, it was also a problem with `Matrix` package. I was too quick in checking it. I think upgrading my devtools and roxygen2 may have fixed it. Thanks for helping me pinpoint where the problem was.

> On Oct 19, 2018, at 12:37 PM, Elizabeth Purdom <epurdom using stat.berkeley.edu> wrote:
> 
> Thanks Martin. And of course you’re right! The errors I was getting came from devtools functions— I didn’t think to check it outside of there and assumed it was a general problem with my package setup. But it's actually a problem in devtools. 
> 
> When I set up your example (thanks!) with Roxygen as follows:
> 
> #' @import methods
> #' @importMethodsFrom phylobase nNodes
> .A = setClass("A", slots = c(x="numeric"))
> 
> #' @export
> setMethod("nNodes", "A", function(x) "I'm an 'A’")
> 
> Then I get the following errors with `document` and `load_all`
> 
>> document()
> Updating PkgA documentation
> Loading PkgA
> Error in setMethod("nNodes", "A", function(x) "I'm an 'A'") : 
>  no existing definition for function ‘nNodes’
> 
>> load_all()
> Loading PkgA
> Error in setMethod("nNodes", "A", function(x) "I'm an 'A'") : 
>  no existing definition for function ‘nNodes’
> 
> But it does seem related to the `nonStandardGeneric`, since I don’t have this problem when I use the Matrix package instead, which creates `standardGeneric`:
> 
> #' @import methods
> #' @importMethodsFrom Matrix isDiagonal
> .A = setClass("A", slots = c(x="numeric"))
> 
> #' @export
> setMethod("isDiagonal", "A", function(object) "I'm an 'A'")
> 
>> document()
> Updating PkgA documentation
> Loading PkgA
> Writing NAMESPACE
> Writing NAMESPACE
> 
> I’ll submit the problem in devtools.
> 
> I guess for the upcoming Bioconductor release I’ll switch the package to `Depends` to get my documentation and any final bugs, and at the last minute I’ll put it back to `Imports`. 
> 
> Thanks,
> Elizabeth
> 
>> On Oct 19, 2018, at 12:03 PM, Martin Morgan <mtmorgan.bioc using gmail.com> wrote:
>> 
>> 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 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
>> 
>> 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-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) {
>>       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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