[Rd] Correct NAMESPACE approach when writing an S3 method for a generic in another package

[Gavin Simpson]

I'm not familiar enough with S4 to know what is going on there. With
S3 methods, the package that defines the generic needs to be loaded
and attached, otherwise you can't do

foo(bar)

when

foo.myclass(bar)

is what you want to be called and you export that method from your
package. Calling `foo()` will result in an error. As long as the
package containing the definition of the generic is not attached,
there is no function `foo()` and hence the user gets an error.

G

On 26 August 2013 13:12, Paul Gilbert <pgilbert902 at gmail.com> wrote:
>
>
> On 13-08-26 12:04 PM, Gavin Simpson wrote:
>>
>> Right Henrik, but then you have to document it or R CMD check raises a
>> Warning, which is less likely to pass muster when submitting to CRAN.
>> So you document that method on your existing method's Rd page (just
>> via an \alias{}), which is fine until the user does end up attaching
>> the original source of the method, and then you get the annoying
>> warnings about masking and `?plot3d` will bring up a dialogue asking
>> which version of the help you want to read.
>>
>> Part of me thinks it would be better if there was a mechanism whereby
>> a generic will just work if package foo imports that generic and
>> exports a method for it.
>
>
> Either I am messing up something again (reasonably likely) or it does just
> work with S4 methods. I can import the namespace that has the generic and
> the methods work, I do not seem to need to export the generic.  Is S3
> working differently? I do have the documentation problem when I try to
> export other imported functions that I would like available to users.
>
> Paul
>
>>
>> Cheers,
>>
>> G
>>
>> On 26 August 2013 09:42, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
>>>
>>> On Mon, Aug 26, 2013 at 1:28 AM, Martyn Plummer <plummerm at iarc.fr> wrote:
>>>>
>>>> I think rgl should be in Depends.  You are providing a method for a
>>>> generic function from another package. In order to use your method, you
>>>> want the user to be able to call the generic function without scoping
>>>> (i.e. without calling rgl::plot3d), so the generic should be on the
>>>> search path, so the package that provides it should be listed in Depends
>>>> in the NAMESPACE file.
>>>
>>>
>>> You can re-export an imported object, but it has to be done via an
>>> explicit export(), cf. "It is possible to export variables from a
>>> namespace which it has imported from other namespaces: this has to be
>>> done explicitly and not via exportPattern" [Writing R Extensions].
>>>
>>> /H
>>>
>>>>
>>>> Martyn
>>>>
>>>> On Fri, 2013-08-23 at 22:01 -0600, Gavin Simpson wrote:
>>>>>
>>>>> Dear List,
>>>>>
>>>>> In one of my packages I have an S3 method for the plot3d generic
>>>>> function from package rgl. I am trying to streamline my Depends
>>>>> entries but don't know how to have
>>>>>
>>>>> plot3d(foo)
>>>>>
>>>>> in the examples section for the plot3d method in my package, without
>>>>> rgl being in Depends.
>>>>>
>>>>> Note that I importFrom(rgl, plotd3d) and register my S3 method via
>>>>> S3Method() in the NAMESPACE.
>>>>>
>>>>> If rgl is not in Depends but in Imports, I see this when checking the
>>>>> package
>>>>>
>>>>>> ## 3D plot of data with curve superimposed
>>>>>> plot3d(aber.pc, abernethy2)
>>>>>
>>>>> Error: could not find function "plot3d"
>>>>>
>>>>> I presume this is because rgl's namespace is only loaded but the
>>>>> package is not attached to the search path.
>>>>>
>>>>> Writing R extensions indicates that one can export from a namespace
>>>>> something that was imported from another package namespace. I thought
>>>>> that might help the situation, and now the code doesn't raise an
>>>>> error, I get
>>>>>
>>>>> * checking for missing documentation entries ... WARNING
>>>>> Undocumented code objects:
>>>>>    ‘plot3d’
>>>>> All user-level objects in a package should have documentation entries.
>>>>> See the chapter ‘Writing R documentation files’ in the ‘Writing R
>>>>> Extensions’ manual.
>>>>>
>>>>> as I don't document plot3d() itself.
>>>>>
>>>>> What is the recommended combination of Depends and Imports plus
>>>>> NAMESPACE directives etc that one should use in this situation? Or am
>>>>> I missing something else?
>>>>>
>>>>> I have a similar issue with my package including an S3 method for a
>>>>> generic in the lattice package, so if possible I could get rid of both
>>>>> of these from Depends if I can solve the above issue.
>>>>>
>>>>> Thanks in advance.
>>>>>
>>>>> Gavin
>>>>>
>>>>
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>>
>>
>



-- 
Gavin Simpson, PhD