[R-pkg-devel] Define S4 method for generic in other package

[Thierry Onkelinx]

Hi Hadley,

Thanks for the workaround.

Best regards,

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data. ~ John Tukey


2015-09-01 15:10 GMT+02:00 Hadley Wickham <h.wickham at gmail.com>:
> Ah, the problem is because of roxyen2 because:
>
> * To document your code, roxygen2 needs to load it first
> * But it can't load it without the definition of git2r::pull
>
> So you're stuck in a bit of a vicious circle. I usually break out of
> this circle by temporarily patching the NAMESPACE by hand (in this
> case with importFrom(git2r,pull) and then re-generating once I can get
> the package loading.
>
> It would be nice to have a more general solution, but I'm not sure how
> to do it, because (e.g.) @export needs the loaded object so it can
> generate the correct directives. Maybe I need a separate roclet that
> only does import namespaces and can run by only inspecting the
> comments, not by running the code. I filed an issue at
> https://github.com/klutometis/roxygen/issues/372
>
> Hadley
>
> On Tue, Sep 1, 2015 at 3:53 AM, Thierry Onkelinx
> <thierry.onkelinx at inbo.be> wrote:
>> Dear Hadley,
>>
>> I've put a reproducible example at https://github.com/ThierryO/testS4
>>
>> Best regards,
>> ir. Thierry Onkelinx
>> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
>> and Forest
>> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
>> Kliniekstraat 25
>> 1070 Anderlecht
>> Belgium
>>
>> To call in the statistician after the experiment is done may be no
>> more than asking him to perform a post-mortem examination: he may be
>> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
>> The plural of anecdote is not data. ~ Roger Brinner
>> The combination of some data and an aching desire for an answer does
>> not ensure that a reasonable answer can be extracted from a given body
>> of data. ~ John Tukey
>>
>>
>> 2015-09-01 0:32 GMT+02:00 Hadley Wickham <h.wickham at gmail.com>:
>>> I'd recommend creating a minimal package that illustrates the problem
>>> using an existing S4 generic in a base package (e.g. stats4::AIC).
>>> That makes it easier to figure out what's gone wrong.
>>>
>>> It's unlikely to be a roxygen2 problem since the translation from
>>> @importFrom foo bar (etc) to importFrom(foo, bar) is quite
>>> straightforward.
>>>
>>> Hadley
>>>
>>> On Fri, Aug 28, 2015 at 3:23 AM, Thierry Onkelinx
>>> <thierry.onkelinx at inbo.be> wrote:
>>>> Dear all,
>>>>
>>>> I'm trying to define a new S4 method for a generics defined in an
>>>> other package. Here is my attempt, but that isn't working.
>>>>
>>>> bar <- function(a, b) is defined as generic and S4 method in the package foo
>>>>
>>>> #' @importFrom foo bar
>>>> #' @importMethodsFrom foo bar
>>>> setMethod(
>>>>   f = "bar",
>>>>   signature = signature(A = "myClass"),
>>>>   definition = function(
>>>>     a,
>>>>     b
>>>>   ){
>>>>     bar(
>>>>       a = myClass at A,
>>>>       b = myClass at B
>>>>     )
>>>>   }
>>>> )
>>>>
>>>> When I build my package I get the error "no existing definition for
>>>> function 'bar'".
>>>>
>>>> Any suggestions?
>>>>
>>>> Best regards,
>>>>
>>>> ir. Thierry Onkelinx
>>>> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
>>>> and Forest
>>>> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
>>>> Kliniekstraat 25
>>>> 1070 Anderlecht
>>>> Belgium
>>>>
>>>> To call in the statistician after the experiment is done may be no
>>>> more than asking him to perform a post-mortem examination: he may be
>>>> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
>>>> The plural of anecdote is not data. ~ Roger Brinner
>>>> The combination of some data and an aching desire for an answer does
>>>> not ensure that a reasonable answer can be extracted from a given body
>>>> of data. ~ John Tukey
>>>>
>>>> ______________________________________________
>>>> R-package-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>>
>>>
>>> --
>>> http://had.co.nz/
>
>
>
> --
> http://had.co.nz/