[R-pkg-devel] Exporting S3 methods for base generics

[Joris Meys]

Hi Charles,

my mistake. I forgot that pmax has an extra argument na.rm. I'm surprised
you could define the method, as this normally should return an error from
conformMethod().

So:
#' @rdname pmax
setGeneric("pmax", signature = "...")

should work. I've used this myself in quite a number of packages.

Cheers
Joris

On Mon, Jun 26, 2017 at 7:20 PM, Charles Determan <cdetermanjr at gmail.com>
wrote:

> Thanks for the reply Joris, although I am not sure what I could be doing
> wrong.  I implement exactly the lines you show and yet I just get the
> following error when I call 'pmax' on the class.
>
> > pmax(x, 0)
>
> Error in mmm < each :
>   comparison (3) is possible only for atomic and list types
> In addition: Warning message:
> In is.na(mmm) : is.na() applied to non-(list or vector) of type 'S4'
>
> Regards,
> Charles
>
> On Mon, Jun 26, 2017 at 12:10 PM, Joris Meys <Joris.Meys at ugent.be> wrote:
>
>> Hi Charles,
>>
>> if a generic exists already in the base, you only have to export the
>> actual S3 method. Your problem is that base::pmax() is not a generic S3
>> function. So R gives you the correct warning: the S3 generic in your
>> package will always mask the base pmax function. And that's not really a
>> problem, especially since you ensured the base functionality with your
>> default method.
>>
>> If you want to avoid that warning, use S4.
>>
>> #' @rdname
>> setGeneric("pmax")
>>
>> #' @rdname pmax
>> #' @method pmax myclass
>> #' @export
>> setMethod("pmax",
>>                   "myclass",
>>                   function(...){
>>                      # do some stuff
>> })
>>
>> More information on how to deal with dots can be found on the help page
>> ?dotsMethods.
>>
>> If you have a generic in the base package (eg plot is such one), you only
>> define the method and use:
>>
>> #' @export
>> plot.myclass <- function(x, y, ...){
>>    # do some more stuff
>> }
>>
>> Cheers
>> Joris
>>
>>
>>
>> On Mon, Jun 26, 2017 at 6:28 PM, Charles Determan <cdetermanjr at gmail.com>
>> wrote:
>>
>>> Greetings R users,
>>>
>>> I was wondering how others are exporting S3 methods in their packages
>>> when
>>> the generic is in 'base'.  For example, let's say I want to export a new
>>> pmax method.  The only way I have found to get this to work is by
>>> redefining the function with 'UseMethod' and setting the default method.
>>>
>>> #' @export
>>> pmax <- function(...){ UseMethod("pmax") }
>>> #' @export
>>> pmax.default <- function(..., na.rm=FALSE){ base::pmax(..., na.rm=FALSE)
>>> }
>>>
>>> setClass("myclass")
>>>
>>> #' @export
>>> pmax.myclass <- function(..., na.rm = FALSE){
>>>     print('myclass pmax!')
>>> }
>>>
>>> Although this works, I get the 'warning'
>>>
>>> The following objects are masked from 'package:base':
>>>
>>>     pmax
>>>
>>>
>>> I would like the package build and loading to be as clean as possible but
>>> if this is acceptable and not considered a problem I will let it go.  It
>>> just seems odd that one would to redefine a the generic when in states in
>>> the docs for 'pmax' that it will also work on classed S3 objects but
>>> perhaps I am reading this incorrectly.
>>>
>>> Thanks,
>>> Charles
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-package-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>
>>
>>
>> --
>> Joris Meys
>> Statistical consultant
>>
>> Ghent University
>> Faculty of Bioscience Engineering
>> Department of Mathematical Modelling, Statistics and Bio-Informatics
>>
>> tel : +32 9 264 59 87 <+32%209%20264%2059%2087>
>> Joris.Meys at Ugent.be
>> -------------------------------
>> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>>
>
>


-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Mathematical Modelling, Statistics and Bio-Informatics

tel : +32 9 264 59 87
Joris.Meys at Ugent.be
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

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