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

[Charles Determan]

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
>

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