[R] S4 : setGeneric for classical methods

[cgenolin at u-paris10.fr]

Martin Maechler <maechler at stat.math.ethz.ch> a écrit :

>>>>>> "CG" == Christophe Genolini <cgenolin at u-paris10.fr>
>>>>>>     on Sat, 26 Jul 2008 12:12:12 +0200 writes:
>
> 	CG> Martin Maechler <maechler at stat.math.ethz.ch> a écrit :
> 	>>>>>>> "CG" == Christophe Genolini <cgenolin at u-paris10.fr>
> 	>>>>>>> on Tue, 22 Jul 2008 19:04:37 +0200 writes:
> 	>>
> 	CG> Prof Brian Ripley <ripley at stats.ox.ac.uk> a écrit :
> 	>> >> On Tue, 22 Jul 2008, cgenolin at u-paris10.fr wrote:
> 	>> >>
> 	>> >>> Hi the list (well, half of the list, only the one who
> 	>> >>> are not on holidays...)
> 	>> >>>
> 	>> >>> I am trying to make an S4 package. When I run it on a
> 	>> >>> console, everything seems ok. When I run R CMD check, I
> 	>> >>> got an error --- 8<
> 	>> >>> ----------------------
> 	>> >>> Error in setMethod("plot", "ClassX", function(x, y) { :
> 	>> >>> no existing definition for function "plot" --- 8<
> 	>> >>> ----------------------
> 	>> >>>
> 	>> >>> If I add
> 	>> >>> setGeneric("plot",function(x,y,...){standardGeneric("plot")})
> 	>> >>> in my code, then everything is OK.
> 	>> >>>
> 	>> >>> This is a surprise for me since I taught that we do not
> 	>> >>> need to redefine as generic the function that are
> 	>> >>> already generic, like "plot". Am I wrong ?
> 	>> >>
> 	>> >> Yes. And do read the error message.  It says
> 	>> >>
> 	>> >> no existing definition for function "plot"
> 	>> >>
> 	>> >> so this is not if the function is S3 or S4 generic, but
> 	>> >> that no such function is visible.
> 	>> >>
> 	>> >> Looks like you forgot to declare a dependence on (or
> 	>> >> import) package graphics.
> 	>>
> 	CG> I would have forgot if I knew that I have to declare
> 	CG> such a dependence...  Do we have to declare all the
> 	CG> depence to all the package ? To base ? To stats ?
> 	>>
> 	>> not to base, but to all other packages (since R can be loaded
> 	>> without any packages but base).
> 	>>
> 	CG> I thaught that the package that are include in R when we
> 	CG> start it had not to be include.
> 	>>
> 	>> You thought wrongly, and all our documentation mentions that you
> 	>> need to use 'Depends:' correctly (and  'Imports(..)' in
> 	>> NAMESPACE if you make use of one).
> 	>>
> 	>> {and please strongly note the correct spelling of "thought" !}
> 	>>
> 	>> Martin
>
>    CG> I correct DESCRIPTION and NAMESPACE adding Depends and import.
>    CG> But I still get the message :
>
>    CG> checking for missing documentation entries ... WARNING
>    CG> Undocumented S4 methods:
>    CG> generic 'plot' and siglist 'ClassX'
>
>    CG> I can't find what is wrong...
>
> well, it's  a message about *documentation*
> and therefore not related to DESCRIPTION
> and not much related to NAMESPACE.
>
> It tells you that you don't have correct documentation for the
> plot method for ClassX.
>

What if I don't want to document this method? I did not put ClassX in 
the export, I do not want the user to acces to it.
I want :

  plot,ClassX-method -> private
  ClassY-class       -> public
  plot,ClassY-method -> public

Is it possible ?

Christophe

> --> "Writing R Extensions",
>    section 2.1.3 'Documenting S4 classes and methods'
>
> Regards,
> Martin
>
>    CG> ----- DESCRIPTION ----- Package: packS4
>    CG> Type: Package
>    CG> Title: Toy example of S4 package
>    CG> Version: 0.5
>    CG> Date: 2008-07-22
>    CG> Author: Christophe Genolini / INSERM U669
>    CG> Maintainer: <genolini at u-paris10.fr>
>    CG> Description: Package built to illustration package 
> construction with S4
>    CG> License: GPL (>=2)
>    CG> LazyLoad: yes
>    CG> Depends: methods, graphics
>    CG> Collate: global.R ClassX.R ClassY.R ClassX-ClassY.R ClassZ.R
>
>
>    CG> ------ NAMESPACE ------
>    CG> export(
>    CG> "classZ",
>    CG> "functionClassicA"
>    CG> )
>    CG> exportMethods(
>    CG> "getZ1",
>    CG> "setZ1<-",
>    CG> "publicA",
>    CG> "plot"
>    CG> )
>    CG> exportClasses(
>    CG> "ClassY",
>    CG> "ClassZ"
>    CG> )
>
>    CG> import(graphics)
>
>    CG> Christophe
>
>
>
>
>    CG> ----------------------------------------------------------------
>    CG> Ce message a ete envoye par IMP, grace a l'Universite Paris 10 
> Nanterre
>
>
>