>>>>> "CG" == Christophe Genolini <[EMAIL PROTECTED]>
>>>>> on Sun, 27 Jul 2008 09:27:34 +0200 writes:
CG> Martin Maechler <[EMAIL PROTECTED]> a écrit :
>>>>>>> "CG" == Christophe Genolini <[EMAIL PROTECTED]>
>>>>>>> on Sat, 26 Jul 2008 12:12:12 +0200 writes:
>>
CG> Martin Maechler <[EMAIL PROTECTED]> a écrit :
>> >>>>>>> "CG" == Christophe Genolini <[EMAIL PROTECTED]>
>> >>>>>>> on Tue, 22 Jul 2008 19:04:37 +0200 writes:
>> >>
CG> Prof Brian Ripley <[EMAIL PROTECTED]> a écrit :
>> >> >> On Tue, 22 Jul 2008, [EMAIL PROTECTED] 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.
CG> What if I don't want to document this method? I did not put ClassX in
CG> the export, I do not want the user to acces to it.
CG> I want :
CG> plot,ClassX-method -> private
CG> ClassY-class -> public
CG> plot,ClassY-method -> public
CG> Is it possible ?
Yes, it is.
Excuse me not having read your previous posting in full detail.
So what you see is a warning in 'R CMD check' that is a so
called "false positive", i.e. warning in a case it should not.
Indeed, we have to acknowledge that the "R CMD check"ing code
in the context of "S4 + NAMESPACE" has not been perfect
recently... and the above is a good test case for improving the
"checking code".
BTW: I have recently started to look into using a few dummy
packages as part of the R-internal 'make check' checks.
Consequently, I'd be quite happy if you could provide (me or
R-devel) with the full packS4_0.5.tar.gz example package
{and maybe other versions of that}.
Merci, Christophe, for your perseverance!
Martin
CG> 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: <[EMAIL PROTECTED]>
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
>>
>>
>>
CG> ______________________________________________
CG> R-help@r-project.org mailing list
CG> https://stat.ethz.ch/mailman/listinfo/r-help
CG> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
CG> and provide commented, minimal, self-contained, reproducible code.
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