I obviously cannot predict the implications as much as John, but would the
followings be solutions:
- setClassUnion looks up for subclasses of its elements and add them up,
and setClass('A', ...) would update the union classes of any superclass of
'A'. removeClass would need to do some cleanup, which it probably does
already.
- OR, extends(class1) could lookup at runtime for union classes that
include a superclass of class1. Caching on class1 could be used, reset by
any subsequent call to setClass(class1, ...) or removeClass(class1). I
guess setClassUnion would also do the same to deal with union of unions.
Renaud
On 8 May 2013 19:02, John Chambers <j...@r-project.org> wrote:
> No need for generic functions and methods. Just looking at the hierarchy
> of the classes shows the problem.
>
> With Martin's simplified version:
>
> > library(PkgA)
> > extends("A")
> [1] "A"
> > library(PkgB)
> > extends("B")
> [1] "B" "A"
>
> > setClassUnion("C", c("matrix", "A"))
> > extends("A")
> [1] "A" "C"
> > extends("B")
> [1] "B" "A"
>
>
> So defining the union does not make all the subclasses of "A" members of
> the union.
>
> The next comments are guesses but plausible. Loading the namespace of
> PkgB may not update the known subclasses of classes from PkgA.
>
> This is one of R's touchier points in general: The state of things with
> respect to classes and methods changes dynamically as packages are loaded.
> Until PkgB is loaded, "A" has no known subclasses.
>
> If the guess is correct, then when the class union is formed, nothing
> tells us that "A" has a subclass "B" that should be added to the union.
>
> Fixing this properly may involve the load-time actions and not be quite
> trivial.
>
> John
>
>
>
> On 5/7/13 11:05 PM, Renaud Gaujoux wrote:
>
>> Hi,
>>
>> I started this post on bioc-devel but this seems to be more general:
>>
>> https://stat.ethz.ch/**pipermail/bioc-devel/2013-May/**004311.html<https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html>
>>
>> See reproducible example from Martin below.
>>
>> Thank you.
>>
>> Renaud
>>
>> ---------- Forwarded message ----------
>> From: Martin Morgan <mtmor...@fhcrc.org>
>> Date: 7 May 2013 19:55
>> Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem
>> in S4 methods for union class
>> To: Renaud Gaujoux <ren...@mancala.cbio.uct.ac.za**>
>> Cc: bioc-de...@r-project.org, dupan.m...@gmail.com
>>
>> I can replicate this with a simpler example, where PkgA has
>>
>> setClass("A", representation(x="numeric"))
>>
>> with NAMESPACE
>>
>> import(methods)
>> exportClasses("A")
>>
>> PkgB has
>>
>> setClass("B", contains="A")
>>
>> NAMESPACE
>>
>> import(methods)
>> importClassesFrom("PkgA", "A")
>> exportClasses("B")
>>
>> and then
>>
>> library(PkgA); library(PkgB)
>> setClassUnion("C", c("matrix", "A"))
>> setGeneric("do", function(x) standardGeneric("do"))
>> setMethod("do", "C", function(x) "done")
>>
>> leading to
>>
>> > do(new("A"))
>> [1] "done"
>> > do(new("B"))
>>
>> Error in (function (classes, fdef, mtable) :
>> unable to find an inherited method for function do for signature
>> "B"
>>
>> suggesting name space issues rather than something about ExpressionSet.
>> The
>> sample packages and test script are attached; it would be appropriate to
>> pursue this on the R-devel mailing list.
>>
>> Martin
>>
>>
>>
>> ______________________________**________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/**listinfo/r-devel<https://stat.ethz.ch/mailman/listinfo/r-devel>
>>
>>
>
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