[Rd] S3 objects in S4 slots
Duncan Murdoch
murdoch at stats.uwo.ca
Tue Sep 15 13:42:29 CEST 2009
On 15/09/2009 7:34 AM, Martin Maechler wrote:
>>>>>> Duncan Murdoch <murdoch at stats.uwo.ca>
>>>>>> on Tue, 15 Sep 2009 06:26:32 -0400 writes:
>
> > Martin Kober wrote:
> >> Hello,
> >>
> >> I am the maintainer of the stringkernels package and have come across
> >> a problem with using S3 objects in my S4 classes.
> >>
> >> Specifically, I have an S4 class with a slot that takes a text corpus
> >> as a list of character vectors. tm (version 0.5) saves corpora as
> >> lists with a class attribute of c("VCorpus", "Corpus", "list"). I
> >> don't actually need the class-specific attributes, I only care about
> >> the list itself.
> >>
> >> Here's a simplified example of my problem:
> >>
> >>
> >>> setClass("testclass", representation(slot="list"))
> >>>
> >> [1] "testclass"
> >>
> >>> a = list(a="1", b="2")
> >>> class(a) = c("VCorpus", "Corpus", "list") # same as corpora in tm v0.5
> >>> x = new("testclass", slot=a)
> >>>
> >> Error in validObject(.Object) :
> >> invalid class "testclass" object: 1: invalid object for slot "slot"
> >> in class "testclass": got class "VCorpus", should be or extend class
> >> "list"
> >> invalid class "testclass" object: 2: invalid object for slot "slot" in
> >> class "testclass": got class "Corpus", should be or extend class
> >> "list"
> >> invalid class "testclass" object: 3: invalid object for slot "slot" in
> >> class "testclass": got class "list", should be or extend class "list"
> >>
> >> The last line is a bit confusing here (``got class "list", should be
> >> or extend class "list"''). There's an even more confusing error
> >> message when I try to assign the slot later on:
> >>
> >>
> >>> y = new("testclass")
> >>> y at slot = a
> >>>
> >> Error in checkSlotAssignment(object, name, value) :
> >> c("assignment of an object of class \"VCorpus\" is not valid for
> >> slot \"slot\" in an object of class \"testclass\"; is(value, \"list\")
> >> is not TRUE", "assignment of an object of class \"Corpus\" is not
> >> valid for slot \"slot\" in an object of class \"testclass\"; is(value,
> >> \"list\") is not TRUE", "assignment of an object of class \"list\" is
> >> not valid for slot \"slot\" in an object of class \"testclass\";
> >> is(value, \"list\") is not TRUE")
> >>
> >> The last part of the message claims that ``is(value, "list") is not
> >> TRUE'', but is(a, "list") is certainly TRUE. (??)
> >>
> >> On a side note, it does work when "list" is the first entry in class().
> >>
> >>
> >> I tried to use setOldClass, but seemingly using list is not possible
> >> because it does not extend oldClass, or I didn't find out how to do
> >> it:
> >>
> >>> setOldClass(c("VCorpus", "Corpus", "list"))
> >>>
> >> Error in setOldClass(c("VCorpus", "Corpus", "list")) :
> >> inconsistent old-style class information for "list"; the class is
> >> defined but does not extend "oldClass"
> >>
> >>
> >> Intuitively I would have thought that, because the underlying data is
> >> of type list, it would "fit" into an object slot requiring a list,
> >> irrespective of S3 class attributes. The only thing I can think of is
> >> a manual solution removing the class attribute.
> >>
> >> Is there a way to define lists with S3 class attributes such that they
> >> are accepted as lists in S4 object slots? Or any other ways to solve
> >> this?
> >>
>
> > A possible workaround is to store unclass(a) in that slot, rather than
> > a. You won't be able to use the VCorpus or Corpus methods on it, but it
> > sounds as though you don't want to.
>
> > I would say checkSlotAssignment should be using some variation on
> > inherits(), rather than checking for an exact class match, but probably
> > the real message is that you shouldn't mix S3 and S4 systems.
>
> I don't think so.
> Recent releases of R have had big improvements (instrumented by
> John Chambers) in order to make exactly this (S3 classed objects as
> slots of S4 objects) possible !!
Shouldn't an object that inherits from "list" be allowed to occupy a
slot that wants a list?
Duncan Murdoch
>
> > Convert the VCorpus objects to S4 objects, or use S3 objects everywhere.
>
> Well, no, at least not at all according to what I think has been the
> intentions of the recent years' changes of making S3 objects
> better fit into the S4 frame work.
>
> Martin Maechler
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