From martin.kober at gmail.com  Tue Sep 15 12:00:58 2009
From: martin.kober at gmail.com (Martin Kober)
Date: Tue, 15 Sep 2009 12:00:58 +0200
Subject: [Rd] S3 objects in S4 slots
Message-ID: <116117690909150300v4a703807se7b08b94c3f1a68d@mail.gmail.com>

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?


Thanks in advance
Best Regards
Martin



[Rd] S3 objects in S4 slots
Martin Kober