From murdoch at stats.uwo.ca  Tue Sep 15 12:26:32 2009
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Tue, 15 Sep 2009 06:26:32 -0400
Subject: [Rd] S3 objects in S4 slots
In-Reply-To: <116117690909150300v4a703807se7b08b94c3f1a68d@mail.gmail.com>
References: <116117690909150300v4a703807se7b08b94c3f1a68d@mail.gmail.com>
Message-ID: <4AAF6BD8.1010002@stats.uwo.ca>

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.  Convert 
the VCorpus objects to S4 objects, or use S3 objects everywhere.

Duncan Murdoch



[Rd] S3 objects in S4 slots
Duncan Murdoch