unary class union of an S3 class

Hi,

Short story
-----------

  setClassUnion("ArrayLike", "array")

  showClass("ArrayLike")  # no slot

  setClass("MyArrayLikeConcreteSubclass",
      contains="ArrayLike",
      representation(stuff="ANY")
  )

  showClass("MyArrayLikeConcreteSubclass") # 2 slots!!

That doesn't seem right.

Long story
----------

S4 provides at least 3 ways to create a little class hierarchy
like this:

       FooLike ............. virtual class with no slot
        ^   ^
        |   |
      foo   anotherfoo ..... 2 concrete subclasses

(1) The "standard" way: define FooLike first, then foo and anotherfoo
as subclasses of FooLike:

  setClass("FooLike")

  setClass("foo",
      contains="FooLike",
      representation(stuff="ANY")
  )

  setClass("anotherfoo",
      contains="FooLike",
      representation(stuff="ANY")
  )

  showClass("FooLike")    # displays foo and anotherfoo as
                          # known subclasses

  x1 <- new("foo")
  is(x1, "foo")           # TRUE
  is(x1, "FooLike")       # TRUE
  is(x1, "anotherfoo")    # FALSE

  x2 <- new("anotherfoo")
  is(x2, "anotherfoo")    # TRUE
  is(x2, "FooLike")       # TRUE
  is(x2, "foo")           # FALSE

Everything works as expected.

(2) Using a class union: define foo and anotherfoo first, then FooLike
as the union of foo and anotherfoo:

  setClass("foo", representation(stuff="ANY"))
  setClass("anotherfoo", representation(stuff="ANY"))
  setClassUnion("FooLike", c("foo", "anotherfoo"))

  showClass("FooLike")    # displays foo and anotherfoo as
                          # known subclasses

(3) Using a *unary* class union: define foo first, then FooLike as the
(unary) union of foo, then anotherfoo as a subclass of FooLike:

  setClass("foo", representation(stuff="ANY"))
  setClassUnion("FooLike", "foo")

  showClass("FooLike")   # displays foo as the only known subclass

  setClass("anotherfoo",
      contains="FooLike",
      representation(stuff="ANY")
  )

  showClass("FooLike")   # now displays foo and anotherfoo as
                         # known subclasses

The 3 ways lead to the same hierarchy. However the 3rd way is
interesting because it allows one to define the FooLike virtual
class as the parent of an existing foo class that s/he doesn't
control.

Why not use setIs() for this? Everything then behaves as expected. I don't
think it makes much sense to "contain" a class union. Rather, you just want
to establish the inheritance relationship.
For example, to define an ArrayLike class:

  setClassUnion("ArrayLike", "array")
  showClass("ArrayLike")  # displays array as a known subclass

Note that ArrayLike is virtual with no slots (analog to a Java
Interface), which is what is expected.

  setClass("MyArrayLikeConcreteSubclass",
      contains="ArrayLike",
      representation(stuff="ANY")
  )

  showClass("MyArrayLikeConcreteSubclass")  # shows 2 slots!!

What is the .Data slot doing here? I would expect to see that slot
if MyArrayLikeConcreteSubclass was extending array but this is not
the case here.

  a <- new("MyArrayLikeConcreteSubclass")

  is(a, "MyArrayLikeConcreteSubclass")  # TRUE  --> ok
  is(a, "ArrayLike")                    # TRUE  --> ok
  is(a, "array")                        # FALSE --> ok

But:

  is.array(a)  # TRUE --> not ok!

Is is.array() confused by the presence of the .Data slot?

It looks like the unary union somehow equates ArrayLike and array and thus
makes ArrayLike confer a dim attribute (and thus is.array(a) returns TRUE).
Since S4 objects cannot have attributes that are not slots, it must do this
via a data part, thus the .Data slot.
I can fix it by defining an "is.array" method for
MyArrayLikeConcreteSubclass objects:

  setMethod("is.array", "MyArrayLikeConcreteSubclass",
      function(x) FALSE
  )

However, it feels that I shouldn't have to do this.

Is the presence of the .Data slot in MyArrayLikeConcreteSubclass
objects an unintended feature?

Thanks,
H.

sessionInfo()
R Under development (unstable) (2016-01-07 r69884)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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unary class union of an S3 class

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