[Rd] Pb with validObject(..., complete=TRUE)

Herve Pages hpages at fhcrc.org
Tue Apr 15 09:03:56 CEST 2008


When called with complete=TRUE, validObject() is supposed to work in a
recursive manner. But here is a situation where it doesn't seem to be
the case.

Let's define a class with a validity method:

   setClass("PosInts", representation(ii="integer"))

       if (!all(object at ii > 0))
         return("'ii' slot contains non-positive values")

Let's extend this class (no need to add new slots for illustrating the pb):

   setClass("PosInts2", contains="PosInts")

   broken <- new("PosInts2")
   broken at ii <- 3:0

If "PosInts2" objects don't need to satisfy additional constraints in order to
be considered valid, then I don't need to define a validity method for them.
I can just rely on method dispatch, which works as expected with validity methods:

   > validObject(broken)
   Error in validObject(broken) :
     invalid class "PosInts" object: 'ii' slot contains non-positive values

Unfortunately, this will cause problems later when I try to validate objects
that have slots of type "PosInts2":

   setClass("A", representation(aa="PosInts2"))
   a <- new("A", aa=broken)

This works as expected:

   > validObject(a)
   [1] TRUE

But this is not what I would expect:

   > validObject(a, complete=TRUE)
   [1] TRUE

... given that 'a' has a slot that contains an invalid "PosInts2" instance:

   > validObject(a at aa)
   Error in validObject(a at aa) :
     invalid class "PosInts2" object: 'ii' slot contains non-positive values

So clearly 'a' is broken and I would expect validObject(a, complete=TRUE) to
tell me so...

Now if I define the same validity method for "PosInts2" objects as for "PosInts"
objects, then things work as expected (validObject(a, complete=TRUE) will fail)
but it's not clear to me why I should be forced to do this?



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