On 10/18/12 6:31 AM, Martin Morgan wrote:
Initialization of this simple hierarchy
A = setClass("A", representation(x="numeric"))
setClass("B", contains=c("VIRTUAL", "A"))
C = setClass("C", contains="B")
fails (neat that setClass returns generators; I hadn't realized that
before!)
Yes, from 2.15.0. See ?setClass and the NEWS file.
> C(A())
Error: evaluation nested too deeply: infinite recursion /
options(expressions=)?
because in the default coerce<-,C,A-method
> selectMethod("coerce<-", c("C", "A"))
Method Definition:
function (from, to = "A", value)
{
.value <- as(from, "B", TRUE)
as(.value, "A") <- value
...
as(from, "B", TRUE) correctly returns an instance of C.
Hmm, correct. Direct specification of the slots is fine, but supplying
a superclass object fails as you show. A "harmless" solution to this
may take some thinking (suggestions welcome). Not for 2.15.2 at any rate.
A workaround is to define the inheritance relation directly. In this
example:
setIs("C", "A",
coerce = function(from) new("A", x = from@x),
replace = function(from, value) {from@x = value@x; from})
Or, if it's more natural, supply an initialize() method for "C" to
intercept such arguments.
Also VIRTUAL isn't mentioned on ?Classes or ?setClass and isn't
documented on class?VIRTUAL, making me wonder whether virtual classes
are actually meant to be supported as part of S4 (they are used
regularly in Bioconductor packages)?
Eh?? Of course they are. E.g., section 9.4 of the Software for Data
Analysis reference. In particular, page 353:
"Any ordinary class definition can create a virtual class, by including
the special class "VIRTUAL" in the contains= argument to setClass()."
John
Martin
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