S4 generating function

Can someone explain what the problem is when I use the
generating function? And how to get debug() to stop in
the Superclass initialize method?


---- source -----
setClass("Superclass",
         representation(id = "character"),
         contains = "VIRTUAL")

setMethod("initialize",
          signature(.Object = "Superclass"),
          function(.Object, id = "") {
              cat("initialize (Superclass)", "\n")
              if (length(id) > 0) {
                  cat("\tid =", id, "\n")
                  .Object at id <- id
              }
              .Object
          })

setClass("Subclass",
         contains = "Superclass")

setMethod("initialize",
          signature(.Object = "Subclass"),
          function(.Object, ...) {
              cat("initialize (Subclass)", "\n")
              cat("\t... =");str(list(...));cat("\n")
              callNextMethod(.Object, ...)
          })

Subclass <- function(id = "") {
    new("Subclass", id = id)
}

cat("*** Create class using new() ***\n")
str(new("Subclass", id = "test1"))

cat("*** Create class using generating function ***\n")
str(Subclass(id = "test2"))


---- output -----
*** Create class using new() ***
initialize (Subclass)
        ... =List of 1
 $ id: chr "test1"

initialize (Superclass)
        id = test1
Formal class 'Subclass' [package ".GlobalEnv"] with 1 slots
  ..@ id: chr "test1"
*** Create class using generating function ***
initialize (Subclass)
        ... =List of 1
 $ id: chr "test2"

initialize (Superclass)
Error in .local(.Object, ...) : Object "id" not found


Thanks

----------------------------------------------------------
SIGSIG -- signature too long (core dumped)

Paul Roebuck wrote:

Can someone explain what the problem is when I use the
generating function? And how to get debug() to stop in
the Superclass initialize method?
[SNIP code & output]

Now, the specific example.  There are 3 special features used:
1. Nonstandard arguments for the initialize method (its official
arguments are (.Object, ...))

2. callNextMethod

3. within callNextMethod, providing explicit arguments.  The simple case
is callNextMethod(), which passes on the arguments to the current method.

Turns out that it's the third step that finds a bug in the heuristics
used by callNextMethod to construct the actual call.

In your example, you don't need the explicit arguments since they just
replicate the formal arguments to initialize().  If you omit them, the
computation is simpler & works.

The bug can probably be fixed, but until 2.2 comes out at least, you
need to stick to the simpler callNextMethod().
[SNIP modified code]

On Fri, 5 Aug 2005, John Chambers wrote:

Paul Roebuck wrote:

Can someone explain what the problem is when I use the
generating function? And how to get debug() to stop in
the Superclass initialize method?
[SNIP code & output]

Now, the specific example.  There are 3 special features used:
1. Nonstandard arguments for the initialize method (its official
arguments are (.Object, ...))

2. callNextMethod

3. within callNextMethod, providing explicit arguments.  The simple case
is callNextMethod(), which passes on the arguments to the current method.

Turns out that it's the third step that finds a bug in the heuristics
used by callNextMethod to construct the actual call.

In your example, you don't need the explicit arguments since they just
replicate the formal arguments to initialize().  If you omit them, the
computation is simpler & works.

The bug can probably be fixed, but until 2.2 comes out at least, you
need to stick to the simpler callNextMethod().
[SNIP modified code]

Thank you for your help. Unfortunately, this is a case where
posting the simplest code necessary to display the bug works
against the poster. Actual code uses external pointers but
this revision shows more of the general concept.

If I understand your description correctly, the problem is
passing both named and unnamed arguments to callNextMethod().
Can I [easily] do either of these things to avoid the bug?

  1) somehow add an argument to 'dots' and invoke callNextMethod()
     without arguments?
  2) parse 'dots' and invoke callNextMethod() with a completely
     named argument list?


------ revised source -------
setClass("Superclass",
         representation(.values = "integer",
                        id      = "character"),
         contains = "VIRTUAL")

setMethod("initialize",
          signature(.Object = "Superclass"),
          function(.Object, .values = NULL, id = "") {
              cat("initialize (Superclass)", "\n")
              if (!is.null(.values)) {
                  cat("\t.values =", .values, "\n")
                  .Object at .values <- .values
              }
              if (length(id) > 0) {
                  cat("\tid =", id, "\n")
                  .Object at id <- id
              }
              .Object
          })

setClass("Subclass",
         contains = "Superclass")

setMethod("initialize",
          signature(.Object = "Subclass"),
          function(.Object, count = 1, ...) {
              cat("initialize (Subclass)", "\n")
              dots <- list(...)
              cat("\t... =");str(dots);cat("\n")
              .values = integer(count)
              callNextMethod(.Object, .values = .values, ...)
          })

Subclass <- function(count, id = "") {
    new("Subclass", count, id = id)
}

cat("*** Create class using new() ***\n")
str(new("Subclass", id = "test0"))
str(new("Subclass", count = 3, id = "test1"))

cat("*** Create class using generating function ***\n")
#trace("initialize", signature = "Subclass", browser)
str(Subclass(count = 3, id = "test2"))

----------------------------------------------------------
SIGSIG -- signature too long (core dumped)