R devel - Feb 2010 - S4 setClass / initialize misunderstanding

Hi, I recently ran into this problem. I couldn't find any mention of it in
the setClass documentation.

setClass("Foo", representation(file = "character"))
setMethod("initialize", "Foo", function(.Object, file) {
  print(file)
})
setClass("Bar", contains = "Foo")

And the error:

Error in print(file) : argument "file" is missing, with no default

The workaround is to interchange the setMethod and the second setClass
call, however, it begs the question why is setClass calling an initialize
method? As always, if I have missed documentation concerning this please
point me there.

Thanks, jim

On 02/02/2010 02:12 PM, bullard at stat.berkeley.edu
wrote:
> 
> Hi, I recently ran into this problem. I couldn't find any mention of it
in
> the setClass documentation.
> 
> setClass("Foo", representation(file = "character"))
> setMethod("initialize", "Foo", function(.Object, file)
{
>   print(file)
> })
> setClass("Bar", contains = "Foo")
> 
> And the error:
> 
> Error in print(file) : argument "file" is missing, with no
default
>
> The workaround is to interchange the setMethod and the second setClass
> call, however, it begs the question why is setClass calling an initialize
> method? As always, if I have missed documentation concerning this please
> point me there.
Hi Jim -- The hint is in traceback()
> setClass("Bar", contains="Foo")
Error in print(file) : argument "file" is missing, with no
default
> traceback()
[snip]
5: new(toDef)
4: .simpleCoerceExpr(Class, to, names(slots), classDef2)
3: makeExtends(name, what, slots = slots, classDef2 = whatClassDef,
       package = package)
2: makeClassRepresentation(Class, properties, superClasses, prototype,
       package, validity, access, version, sealed, where = where)
1: setClass("Bar", contains = "Foo")

the source

 if(!isVirtualClass(toDef))
    toClass <- class(new(toDef)) # get it with the package slot correct

subversion

% svn annotate src/library/methods/R/RClassUtils.R

 48221        jmc     if(!isVirtualClass(toDef))
 48221        jmc         toClass <- class(new(toDef)) # get it with

% svn log -r 48221
------------------------------------------------------------------------
r48221 | jmc | 2009-03-26 14:28:03 -0700 (Thu, 26 Mar 2009) | 1 line

fix bug in defining as() methods--got wrong package for simple contains
class with no added slots
------------------------------------------------------------------------

and the mailing list

https://stat.ethz.ch/pipermail/r-devel/2009-March/052829.html

but the bottom line is that you want

  validObject(new("Foo"))

to return TRUE. I'd write (if an initialize method is really required --
what happens if there's a constructor Foo() that constructs the
arguments to new("Foo", <...>) correctlyl?)

  setMethod(initialize, function(.Object, ..., file=character(0)) {
      ## process file, then
      callNextMethod(.Object, ..., file=file)
  })

'file' gets a default argument. '...' allows derived classes to
callNextMethod (explicitly, or implicitly by a call to new("Bar",
<...>)) and get the expected 'initialize' behavior. Placing
'file' after
'...' means that 'file' doesn't capture unnamed arguments,
which are
supposed to be prototypes for classes that .Object extends.

Martin

> 
> Thanks, jim
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793