[Rd] S4 setClass with prototypes " issues" (PR#8053)

gunter.berton@gene.com gunter.berton at gene.com
Fri Aug 5 19:07:08 CEST 2005

To R-Developers:

I wish to report what I believe are inconsistencies between Green Book
descriptions and R methods behaviors. I **realize** that R does not
guarantee total consistency with the Green Book; therefore I leave it to you
to decide whether any of this is a bug, design choice, or a need for
additional documentation -- or whether I have simply misread or overlooked
existing explanations. If the latter, I apologize for the error, but it was
not for a want of effort.

The issues all revolve around the setClass('xxx',prototype=...) without any
slots construction. All references are to the Green Book. R 2.1.1 (on

1. Classes so defined (with protype, no slots) are not instantiated as
described on the bottom of p.289. In particular, the following example from
the book fails:

> setClass('sequence',prototype=numeric(3))
[1] "sequence"
> new('sequence',c(1,51,10))
Error in initialize(value, ...) : cannot use object of class "numeric" in
new():  class "sequence" does not extend that class
2. I have been unable to find any Help documentation about the proper method
to instantiate classes defined by prototypes without slots. Experimentation
showed that only one of the two approaches on the bottom of p.289 worked:

> setClass('foo',prototype=numeric())
[1] "foo"
> z<-new('foo')
## new() works as it should
> z
An object of class "foo"

## But now try this ...
> z<-1:3
> is(z,'numeric')
[1] TRUE
## Hence, if R followed the book's statement that "For this to work,
'object' must either be suitable as a prototype for 'myClass or belong to a
class that can be coerced to 'myClass.'" (Note, I interpret this to mean
that either of these conditions are sufficient for either of the approaches

> as(z,'foo')
Error in as(z, "foo") : no method or default for coercing "integer" to "foo"

## But
> class(z)<-'foo'
> z
An object of class "foo"
[1] 1 2 3

I was unable to find documentation for this behavior in R, assuming that
this is not a bug. If it's a bug, it should be fixed, of course; if not, I
think the behavior should be documented, perhaps in setClass.

3. Finally, and most disconcertingly, The Green Book says (p.288):

"... We do NOT want a 'sequence' object to be interpreted as a numeric
vector ... Doing arbitrary arithmetic on the object, for example would be

The use of prototypes without representations allows the class designer to
limit the legal computations on objects made up of numeric data..."

As I read this, this should mean that the following should fail, but it
doesn't (continuing the above example):

> z+1
An object of class "foo"
[1] 2 3 4

Again, if this is not a bug, I think that this lack of adherence to the
Green book should be documented in R. May I say, however, that I wish R had
implemented the book's prescription.

-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
"The business of the statistician is to catalyze the scientific learning
process."  - George E. P. Box

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