[Rd] valid objects -> using S4 {was "Re: c.factor"}

From: Martin Maechler <maechler_at_stat.math.ethz.ch>
Date: Thu 16 Nov 2006 - 09:07:51 GMT

>>>>> "Roger" == Roger Bivand <Roger.Bivand@nhh.no> >>>>> on Wed, 15 Nov 2006 19:27:11 +0100 (CET) writes:

    Roger> On Wed, 15 Nov 2006, "BaRow" == Barry Rowlingson wrote:

> BillD> It does not remove names in Splus either, just all
> BillD> other attributes. I see c() used in several Splus
> BillD> functions as a way to convert a matrix into a vector
> BillD> (by removing the .Dims and .Dimnames attributes).

      >> 
      BaRow> I dont see the logic in certain attribute names
      BaRow> (?attr lists 'class', 'comment', 'dim', 'dimnames',
      BaRow> 'names', 'row.names' and 'tsp') being 'special'. Why
      BaRow> are matrices vectors with some 'magic' attribute
      BaRow> 'dim', and possibly some non-magic attributes like
      BaRow> 'umbongo' and 'fnord'? I'd have the dim (and other
      BaRow> essential properties of data structures) more tightly
      BaRow> bound to the data. attr(M,'dim')=NULL seems a very
      BaRow> odd way of turning a matrix into a vector.
      BaRow> 
      BaRow> If I was the R bdfl[1] I'd deprecate using 'attr' to
      BaRow> access these aspects of data objects and insist on
      BaRow> using "dim(M)" or "row.names(M)=foo".

    Roger> I have a less than vague feeling that you as bdfl are     Roger> describing new-style classes:

indeed, thank you, Roger!

    Roger> library(Matrix)
    Roger> x <- Matrix(1:6, nrow=2, ncol=3)
    Roger> getSlots(class(x))
    Roger> slot(x, "Dim")
    Roger> slot(x, "Dim") <- NULL

which gives

Error in checkSlotAssignment(object, name, value) :

        assignment of an object of class "NULL" is not valid for slot "Dim" in an object of class "dgeMatrix"; is(value, "integer") is not TRUE

    Roger> but perhaps unfortunately:

    Roger> slot(x, "Dim") <- as.integer(c(0,0,0))

    Roger> works! Maybe not quite what was intended?

Indeed it does not signal an error, surprisingly to you and others. Note however that subsequently

 > validObject(x)
 Error in validObject(x) : invalid class "dgeMatrix" object: Dim slot must be of length 2

. . . . .

This seems to have become a QFAQ (quite frequently asked question):

 Q: Why does R not signal an error when I assign invalid contents

    to a slot of an S4 object?

  1. Calling validObject() on every slot assignment would
    • inhibit building S4 objects incrementally ``until they are valid''
    • potentially lead to too slowly executing code.

Consequence:

 Only ``low-level'' programming should use    slot(A, "sn") <- .... or the equivalent

        A @ sn <- ....
 and then the programmeR is solely responsible to construct a  valid object -- or needs to expliclictly call validObject() at  the end of the construction process.

 Normal construction of S4 objects should use

John Chambers has much more to say on this, but I think most of it has already been written in the Green Book.

--
Martin Maechler, ETH Zurich

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