[Rd] Spurious warning in as.data.frame.factor()

[Martin Maechler]

>>>>> Martin Maechler 
>>>>>     on Fri, 15 Mar 2024 11:24:22 +0100 writes:

>>>>> Ivan Krylov 
>>>>>     on Thu, 14 Mar 2024 14:17:38 +0300 writes:

    >> On Thu, 14 Mar 2024 10:41:54 +0100
    >> Martin Maechler <maechler using stat.math.ethz.ch> wrote:

    >>> Anybody trying S7 examples and see if they work w/o producing
    >>> wrong warnings?

    >> It looks like this is not applicable to S7. If I overwrite
    >> as.data.frame with a newly created S7 generic, it fails to dispatch on
    >> existing S3 classes:

    >> new_generic('as.data.frame', 'x')(factor(1))
    >> # Error: Can't find method for `as.data.frame(S3<factor>)`.

    >> But there is no need to overwrite the generic, because S7 classes
    >> should work with existing S3 generics:

    >> foo <- new_class('foo', parent = class_double)
    >> method(as.data.frame, foo) <- function(x) structure(
    >> # this is probably not generally correct
    >> list(x),
    >> names = deparse1(substitute(x)),
    >> row.names = seq_len(length(x)),
    >> class = 'data.frame'
    >> )
    >> str(as.data.frame(foo(pi)))
    >> # 'data.frame':   1 obs. of  1 variable:
    >> #  $ x: <foo> num 3.14

    >> So I think that is nothing to break because S7 methods for
    >> as.data.frame will rely on S3 for dispatch.

    > Yes, as it should be.  Thank you for checking..


    >>> > The patch passes make check-devel, but I'm not sure how to safely
    >>> > put setGeneric('as.data.frame'); as.data.frame(factor(1:10)) in a
    >>> > regression test.  
    >>> 
    >>> {What's the danger/problem?  we do have "similar" tests in both
    >>> src/library/methods/tests/*.R
    >>> tests/reg-S4.R
    >>> 
    >>> -- maybe we can discuss bi-laterally  (or here, as you prefer)
    >>> }

    >> This might be educational for other people wanting to add a regression
    >> test to their patch. I see that tests/reg-tests-1e.R is already running
    >> under options(warn = 2), so if I add the following near line 750
    >> ("Deprecation of *direct* calls to as.data.frame.<someVector>")...

    >> # Should not warn for a call from a derivedDefaultMethod to the raw
    >> # S3 method -- implementation detail of S4 dispatch
    >> setGeneric('as.data.frame')
    >> as.data.frame(factor(1))

    >> ...then as.data.frame will remain an S4 generic. Should the test then
    >> rm(as.data.frame) and keep going? (Or even keep the S4 generic?) Is
    >> there any hidden state I may be breaking for the rest of the test this
    >> way? 
    >> The test does pass like this, so this may be worrying about nothing.

    > Indeed, this could be educational;  I think just adding

    > removeGeneric('as.data.frame')

    > is appropriate here as it is self-explaining and should not leave
    > much traces.

    > I'm about to test this in reg-tests-1e.R and with make check-all
    > and commit later today,
    > thanking you, Ivan!

This has been committed to R-devel svn rev 86139 now.

So these spurious warnings in situations where  as.data.frame()
is an S4 generic --- notably for the many Bioconductor package
depending on {BiocGenerics} ---  should disappear within 24
hours or less.

Martin