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

[Hervé Pagès]

Thanks Martin. We'll update the BioC builders to the latest R devel soon.

Cheers,

H.

On 3/15/24 10:26, Martin Maechler wrote:
>>>>>> 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

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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