From gmbecker at ucdavis.edu  Tue Apr 19 15:51:48 2016
From: gmbecker at ucdavis.edu (Gabriel Becker)
Date: Tue, 19 Apr 2016 06:51:48 -0700
Subject: [Rd] S3 dispatch for S4 subclasses only works if variable
 "extends" is accessible from global environment
In-Reply-To: <CAOQ5NyfBrX=DUVdf66g5fWeubnqNUeaT-yJYYiuQB2-MkHk1Xw@mail.gmail.com>
References: <57156F2B.4000205@ivt.baug.ethz.ch>
	<CAOQ5NyfK-67N6yHgdP-_Nr8=i34d7zkiR9J6OYFnCtN6_A=fjA@mail.gmail.com>
	<5715D528.6030101@ivt.baug.ethz.ch>
	<CAOQ5NyfBrX=DUVdf66g5fWeubnqNUeaT-yJYYiuQB2-MkHk1Xw@mail.gmail.com>
Message-ID: <CADwqtCNTFaEXauZKfgMX5tV0=b5L2N4gdCG+ZtCn2RGijo4B-w@mail.gmail.com>

See also .isMethodsDispatchOn, which is what trace uses to decide if the
methods package needs to be loaded.

~G

On Tue, Apr 19, 2016 at 5:34 AM, Michael Lawrence <lawrence.michael at gene.com
> wrote:

> Not sure why R_has_methods_attached() exists. Maybe Martin could shed
> some light on that.
>
> On Mon, Apr 18, 2016 at 11:50 PM, Kirill M?ller
> <kirill.mueller at ivt.baug.ethz.ch> wrote:
> > Thanks for looking into it, your approach sounds good to me. See also
> > R_has_methods_attached()
> > (
> https://github.com/wch/r-source/blob/42ecf5f492a005f5398cbb4c9becd4aa5af9d05c/src/main/objects.c#L258-L265
> ).
> >
> > I'm fine with Rscript not loading "methods", as long as everything works
> > properly with "methods" loaded but not attached.
> >
> >
> > -Kirill
> >
> >
> >
> > On 19.04.2016 04:10, Michael Lawrence wrote:
> >>
> >> Right, the methods package is not attached by default when running R
> >> with Rscript. We should probably remove that special case, as it
> >> mostly just leads to confusion, but that won't happen immediately.
> >>
> >> For now, the S4_extends() should probably throw an error when the
> >> methods namespace is not loaded. And the check should be changed to
> >> directly check whether R_MethodsNamespace has been set to something
> >> other than the default (R_GlobalEnv). Agreed?
> >>
> >> On Mon, Apr 18, 2016 at 4:35 PM, Kirill M?ller
> >> <kirill.mueller at ivt.baug.ethz.ch> wrote:
> >>>
> >>> Scenario: An S3 method is declared for an S4 base class but called for
> an
> >>> instance of a derived class.
> >>>
> >>> Steps to reproduce:
> >>>
> >>>> Rscript -e "test <- function(x) UseMethod('test', x); test.Matrix <-
> >>>> function(x) 'Hi'; MatrixDispatchTest::test(Matrix::Matrix())"
> >>>
> >>> Error in UseMethod("test", x) :
> >>>    no applicable method for 'test' applied to an object of class
> >>> "lsyMatrix"
> >>> Calls: <Anonymous>
> >>> 1: MatrixDispatchTest::test(Matrix::Matrix())
> >>>
> >>>> Rscript -e "extends <- 42; test <- function(x) UseMethod('test', x);
> >>>> test.Matrix <- function(x) 'Hi';
> >>>> MatrixDispatchTest::test(Matrix::Matrix())"
> >>>
> >>> [1] "Hi"
> >>>
> >>> To me, it looks like a sanity check in line 655 of src/main/attrib.c is
> >>> making wrong assumptions, but there might be other reasons.
> >>>
> >>> (
> https://github.com/wch/r-source/blob/780021752eb83a71e2198019acf069ba8741103b/src/main/attrib.c#L655-L656
> )
> >>>
> >>> Same behavior in R 3.2.4, R 3.2.5 and R-devel r70420.
> >>>
> >>>
> >>> Best regards
> >>>
> >>> Kirill
> >>>
> >>> ______________________________________________
> >>> R-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>>
> >
> >
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



-- 
Gabriel Becker, PhD
Associate Scientist (Bioinformatics)
Genentech Research

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[Rd] S3 dispatch for S4 subclasses only works if variable "extends" is accessible from global environment
Gabriel Becker