From gmbecker at ucdavis.edu  Tue Apr 19 17:37:59 2016
From: gmbecker at ucdavis.edu (Gabriel Becker)
Date: Tue, 19 Apr 2016 08:37:59 -0700
Subject: [Rd] S3 dispatch for S4 subclasses only works if variable
 "extends" is accessible from global environment
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Does it make sense to be able to load an S4 object without the methods
package being attached? I'm not sure implementation-wise how easy this
would be, but it seems like any time there is an S4 object around, the
methods package should be available to deal with it.

~G

On Tue, Apr 19, 2016 at 7:34 AM, Michael Lawrence <lawrence.michael at gene.com
> wrote:

> Right, R_has_methods_attached() uses that. Probably not the right
> check, since it refers to S4 dispatch, while S4_extends() is used by
> S3 dispatch.
>
> Perhaps S4_extends() should force load the methods package? The above
> example works after fixing the check to ensure that R_MethodsNamespace
> is not R_GlobalEnv, but one could load a serialized S4 object and
> expect S3 dispatch to work with Rscript.
>
> On Tue, Apr 19, 2016 at 6:51 AM, Gabriel Becker <gmbecker at ucdavis.edu>
> wrote:
> > 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
>



-- 
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