From lawrence.michael at gene.com  Tue Apr 19 16:34:00 2016
From: lawrence.michael at gene.com (Michael Lawrence)
Date: Tue, 19 Apr 2016 07:34:00 -0700
Subject: [Rd] S3 dispatch for S4 subclasses only works if variable
 "extends" is accessible from global environment
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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



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