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

[Michael Lawrence]

Agreed about Rscript being consistent R.

For now, I'll modify S4_extends() so that it leads to S4 dispatch when
dispatch is turned on (not just when methods is attached).

On Tue, Apr 19, 2016 at 8:37 AM, Gabriel Becker <gmbecker at ucdavis.edu> wrote:
> 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 Müller
>> >> <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 Müller
>> >> >> <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