R devel - Apr 2016 - S3 dispatch for S4 subclasses only works if variable "extends" is accessible from global environment

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
>>

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
>>>
>
>

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

	[[alternative HTML version deleted]]

>>>>> Michael Lawrence <lawrence.michael at gene.com>
>>>>>     on Tue, 19 Apr 2016 05:34:41 -0700 writes:
    > Not sure why R_has_methods_attached() exists. Maybe Martin could shed
    > some light on that.

It was to support (via 'classgets' in attrib.c) a very fast

   class(.) <- "<newclass>"

for S4 objects... to be used in  setAs(......)  methods,
e.g., for the Matrix package where you have many classes with
most slots the same, and I would have wanted to be clearly
faster than calling
   new("<newclass>", x=.., y=.., z=.., u=..,v=.. ..)

But that experiment has not finalized, maybe because it was a too hackish idea.

I may have started writing that at a time where we still mostly
thought that it was not possible to have a working S4 R
"environment" where methods was only loaded but not attached.

In conclusion, you can consider R_has_methods_attached as non-existent.


    > 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