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

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

Please omit "MatrixDispatchTest::" from the test scripts:

Rscript -e "test <- function(x) UseMethod('test', x);
test.Matrix <-
function(x) 'Hi'; test(Matrix::Matrix())"

Rscript -e "extends <- 42; test <- function(x)
UseMethod('test', x);
test.Matrix <- function(x) 'Hi'; test(Matrix::Matrix())"


-Kirill


On 19.04.2016 01:35, Kirill M?ller 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

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
>

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
>>