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

This might be too big a change - but is it worth reconsidering the
behaviour of Rscript? Maybe the simplest fix would be simply to always
load the methods package.  (I think historically it didn't because
loading methods took a long time, but that is no longer true)

getOption('defaultPackages')

getOption('defaultPackages')

Hadley

On Tue, Apr 19, 2016 at 10:37 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 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

--
Gabriel Becker, PhD
Associate Scientist (Bioinformatics)
Genentech Research

--
Gabriel Becker, PhD
Associate Scientist (Bioinformatics)
Genentech Research

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--
http://hadley.nz