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.mich...@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 <gmbec...@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.mich...@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.muel...@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.muel...@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@r-project.org mailing list > >> >>> https://stat.ethz.ch/mailman/listinfo/r-devel > >> >>> > >> > > >> > > >> > >> ______________________________________________ > >> R-devel@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 [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
