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 <gmbec...@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.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 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
