From henrik.bengtsson at gmail.com  Tue Apr 19 20:10:06 2016
From: henrik.bengtsson at gmail.com (Henrik Bengtsson)
Date: Tue, 19 Apr 2016 11:10:06 -0700
Subject: [Rd] S3 dispatch for S4 subclasses only works if variable
 "extends" is accessible from global environment
In-Reply-To: <CABdHhvF5K2eU5_kHhxvx++hjKEZsx7hi3j9PxW3fGZCpJ_nLuQ@mail.gmail.com>
References: <57156F2B.4000205@ivt.baug.ethz.ch>
	<CAOQ5NyfK-67N6yHgdP-_Nr8=i34d7zkiR9J6OYFnCtN6_A=fjA@mail.gmail.com>
	<5715D528.6030101@ivt.baug.ethz.ch>
	<CAOQ5NyfBrX=DUVdf66g5fWeubnqNUeaT-yJYYiuQB2-MkHk1Xw@mail.gmail.com>
	<CADwqtCNTFaEXauZKfgMX5tV0=b5L2N4gdCG+ZtCn2RGijo4B-w@mail.gmail.com>
	<CAOQ5NycZgF_sF6Ef90etRkEYL2-GzFGM08+Ff8RRjtURJYk=yA@mail.gmail.com>
	<CADwqtCP9Vk4U-axT0_4CiiOx0T_Ance9=L7yVz-B0RJK+bgfvA@mail.gmail.com>
	<CABdHhvF5K2eU5_kHhxvx++hjKEZsx7hi3j9PxW3fGZCpJ_nLuQ@mail.gmail.com>
Message-ID: <CAFDcVCSNH7xh1gdoHFXEEAuQgKHmC_Jf5dV6OQXBe6bgS=LTYQ@mail.gmail.com>

On Tue, Apr 19, 2016 at 9:21 AM, Hadley Wickham <h.wickham at gmail.com> wrote:
>
> 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)

Slightly weaker version of this wish (that would also remove
confusion): At least make R and Rscript load the same set of packages
by default.


More clarification (in case some is new to this topic):

The packages loaded by default when R and Rscript is loaded can be
controlled by environment variable 'R_DEFAULT_PACKAGES' and/or option
'defaultPackages', cf. help("Startup").  When this is empty or
undefined, the built-in defaults kick in, and it's these built-in
defaults that differ between the R and the Rscript executable:

$ R --quiet --vanilla -e "getOption('defaultPackages')"
> getOption('defaultPackages')
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods"

$ Rscript --vanilla -e "getOption('defaultPackages')"
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"

Thus, a user can enforce the same set of default packages by using:

$ export R_DEFAULT_PACKAGES=datasets,utils,grDevices,graphics,stats,methods

$ R --quiet --vanilla -e "getOption('defaultPackages')"
> getOption('defaultPackages')
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods"

$ Rscript --vanilla -e "getOption('defaultPackages')"
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods"

/Henrik

>
> 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
> >> >> >>>
> >> >> >>> ______________________________________________
> >> >> >>> 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
> >>
> >
> >
> >
> > --
> > Gabriel Becker, PhD
> > Associate Scientist (Bioinformatics)
> > Genentech Research
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
> --
> http://hadley.nz
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] S3 dispatch for S4 subclasses only works if variable "extends" is accessible from global environment
Henrik Bengtsson