[R-pkg-devel] [EXTERNAL] Re: slightly polemic question re R CMD check

Mon Mar 9 17:51:47 CET 2020

I tend to agree. Having ... as an argument for a specific method is often unnecessary, and furthermore, can result in errors being hidden. Eg you think you're calling

methodname(arg1, arg2="whatever")

but you're really calling

methodname(arg1, ar2="whatever")

and the misspelling isn't picked up, because it gets swallowed by the ... .

IMO the whole reason for the current state of affairs is because of a wart in how lm and glm were implemented back in the S-Plus days. A glm object inherits from lm, which doesn't make a lot of sense. It should really be the other way round: the specific case should inherit from the general, so that an lm is a glm, not a glm is an lm. It's way too late to change this now, of course.

-----Original Message-----
From: R-package-devel <r-package-devel-bounces using r-project.org> On Behalf Of David Hugh-Jones
Sent: Sunday, 8 March 2020 6:28 PM
To: Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
Cc: R package devel <r-package-devel using r-project.org>
Subject: [EXTERNAL] Re: [R-pkg-devel] slightly polemic question re R CMD check

I see the logic, but it seems in practice people often write specific
methods with their own specific arguments. (Think of the many plot or print
methods for different objects, for example.) Here, enforcing a ... argument
does not buy us much. All that we really need is that plot(x) will work for
many classes of x. Beyond that, we expect users to read the method-specific
documentation.

Maybe this is an antipattern. It just seems that S3 methods have turned out
to be often used that way. Enforcing ... hasn't stopped it, and causes some
awkwardnesses in documentation and error checking. To be clear, I'm not
arguing against the generic having flexibility. I'm arguing against
enforcing that the method always accepts every argument that the generic
could accept.

On Sun, 8 Mar 2020, 17:14 Jeff Newmiller, <jdnewmil using dcn.davis.ca.us> wrote:

> R encourages the use of ... particularly in S3 generics, to avoid
> over-depending on inheritance to enable flexible use of these generics.
> That is, when you call the generic without knowing which class you are
> giving it, you cannot specify class-specific arguments. However, some
> methods have obvious alternative class-specific behaviors that are
> typically enabled using class-specific arguments (e.g. plot). You cannot
> support both fully-generic calls and class-specific calls without giving
> the generic some flexibility that won't get used in some cases.
>
>
> On March 8, 2020 9:41:51 AM PDT, David Hugh-Jones <
> davidhughjones using gmail.com> wrote:
> >Hi Jeff,
> >
> >I wouldn't say R encourages that in general. Non-generic functions will
> >throw an error if you use a non-existent argument. And some generic
> >functions check for it:
> >
> >seq(1, 3, blah = 1)
> >[1] 1 2 3
> >Warning message:
> >In seq.default(1, 3, blah = 1) :
> > extra argument ‘blah’ will be disregarded
> >
> >In fact there is even a `chkDots()` function to help with this - which,
> >despite having used R or 17 years, I first discovered today :-). So, it
> >seems the R base developers thought lenient argument checking could be
> >a
> >bad thing, presumably because it lets errors go undetected.
> >
> >Maybe chkDots is a reasonable workaround. But I wonder what the
> >rationale
> >is for R CMD check enforcing that methods *must* be as lenient as the
> >generic. It seems to lead to a lot of documentation of the form:
> >
> >@param ... Not used.
> >
> >Cheers,
> >David
> >
> >
> >On Sun, 8 Mar 2020 at 16:24, Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
> >wrote:
> >
> >> You seem to think this is a bad thing. R does encourage lenient
> >argument
> >> checking... what rock have you been under for the last 20 years?
> >>
> >> On March 8, 2020 5:41:51 AM PDT, David Hugh-Jones <
> >> davidhughjones using gmail.com> wrote:
> >> >You're quite right :-) But I think the polemic still holds, because
> >I
> >> >have
> >> >to add manual argument checking to all my methods, which has a cost
> >in
> >> >lines of code. Indeed, few base R methods have chosen to do this. In
> >> >effect, the current setup encourages writing methods with "lenient"
> >> >argument specifications.
> >> >
> >> >Thank you for the suggestion about ellipsis.
> >> >
> >> >On Sun, 8 Mar 2020, 11:04 Gábor Csárdi, <csardi.gabor using gmail.com>
> >wrote:
> >> >
> >> >> You can add the ... argument to chop.default(), and then check
> >that
> >> >> length(list(...)) is zero.
> >> >>
> >> >> Also, you might be interested in the ellipsis package.
> >> >>
> >> >> Gabor
> >> >>
> >> >> On Sun, Mar 8, 2020 at 10:56 AM David Hugh-Jones
> >> >> <davidhughjones using gmail.com> wrote:
> >> >> >
> >> >> > Hi all,
> >> >> >
> >> >> > My package defines the following method and generic:
> >> >> >
> >> >> > chop <- function (x, ...) UseMethod("chop")
> >> >> >
> >> >> > chop.default <- function (x, breaks, labels, extend = NULL, drop
> >=
> >> >TRUE)
> >> >> {
> >> >> > ... }
> >> >> >
> >> >> > R CMD check then gives a warning:
> >> >> >
> >> >> > W  checking S3 generic/method consistency (695ms)
> >> >> >    chop:
> >> >> >      function(x, ...)
> >> >> >    chop.default:
> >> >> >      function(x, breaks, labels, extend, drop)
> >> >> >
> >> >> >    See section ‘Generic functions and methods’ in the ‘Writing R
> >> >> >    Extensions’ manual.
> >> >> >
> >> >> > I can fix this by adding a ... argument to chop.default:
> >> >> >
> >> >> > chop.default <- function (x, breaks, labels, extend = NULL, drop
> >=
> >> >> > TRUE, ...)
> >> >> >
> >> >> > But that makes the code less robust because e.g.
> >> >> >
> >> >> > chop(x, Breaks = 1:3)
> >> >> >
> >> >> > will no longer throw an error from the misspelled argument.
> >> >> >
> >> >> > Or I can write:
> >> >> >
> >> >> > chop(x, breaks, labels, extend, drop) UseMethod("chop")
> >> >> >
> >> >> > but this means I cannot use a different interface for a
> >different
> >> >method.
> >> >> >
> >> >> > This seems like a mistake. (That's the polemic.) Or am I missing
> >a
> >> >better
> >> >> > way? (That's the question.)
> >> >> >
> >> >> > David
> >> >> >
> >> >> >         [[alternative HTML version deleted]]
> >> >> >
> >> >> > ______________________________________________
> >> >> > R-package-devel using r-project.org mailing list
> >> >> > https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-package-devel&data=02%7C01%7Chongooi%40microsoft.com%7C0ad9cebc4ce24e7d50e508d7c3b006de%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637193033116746685&sdata=CJ8fTRpoMUxAaJJkI7QSQylGZE3dtd8YLodIZn4C5xA%3D&reserved=0
> >> >>
> >> >
> >> >       [[alternative HTML version deleted]]
> >> >
> >> >______________________________________________
> >> >R-package-devel using r-project.org mailing list
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> >>
> >> --
> >> Sent from my phone. Please excuse my brevity.
> >>
>
> --
> Sent from my phone. Please excuse my brevity.
>

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