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

[Jeff Newmiller]

Re backwards specialization... you could also say that a vector is a special kind of matrix... but it most definitely is not that way in R.

On March 9, 2020 9:51:47 AM PDT, Hong Ooi <hongooi using microsoft.com> wrote:
>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
>> >>
>>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%7C637193033116751662&sdata=%2Ba6YarFqDW9nleC7EZjVStMzHwnpQMTTV69CPEEP7eg%3D&reserved=0
>> >>
>> >> --
>> >> Sent from my phone. Please excuse my brevity.
>> >>
>>
>> --
>> Sent from my phone. Please excuse my brevity.
>>
>
>	[[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%7C637193033116751662&sdata=%2Ba6YarFqDW9nleC7EZjVStMzHwnpQMTTV69CPEEP7eg%3D&reserved=0

-- 
Sent from my phone. Please excuse my brevity.