[R-pkg-devel] [External] Re: Two packages with the same generic function

On Tue, 23 Jun 2020, Bert Gunter wrote:

"Users don't get warned about overriding names in packages they've
loaded, because that would just be irritating."

All Duncan is saying is that you don't get a notification if you do

     mean <- log

in the interpreter. If you attach a package that does this you would
get a notification (or an error if you configure your conflict
resolution options appropriately).

Best,

luke

Is that also true if the package or generic is imported by another that
they load; or is a dependency of a package they load? If so, I would not
call it "just irritating" because if silent, how would they know?


Bert Gunter

"The trouble with having an open mind is that people keep coming along

and

sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Mon, Jun 22, 2020 at 5:58 PM Mark Leeds <markleeds2 at gmail.com> wrote:

Hi Duncan: I maintain dynlm and your example is the exact reason I've

been

getting emails from people regarding
it not working correctly. I've been telling them to load dplyr by using

library(dplyr, exclude = c("filter", "lag"))





On Mon, Jun 22, 2020 at 7:57 PM Duncan Murdoch <

murdoch.duncan at gmail.com>

wrote:

On 22/06/2020 3:48 p.m., Tom Wainwright wrote:

Yet another alternative is simply to prevent your second package from
overriding the previously defined generic. The basic problem is the

ease

with which R allows overriding prior generic definitions (one of those

bits

of bad behavior we in the USA used to call "a Bozo No-No"), which

hides

all

the previous methods, as demonstrated by the following code:

plot(1:3)

plot <- function(x, ...) UseMethod("plot")
plot(1:3)

Error in UseMethod("plot") :
   no applicable method for 'plot' applied to an object of class
"c('integer', 'numeric')"

rm(plot)
plot(1:3)

(Despite Murdoch's suggestion that overriding the generic SHOULD issue

a

warning, it doesn't seem to in R 4.0.1.)

Sure it does, if pkgA and pkgB both export the same name, then you get

a

warning when you attach the second one.  For example,

library(MASS)
library(dplyr)

Attaching package: ?dplyr?

The following object is masked from ?package:MASS?:

     select

The following objects are masked from ?package:stats?:

     filter, lag

The following objects are masked from ?package:base?:

     intersect, setdiff, setequal, union

Users don't get warned about overriding names in packages they've
loaded, because that would just be irritating.

Duncan Murdoch

So, we might try protecting the generic definitions of "foo" in both
packages by enclosing them in something like:

tryCatch(invisible(methods("foo")), error = {foo <- function(x,...)

UseMethod("foo")}, finally=NULL)

There's probably a more elegant way to accomplish this. This relies on
"methods" returning an error if "foo" has no defined methods, so it is

not

redefined if their are previous methods. I haven't had time to try

this

in

the two-package example, but it might work, although I'm not sure how

to

handle the Namespace declarations.

   Tom Wainwright

On Mon, Jun 22, 2020 at 10:41 AM Bert Gunter <bgunter.4567 at gmail.com>

wrote:

...
and just to add to the query, assume the author of pkg B did (does)

not

know of pkg A and so, for example, could (did) not import any of pkg

A's

content into B. Given that there are at the moment ~20,000 packages

out

there, this does not seem to be an unreasonable assumption. One may

even

further assume that the user may not know that (s)he has package B

loaded,

as it may be a dependency of another package that (s)he uses. I

certainly

don't keep track of all the dependencies of packages I use.

Under these assumptions, is there any more convenient alternative to
Wolfgang's pkgA:foo(x) explicit call under such assumptions? If pkgA

has a

long name, what might one do?

Bert Gunter

"The trouble with having an open mind is that people keep coming

along

and

sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Mon, Jun 22, 2020 at 10:00 AM Viechtbauer, Wolfgang (SP) <
wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:

Hi All,

Let's say there are two packages pkgA and pkgB, both of which have a
generic function

foo <- function(x, ...)
    UseMethod("foo")

and pkgA has a method for objects of class "A":

foo.A <- function(x, ...)
    print(x)

and pkgB has a method for objects of class "B":

foo.B <- function(x, ...)
    plot(x)

Both packages export foo and their method and declare their

respective

S3

methods, so:

export(foo)
export(foo.A)
S3method(foo, A)

in NAMESPACE of pkgA and

export(foo)
export(foo.B)
S3method(foo, B)

in NAMESPACE of pkgB.

If a user loads pkgA first and then pkgB, this fails:

library(pkgA)
library(pkgB)
x <- 1:4
class(x) <- "A"
foo(x)

Error in UseMethod("foo") :
   no applicable method for 'foo' applied to an object of class "A"

and vice-versa. Of course, pkgA::foo(x) works. Aside from pkgA

importing

foo() or vice-versa, is there some other clever way to make this

work?

In

earlier versions of R (at least in 3.6.3), this used to work (i.e.,

the

generic foo() from pkgB would find method foo.A() and vice-versa),

but

not

since 4.0.0.

Best,
Wolfgang

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--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
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