[R-pkg-devel] Courtesy methods and explosive dependencies

[Neal Fultz]

In the estimatr package, we provided a shim to support broom without
transitively depending on the tidyverse:


tidy <- function(object, ...) {
  if (requireNamespace("broom", quietly = TRUE)) broom::tidy(object, ...)
else UseMethod("tidy")
}

https://github.com/DeclareDesign/estimatr/blob/master/R/S3_tidy.R

It's not ideal but it seems to make our functions work whether or not the
end user has broom.


S4 methods (eg texreg) were more difficult, and we ended up registering the
generics in .onLoad:


.onLoad <- function(libname, pkgname) {
  if (suppressWarnings(requireNamespace("texreg", quietly = TRUE))) {
    setGeneric("extract", function(model, ...) standardGeneric("extract"),
      package = "texreg"
    )
    setMethod("extract",
      signature = className("lm_robust", pkgname),
      definition = extract.lm_robust
    )
  }
  invisible()
}

https://github.com/DeclareDesign/estimatr/blob/master/R/zzz.R


Since this is in .onLoad, it's a little buggy if the user has estimatr and
then installs texreg, but again seems to mostly work.

We would appreciate any feedback the list may have on these design patterns.


-Neal




On Fri, May 25, 2018 at 8:38 AM, Lenth, Russell V <russell-lenth using uiowa.edu>
wrote:

> I agree that most of the package dependencies in multcomp are worth
> having, but that is not the point. The point is that if a developer wants
> to write a method for a generic function offered in another non-base
> package, that creates false dependencies: packages that users are required
> to have, but that aren't actually used by the method. I certainly wasn't
> trying to diss multcomp; that was just a concrete illustration.
>
> Russ
>
> -----Original Message-----
> From: Martin Maechler [mailto:maechler using stat.math.ethz.ch]
> Sent: Friday, May 25, 2018 2:13 AM
> To: Lenth, Russell V <russell-lenth using uiowa.edu>
> Cc: r-package-devel using r-project.org
> Subject: Re: [R-pkg-devel] Courtesy methods and explosive dependencies
>
> >>>>> Lenth, Russell V
> >>>>>     on Thu, 24 May 2018 23:14:42 +0000 writes:
>
>     > Package developers, I am trying to severely cut down on
>     > the number of dependencies of my package emmeans. It is
>     > now 48, which is quite a few (but that is down from over
>     > 100 in the preceding version, where I made the unwise
>     > choice of including a particularly greedy package in
>     > Imports). I hate to force users to install dozens of
>     > packages that they don't really need or want, but it seems
>     > very hard to avoid.
>
>     > Case in point: emmeans provides additional methods for
>     > 'cld' and 'glht' from the multcomp package. Accordingly, I
>     > import their generics, and register my additional
>     > methods. But because I import the generics, I must list
>     > multcomp in Imports, and that results in the addition of
>     > 16 required packages, some of which I never use. More
>     > important, I believe that NONE of those 16 packages are
>     > required for the correct functioning of my courtesy
>     > methods. The only things I really need are the generics.
>
> There must be a mistake here -- I think in your perception:
>
> 'multcomp' does *not* have excessive dependencies (though I'd say one too
> much):
>
> > tools::package_dependencies("multcomp")
> $multcomp
> [1] "stats"     "graphics"  "mvtnorm"   "survival"  "TH.data"   "sandwich"
> [7] "codetools"
>
> > tools::package_dependencies("multcomp", recursive=TRUE)
> $multcomp
>  [1] "stats"     "graphics"  "mvtnorm"   "survival"  "TH.data"
>  "sandwich"
>  [7] "codetools" "methods"   "utils"     "zoo"       "Matrix"
> "splines"
> [13] "MASS"      "grDevices" "grid"      "lattice"
>
> >
>
> Apart from "base + recommended" packages (which *everyone* has installed),
> these are just 4 packages:
>
>      mvtnorm
>      TH.data
>      sandwich
>      zoo
>
> where  mvtnorm, sandwich, and zoo  really are among the (formally
> undefined) recommended-level-2 R packages... so I do wonder if you really
> had needed to install.
>
> The 'TH.data' { TH <==>  maintainer("multcomp") } package I think should
> not be in the strict dependencies of 'multcomp' but rather in its
> "Suggests".... something I'd say must be true for all data packages:
> The whole idea of data packages is that they should be needed for
> interesting help page examples, vignettes, maybe even tests, but not for
> package functionality.
>
> In sum: I'd strongly advise to not change from keeping multcomp among your
> imports.
>
> Martin Maechler
> ETH Zurich
>
>     > On the flip side, emmeans defines some generics of its own
>     > that I invite other package developers to extend so that
>     > emmeans supports their models. If those packages import
>     > emmeans, there is an overhead of 48 dependencies; again,
>     > most of these are packages that are not needed at all for
>     > those packages' methods to work. I don't like being
>     > responsible for that.
>
>     > I believe this is a very common problem, not just with my
>     > own packages. It's one thing to extend a base method like
>     > 'print'; but extending methods in contributed packages
>     > creates these dependency explosions. I have hundreds of
>     > packages installed on my system - a couple dozen I care
>     > about, another few dozen that seem fairly desirable, and a
>     > couple hundred that I don't even know what they're for,
>     > other than that things will break if I uninstall them.
>
>     > I do know of a couple ways to reduce these dependencies in
>     > the case of my multcomp dependencies:
>
>     > 1. I could simply export my S3 methods for cld and glht as
>     > functions, rather than registering them as S3 methods.
>     > Then I could move multcomp to Suggests. The downside is
>     > that it clutters the namespace for emmeans.
>
>     > 2. I could define the generics for cld and glht in my own
>     > package, and export them; and move multcomp to Suggests.
>     > Again, it clutters the namespace, and creates warning
>     > messages about (if not real issues with) masking.
>
>     > Probably (1) is better than (2), but is it better than
>     > what I do now? Is there something else that I (and
>     > probably a whole lot of other people) don't know?
>
>     > I wish there were an ImportGenerics or an
>     > ImportWithoutDependencies or some such field possible in
>     > DESCRIPTION.
>
>     > I appreciate any suggestions. Thanks
>
>     > Russ
>
>     > --
>     > Russell V. Lenth  -  Professor Emeritus Department of
>     > Statistics and Actuarial Science    The University of Iowa
>     >  -  Iowa City, IA 52242  USA    Voice (319)335-0712  -
>     >  FAX (319)335-3017 russell-lenth using uiowa.edu  -
>     >  http://www.stat.uiowa.edu/~rlenth/
>
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>
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