[R-pkg-devel] Use of `:::` in a package for code run in a parallel cluster

[David Kepplinger]

Yes, my view is certainly rigid and I agree that in the cases where the
function is actually used directly by the user, exporting it is the correct
step.

However, it seems some packages actually need to access internal functions
from an outside context, but the code that accesses the function is
logically contained completely inside the package. In these cases, package
maintainers seem to be looking for alternatives to `:::` for the sake of
avoiding the R CMD check note. I argue that the work arounds, however,
either (a) achieve the exact same result as `:::`, but in a less
transparent and likely more error prone way, or (b) unnecessarily making an
internal function available to the user.

I also agree with the CRAN team that package maintainers need to be made
aware of the issue when using `:::` inside their package as it is most
likely unnecessary. But the phrasing of the note ("almost never needs to
use :::") combined with a lack of transparent guidelines on when it is
acceptable leads to maintainers looking for alternatives mimicking the
behavior of `:::`. I haven't found any official instructions in Writing R
extensions or on the mailing list under what circumstances `:::` is deemed
to be acceptable by the CRAN team (I have to admit searching for `:::` in
the archives yields so many results I haven't looked at all of them). It's
probably impossible to conceive every possible use case for `:::`, but a
good start may be to have something in the documentation explicitly
mentioning commonly observed patterns where `:::` is not acceptable, and
the common exceptions to the rule (if there are any).

Maybe this issue is so miniscule and almost never comes up that it's not
worth mentioning in the documentation.

Best,
David



On Mon, Sep 14, 2020 at 3:19 AM Georgi Boshnakov <
georgi.boshnakov using manchester.ac.uk> wrote:

> You may have a case to argue to CRAN that you can get the "almost"
> exemption (can't say without details) but your views look overly rigid.
>
> Exporting an object and marking it as internal is not a "work around",
> even less a "dirty trick".
> Export makes the object available outside the package's namespace and
> makes it clear that this is intentional.
> If you can't drop the 'package:::' prefix in your use case, this means
> that this is what you actually do (i.e. use those objects outside the
> namespace of the package). I would be grateful to CRAN for asking me to
> export and hence document this.
>
>
> Georgi Boshnakov
>
> PS Note that there is no such thing as "public namespace".
>
>
> -----Original Message-----
> From: R-package-devel <r-package-devel-bounces using r-project.org> On Behalf
> Of David Kepplinger
> Sent: 13 September 2020 20:52
> To: R Package Devel <r-package-devel using r-project.org>
> Subject: [R-pkg-devel] Use of `:::` in a package for code run in a
> parallel cluster
>
> Dear list members,
>
> I submitted an update for my package and got automatically rejected by the
> incoming checks (as expected from my own checks) for using `:::` calls to
> access the package's namespace.
> "There are ::: calls to the package's namespace in its code. A package
> *almost* never needs to use ::: for its own objects:…" (emphasis mine)
>
> This was a conscious decision on my part as the package runs code on a
> user-supplied parallel cluster and I consider cluster-exporting the
> required functions a no-go as it would potentially overwrite objects in the
> clusters R sessions. The package code does not own the cluster and hence
> the R sessions. Therefore overwriting objects could potentially lead to
> unintended behaviour which is opaque to the user and difficult to debug.
>
> Another solution to circumvent the R CMD check note is to export the
> functions to the public namespace but mark them as internal. This was also
> suggested in another thread on this mailing list (c.f. "Etiquette for
> package submissions that do not automatically pass checks?"). I do not
> agree with this work-around as the methods are indeed internal and should
> never be used by users. Exporting truly internal functions for the sake of
> satisfying R CMD check is a bad argument, in particular if there is a
> clean, well-documented, solution by using `:::`.
>
> I argue `:::` is the only clean solution to this problem and no dirty
> work-arounds are necessary. This is a prime example of where `:::` is
> actually useful and needed inside a package. If the R community disagrees,
> I think R CMD check should at least emit a WARNING instead of a NOTE and
> elaborate on the problem and accepted work-arounds in "Writing R
> extensions". Or keep emitting a NOTE but listing those nebulous reasons
> where `:::` would be tolerated inside a package. Having more transparent
> criteria for submitting to CRAN would be really helpful to the entire R
> community and probably also reduce the traffic on this mailing list.
>
> Best,
> David
>
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