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

[Joshua Ulrich]

On Sun, Sep 13, 2020 at 3:19 PM Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>
> On 13/09/2020 3:51 p.m., David Kepplinger wrote:
> > 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 `:::`
>
> Who is calling this function:  package code or user code?  I assume it's
> a bit of a mix:  your package writes a script that calls the function
> when it runs in user space.  (It would help if you gave an explicit
> example of when you need to use this technique.)
>
> If my assumption is correct, there are other simple workarounds besides
> exporting the functions.  Instead of putting
>
>     pkg:::foo(args)
>
> into your script, put
>
>     pkg::callInternal("foo", args)
>
> where pkg::callInternal is an exported function that can look up
> unexported functions in the namespace.
>
Another possibility is what quantmod::newTA() does.
https://github.com/joshuaulrich/quantmod/blob/a8e9cb87825c0997a8468f5105db6c507b26ac5d/R/newTA.

It's a function that creates a user-facing function.  The created
function needs to access unexported objects from the quantmod
namespace.  newTA() accomplishes that by setting the environment of
the function it returns to the quantmod namespace.

https://github.com/joshuaulrich/quantmod/blob/a8e9cb87825c0997a8468f5105db6c507b26ac5d/R/newTA.R#L98

That gives the user's new function access to the unexported charting
objects it needs to work.

Hope that helps.

Best,
Josh


> You may argue that you prefer pkg:::foo for some reason:  to which I'd
> respond that you are being rude to the CRAN volunteers.  I've offered
> two options (one in the previous thread, a different one here), and
> there was a third one in that thread offered by Ivan Krylov.  Surely one
> of these is good enough for your needs, and you shouldn't force CRAN to
> handle you specially.
>
> Duncan
>
> >
> > 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
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
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