[Rd] Re R CMD check checking in development version of R

Martin Morgan mtmorgan at fhcrc.org
Thu Aug 28 14:29:48 CEST 2014

On 08/27/2014 08:33 PM, Gavin Simpson wrote:
> On Aug 27, 2014 5:24 PM, "Hadley Wickham"
> <snip />
>> I'd say: Depends is a historical artefact from ye old days before
>> package namespaces. Apart from depending on a specific version of R,
>> you should basically never use depends.  (The one exception is, as
>> mentioned in R-exts, if you're writing something like latticeExtras
>> that doesn't make sense unless lattice is already loaded).
> Keeping this nuance in mind when when discussing Depends vs Imports is
> important so as to not suggest that there isn't any reason to use Depends
> any longer.

A common case in Bioconductor is that a package defines a class and methods 
intended for the user; this requires the package to be on the search path (else 
the user wouldn't be able to do anything with the returned object). A class and 
supporting methods can represent significant infrastructure, so that it makes 
sense to separate these in distinct packages. It is not uncommon to find 3-5 or 
more packages in the Depends: field of derived packages for this reason.


> I am in full agreement that its use should be limited to exceptional
> situations, and have modified my packages accordingly.
> Cheers,
> G
>>> This check (whilst having found some things I should have imported and
>>> didn't - which is a good thing!) seems to be circumventing the
> intention of
>>> having something in Depends. Is Depends going to go away?
>> I don't think it's going to go away anytime soon, but you should
>> consider it to be largely deprecated and you should avoid it wherever
>> possible.
>>>> (And really you shouldn't have any packages in depends, they should
>>>> all be in imports)
>>> I disagree with *any*; having say vegan loaded when one is using
> analogue is
>>> a design decision as the latter borrows heavily from and builds upon
> vegan.
>>> In general I have moved packages that didn't need to be in Depends into
>>> Imports; in the version I am currently doing final tweaks on before it
> goes
>>> to CRAN I have remove all but vegan from Depends.
>> I think that is a reasonable use case for depends. Here's the exact
>> text from R-exts: "Field ‘Depends’ should nowadays be used rarely,
>> only for packages which are intended to be put on the search path to
>> make their facilities available to the end user (and not to the
>> package itself): for example it makes sense that a user of package
>> latticeExtra would want the functions of package lattice made
>> available."
>> Personally I avoid even this use, requiring users of my packages to be
>> explicit about exactly what packages are on the search path.  You are
>> of course welcome to your own approach, but I think you'll find it
>> will become more and more difficult to maintain in time. I recommend
>> that you bite the bullet now.
>> Put another way, packages should be extremely conservative about
>> global side effects (and modifying the search path is such a
>> side-effect)
>> Hadley
>> --
>> http://had.co.nz/
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