From ucfagls at gmail.com  Thu Aug 28 23:42:28 2014
From: ucfagls at gmail.com (Gavin Simpson)
Date: Thu, 28 Aug 2014 15:42:28 -0600
Subject: [Rd] Re R CMD check checking in development version of R
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Gabriel,

That is not my understanding of this at all. I could hide the fact that I
was using vegan under the hood, supplying methods for its generics and by
exporting the generic I imported from vegan, etc. But you are missing the
point that I see users of my package, because I envisioned close
interlinking with the functionality provided by vegan, wanting to use vegan
interactively with many of the objects that functions in analogue create.

I do feel this aversion to Depends is being taken too far by some. Simon's
articulation in this thread of what Depends means (to him) is the closest I
have seen to how I have interpreted things. That's also about as close to
official wisdom that I have seen beyond what is in Writing R Extensions.

Analogue also uses Lattice, but I have moved this to Imports as I don't
expect users to be manipulating the few plot alternatives analogue provides
using this graphics package and if they want to they can load lattice
themselves. So, I fully understand the differences and nuances of Depends
and Imports etc. I just don't agree with those that claim no packages
should be in Depends, or that my use case is somehow wrong or not best
practice.

G


On 28 August 2014 15:14, Gabriel Becker <gmbecker at ucdavis.edu> wrote:

> Gavin,
>
> I admit to not knowing the details of your package, but do users commonly
> need to use symbols from other package *in calls to functions exported by
> your package*? If so, you're in the situation Martin (Morgan) described,
> which is one I think everyone agrees Depends is appropriate for.
>
> If the above is not the case, and you're arguing it's simply convenient
> for users because it's very common for them to use top level functions from
> both in the same analysis, the case for Depends is not as strong. In that
> case, the official wisdom, AFAIK, is that Depends is not warranted.
>
> ~G
>
>
> On Thu, Aug 28, 2014 at 11:43 AM, Gavin Simpson <ucfagls at gmail.com> wrote:
>
>> I fully agree.
>>
>> This is how I have come to understand Depends vs Imports and why I
>> currently will not be removing vegan from Depends for my analogue package.
>> This is also why I was pushing back against the notion that was voiced
>> early in this thread that *nothing* should be in Depends.
>>
>> Cheers
>>
>> G
>>
>>
>> On 28 August 2014 08:47, Bert Gunter <bgunter at gene.com> wrote:
>>
>> > This is a nice explanation of the Imports/Depends distinction. It
>> > ought to go into the Extensions ref manual imho.
>> >
>> > Cheers,
>> > Bert
>> >
>> > Bert Gunter
>> > Genentech Nonclinical Biostatistics
>> > (650) 467-7374
>> >
>> > "Data is not information. Information is not knowledge. And knowledge
>> > is certainly not wisdom."
>> > Clifford Stoll
>> >
>> >
>> >
>> >
>> > On Thu, Aug 28, 2014 at 7:39 AM, Simon Urbanek
>> > <simon.urbanek at r-project.org> wrote:
>> > >
>> > > On Aug 27, 2014, at 6:01 PM, Gavin Simpson <ucfagls at gmail.com> wrote:
>> > >
>> > >> On 27 August 2014 15:24, Hadley Wickham <h.wickham at gmail.com> wrote:
>> > >>
>> > >>>> Is that the cause of these NOTEs? Is the expectation that if I am
>> > using a
>> > >>>> function from a package, even a package that I have in Depends:,
>> that
>> > I
>> > >>>> have to explicitly declare these imports in NAMESPACE?
>> > >>>
>> > >>> Yes.
>> > >>>
>> > >>> (Otherwise your package won't work if it's only attached and not
>> > >>> loaded. i.e. if someone does analogue::foo() only the imported
>> > >>> functions are available, not the functions in packages you depend
>> on)
>> > >>>
>> > >>
>> > >> Cheers Hadley. Thanks for the confirmation, but...
>> > >>
>> > >> ...I don't get this; what is the point of Depends? I thought it was
>> "my
>> > >> package needs these other packages to work, i.e. be loaded". Hence
>> it is
>> > >> user error (IMHO ;-) to do `analogue::foo()` without having the
>> > >> dependencies loaded too.
>> > >>
>> > >
>> > > No. The point of Depends is that if your package is attached, it also
>> > attaches the other packages to make them available for the user.
>> > Essentially you're saying "if you want to use my package interactively,
>> you
>> > will also want to use those other packages interactively". You still
>> need
>> > to use import() to define what exactly is used by your package - as
>> opposed
>> > to what you want to be available to the user in case it is attached.
>> > >
>> > > Cheers,
>> > > Simon
>> > >
>> > >
>> > >
>> > >> 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?
>> > >>
>> > >>
>> > >>> (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.
>> > >>
>> > >> Or am I thinking about this in the wrong way?
>> > >>
>> > >> Thanks again
>> > >>
>> > >> Gavin
>> > >>
>> > >>
>> > >>>
>> > >>> Hadley
>> > >>>
>> > >>>
>> > >>> --
>> > >>> http://had.co.nz/
>> > >>>
>> > >>
>> > >>
>> > >>
>> > >> --
>> > >> Gavin Simpson, PhD
>> > >>
>> > >>       [[alternative HTML version deleted]]
>> > >>
>> > >> ______________________________________________
>> > >> R-devel at r-project.org mailing list
>> > >> https://stat.ethz.ch/mailman/listinfo/r-devel
>> > >>
>> > >
>> > > ______________________________________________
>> > > R-devel at r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/r-devel
>> >
>>
>>
>>
>> --
>> Gavin Simpson, PhD
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>
>
> --
> Gabriel Becker
> Graduate Student
> Statistics Department
> University of California, Davis
>



-- 
Gavin Simpson, PhD

	[[alternative HTML version deleted]]



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