From gmbecker at ucdavis.edu  Thu Aug 28 23:14:43 2014
From: gmbecker at ucdavis.edu (Gabriel Becker)
Date: Thu, 28 Aug 2014 14:14:43 -0700
Subject: [Rd] Re R CMD check checking in development version of R
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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

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