[Rd] NOTE: unstated dependencies in examples
Duncan Murdoch
murdoch.duncan at gmail.com
Fri Oct 14 15:26:38 CEST 2011
On 14/10/2011 9:18 AM, Jari Oksanen wrote:
> On Thu, 2011-10-13 at 17:34 +0200, Uwe Ligges wrote:
> > I looked at the code and since this is not that trivial to change, I
> > think we can well live with typing
> >
> > grep -r gplots ./man
> >
> > which is not too hard to run on the source package, I believe.
> >
> > Best wishes,
> > Uwe
> >
> Uwe& others,
>
> This is OK if you want to identify the cause of the problems. However,
> the basic problem was that checking required something that is not
> required: there was one example that was not run, and one case where the
> loading of the package was not necessary (if(require(<package>))). I do
> believe that handling this kind of cases is difficult in automatic
> checking. However, I think they need not be checked: there should be a
> new case of package reference in addition to 'depends', 'suggests' and
> 'enhances' -- something like 'benefitsfrom'.
Users use those declarations when they ask to install dependencies. If
you don't declare a dependence on a contributed package, users will have
to manually install it.
> This is now actual to me, since I'm adding 'parallel' support to my
> package, but there seems to be no clean way of doing this with the
> current checking procedures. I use the 'parallel' support only if the
> package is available (in R>= 2.14.0, not yet released), and there are
> multiple cores.
Temporarily maintain two releases of your package: one for R < 2.14.0
that doesn't mention parallel, and one for R >= 2.14.0 that does. The
second one should declare its dependence on R >= 2.14.0. If support for
parallel is your only change, you don't need to do anything for the
previous one: CRAN will not replace it in the 2.13.x repository if the
new one needs a newer R.
Duncan Murdoch
> If there is only once cpu or there is not yet
> 'parallel' package, nothing bad will happen: things will only work like
> they worked earlier without 'parallel' package. I haven't found out how
> to do this cleanly for R CMD check (it is clean for my code since there
> the usage is checked). If I add "suggests: parallel" I get R CMD check
> error for the current and previous R -- for no reason. So currently I
> don't mention 'parallel' at all in DESCRIPTION: I get a NOTE and
> Warnings ('require' call not declared, no visible definitions), but this
> is a smaller problem than having a spurious failure, and failing to
> have this package for a system where it works quite normally.
>
> The new DESCRIPTION keyword could be used for packages that are useful
> but not necessary, so that the package can be quite well be used without
> these packages, but it may have some extra options or functionality with
> those packages. This sounds like a suggestion to me, but in R language
> suggestions cannot be refused.
>
> Cheers, jari oksanen
>
> >
> > On 13.10.2011 03:00, Yihui Xie wrote:
> > > You have this in Jevons.Rd:
> > >
> > > # show as balloonplots
> > >
> > > if (require(gplots)) {
> > >
> > >
> > > and this in Snow.Rd:
> > >
> > > %\dontrun{
> > >
> > > library(sp)
> > >
> > >
> > > It will certainly be helpful if R CMD check can provide more
> > > informative messages (in this case, e.g, point out the Rd files).
> > >
> > > Regards,
> > > Yihui
> > > --
> > > Yihui Xie<xieyihui at gmail.com>
> > > Phone: 515-294-2465 Web: http://yihui.name
> > > Department of Statistics, Iowa State University
> > > 2215 Snedecor Hall, Ames, IA
> > >
> > >
> > >
> > > On Wed, Oct 12, 2011 at 11:33 AM, Michael Friendly<friendly at yorku.ca> wrote:
> > >> Using R 2.13.1, I am now getting the following NOTE when I run R CMD check
> > >> on my HistData
> > >> package
> > >>
> > >> * checking for unstated dependencies in examples ... NOTE
> > >> 'library' or 'require' calls not declared from:
> > >> gplots sp
> > >>
> > >> Under R 2.12.x, I didn't get these notes.
> > >>
> > >> I have ~ 25 .Rd files in this package, and AFAICS, every example uses
> > >> library or require for the
> > >> functions used; the DESCRIPTION file has the long list of Suggests, which
> > >> previously was sufficient
> > >> for packages used in examples.
> > >>
> > >> Suggests: gtools, KernSmooth, maps, ggplot2, proto, grid, reshape, plyr,
> > >> lattice, ReadImages, car
> > >>
> > >> But I have no way to find the .Rd file(s) that triggered this note.
> > >>
> > >> What is the tool used in R CMD check to make this diagnosis? It would be
> > >> better
> > >> if this reported the .Rd file(s) that triggered this note.
> > >> Is it possible that this note could be specious?
> > >>
> > >> -Michael
> > >>
> > >> --
> > >> Michael Friendly Email: friendly AT yorku DOT ca
> > >> Professor, Psychology Dept.
> > >> York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
> > >> 4700 Keele Street Web: http://www.datavis.ca
> > >> Toronto, ONT M3J 1P3 CANADA
> > >>
> > >> ______________________________________________
> > >> R-devel at r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/r-devel
> > >>
> > >
> > > ______________________________________________
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> >
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