[Rd] NOTE: unstated dependencies in examples

[Jari Oksanen]

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'.

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. 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
> >>
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> 
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