[Rd] Wish list

Prof Brian Ripley ripley at stats.ox.ac.uk
Mon Jan 19 15:09:58 MET 2004

On Mon, 19 Jan 2004, Frank E Harrell Jr wrote:

> On Sun, 18 Jan 2004 18:47:52 -0500
> Duncan Murdoch <dmurdoch at pair.com> wrote:
> > On Sat, 17 Jan 2004 09:33:10 -0500, you wrote:
> > 
> > >I also share your views about namespaces.  These have caused numerous
> > >problems for me.  It would be nice to have more of a mechanism to put
> > >"feelers" out to the R user community when major changes are planned. 
> > 
> > Changes always show up in r-devel (the main CVS branch, not the
> > mailing list) first.  Package developers should be keeping a
> > relatively up to date copy of it around if they're doing things that
> > are likely to break.
> I need to do that more often.  But sometimes it's hard to know what things
> I do that are likely to break.  That's where there needs to be some other
> mechanism for user communications.

Well, there is a NEWS file that is worth consulting, and we (Kurt in 
particular) run all the CRAN packages after every major change and daily.
See  http://cran.r-project.org/src/contrib/checkSummary.html.  We do also 
tend to tell package authors directly if their packages break, at least if 
they were previously warning-free.

It seems the sort of thing you do is to call methods directly where you 
could equally well call the generic, since that is what is currently 
failing in Design and Hmisc (if survfit.km is a survfit method).

> > >In Hmisc and Design I reference several functions that were not
> > >exported from packages that now use namespaces.  There is an elegant

That's not showing up in failures on the tests under R-patched.  Of the
listed dependencies only grid, lattice and survival have namespaces, and
only survival has been added since 1.8.1.  (I suspect the R-patched tests 
are against the 1.8.1 versions of the recommended packages, not the 
current versions.)

> > >solution with the package:::function notation, 
> > 
> > I'd recommend avoiding that as much as you can.  If things aren't
> > exported from a package, then the package writer is likely to feel
> > free to change them without warning.  It's much better to convince the
> > package writer that they missed something in their export list.
> That's a good solution in general, but I could see legitimate
> disagreements about what should be exported, so this will not always solve
> the problem.

I think it does.  If the package writer wants a function to be private,
would-be users should respect that decision.  Most of the cases we have
encountered have been calling methods directly rather than coercing
objects to the right class and calling the generic.  In extremis, copy
(with permission) the function you want from the package sources and
rename it.

Unless I made a mistake there are no current uses of ::: in CRAN packages, 
and there are very few in base R (and quite a lot of the methods::: should 
probably better be methods::).


Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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