I think the message is accurate [*]: you do however need to have a clear
understanding of the scoping issues involved, and no message is going to
give you that.
In short, implicit generics are converted (or not) into explicit
functions to be dumped during the dump-for-lazy-loading phase of R CMD
INSTALL: loading the namespace finds whatever function of that name is
in scope at that time, and once there are multiple functions of the same
name around, different ones may be in scope at different times.
To take one recent example from CRAN:
library(VGAM) # fine, as VGAM loads stats4 via Depends:
and in another session
loadNamespace('VGAM')
Error: Functions for exporting methods must have been made generic,
explicitly or implicitly; not true when loading ‘VGAM’ for ‘AIC’, ‘logLik’
since the visible function AIC() when the namespace alone is loaded is
the one in stats, not the one in stats4 which was visible when the
package was dumped for lazy-loading.
I have little idea how one could express all the possibilities for user
error in an error message like this: as the CRAN maintainers have found,
some package authors cannot comprehend even several-paragraph
explanations tailored to their specific errors. But I might have
written something like:
The function 'plot' found when exporting methods from the namespace
'pkgB' is not an S4 generic.
Hopefully such experiences will encourage people to write NAMESPACE
files more carefully, and also to import generics from e.g. stats4 which
was long ago provided for that purpose. (Re another message: stats4
*is* methodsGenerics for base packages.)
[*] at least now that it tells you which namespace is involved, unlike
the original version
On 26/02/2012 06:39, Martin Morgan wrote:
pkgA's NAMESPACE has
importFrom(graphics, plot)
exportClasses(A)
exportMethods(plot)
R/foo.R has
setClass(A)
setMethod(plot, A, function(x, y, ...) {})
During R CMD INSTALL pkgA_1.0.tar.gz we are told
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in
package 'pkgA'
** help
No man pages found in package ‘pkgA’
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pkgA)
pkgB has in its DESCRIPTION
Depends; pkgA
with NAMESPACE
importFrom(graphics, plot)
exportClasses(B)
exportMethods(plot)
R/bar.R has
setClass(B)
setMethod(plot, B, function(x, y, ...) {})
During R CMD INSTALL pkgB_1.0.tar.gz we are told
** preparing package for lazy loading
** help
i.e., no implicit generic created (because graphics::plot already has an
implicit generic created, when the pkgA dependency was attached?). and also
** testing if installed package can be loaded
Error : Functions for exporting methods must have been made generic,
explicitly or implicitly; not true when loading 'pkgB' for 'plot'
Error: loading failed
Execution halted
ERROR: loading failed
which doesn't seem accurate, rather 'pkgB' does not import S4 implicit
generic for 'plot' created by 'pkgA'
sessionInfo()
R Under development (unstable) (2012-02-25 r58492)
Platform: x86_64-unknown-linux-gnu (64-bit)
Martin
--
Brian D. Ripley, rip...@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, UKFax: +44 1865 272595
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