R devel - Aug 2013 - "False" warning on "replacing previous import" when re-exporting identical object

Hi,

SETUP:
Consider three packages PkgA, PkgB and PkgC.

PkgA defines a generic function foo() and exports it;

export(foo)

PkgB imports PkgA::foo() and re-exports it;

importFrom(PkgA, foo)
export(foo)

PkgC imports everything from PkgA and PkgB:

imports(PkgA, PkgB)


PROBLEM:
Loading or attaching the namespace of PkgC will generate a warning:

  replacing previous import by 'PkgA::foo' when loading 'PkgC'

This in turn causes 'R CMD check' on PkgC to generate a WARNING (no-go
at CRAN):

* checking whether package 'PkgC' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import by 'PkgA::foo' when loading
'CellularAutomaton'


FALSE?
Isn't it valid to argue that this is a "false" warning, because
identical(PkgB::foo, PkgA::foo) is TRUE and therefore has no effect?


/Henrik

PS. The above can be avoided by using explicit importFrom() on PkgA
and PkgB, but that's really tedious.  In my case this is out of my
reach, because I'm the author of PkgA and PkgB but not many of the
PkgC packages.

This is related to the recent thread on correct NAMESPACE approach when writing
S3 methods. If your methods are S4 I think pkgB does not need to export the
generic. Just export the method and everything works magically and your problem
disappears. For S3 methods there seems to be the difficultly you describe. Of
course, the difference between S3 and S4 on this appears somewhat bug like. (I
have not tested all this very carefully so I may have something wrong.)
Paul

Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
>Hi,
>
>SETUP:
>Consider three packages PkgA, PkgB and PkgC.
>
>PkgA defines a generic function foo() and exports it;
>
>export(foo)
>
>PkgB imports PkgA::foo() and re-exports it;
>
>importFrom(PkgA, foo)
>export(foo)
>
>PkgC imports everything from PkgA and PkgB:
>
>imports(PkgA, PkgB)
>
>
>PROBLEM:
>Loading or attaching the namespace of PkgC will generate a warning:
>
>  replacing previous import by 'PkgA::foo' when loading
'PkgC'
>
>This in turn causes 'R CMD check' on PkgC to generate a WARNING
(no-go at CRAN):
>
>* checking whether package 'PkgC' can be installed ... WARNING
>Found the following significant warnings:
>  Warning: replacing previous import by 'PkgA::foo' when loading
>'CellularAutomaton'
>
>
>FALSE?
>Isn't it valid to argue that this is a "false" warning,
because
>identical(PkgB::foo, PkgA::foo) is TRUE and therefore has no effect?
>
>
>/Henrik
>
>PS. The above can be avoided by using explicit importFrom() on PkgA
>and PkgB, but that's really tedious.  In my case this is out of my
>reach, because I'm the author of PkgA and PkgB but not many of the
>PkgC packages.
>
>______________________________________________
>R-devel at r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-devel

Henrik Bengtsson <hb <at> biostat.ucsf.edu> writes:
> 
> On Fri, Aug 30, 2013 at 11:51 AM, Henrik Bengtsson 
> <hb <at> biostat.ucsf.edu> wrote:
> > Hi.
[snip]

  Bump ... Henrik, did you ever post this as a request/wishlist at
https://bugs.r-project.org/bugzilla3/ ?  (I don't think so, I couldn't
find it there, but maybe I wasn't looking in the right place.) I
would be curious to know what the response was from R-Core, because
these kinds of warnings are starting to pop up in the nlme/lme4/
downstream package complex.  In particular, 

VarCorr
fixef
lmList
ranef

are defined by nlme, imported and re-exported by lme4.  This doesn't
seem to make any trouble for lme4, but it does cause problems for
some of the downstream packages (such as GRRGI:
[broken URL for Gmane]
http://www.r-project.org/nosvn/R.check/
 r-devel-linux-x86_64-fedora-gcc/GRRGI-00check.html )

(Right now GRRGI uses a pretty crude import-all strategy:
import(nlme,lme4,...); exportPattern("."); which might be
tweaked, but I think the issue is still worth resolving.)

  In a perfect world, I guess some of these generics would be moved
upstream to a package that both nlme and lme4 could import from,
but that seems tricky to do without making fairly major architectural
changes.

  Ben Bolker

> > For the record, you're referring to R-devel thread 'Correct
NAMESPACE
> > approach when writing an S3 method for a generic in another
package'
> > started on Aug 24, 2013
> > [https://stat.ethz.ch/pipermail/r-devel/2013-August/067221.html].
> > Yes, it's closely related or possibly the same issue.  However, I
do
> > not find it odd that the S3 generic function needs to be exported
> > from/available via the namespace.  Hence it needs to be export():ed by
> > at least one package/namespace.
> >
> > The real issue is when two package needs to export a generic function
> > with the same name, e.g. foo().   If the two generic functions are
> > defined differently (e.g. different arguments/signatures), they will
> > be in conflict with each other.  If they are identical, this should
> > not be a problem, but here I might be wrong.  However, there is also
> > the special case where one package reexports the generic function from
> > another package, e.g. PkgB::foo() exports PkgA:foo().  In this case,
> > the object 'foo' does actually not existing in the name space
of
> > package PkgB - instead it provides a "redirect" to it, e.g.
> >
> >> PkgA::foo
> > function (...)
> > UseMethod("foo")
> > <environment: namespace:PkgA>
> >
> >> PkgB::foo
> > function (...)
> > UseMethod("foo")
> > <environment: namespace:PkgA>
> >
> >> exists("foo", envir=getNamespace("PkgB"),
inherits=FALSE)
> > [1] FALSE
> >
> >> exists("foo", envir=getNamespace("PkgB"),
inherits=TRUE)
> > [1] TRUE
> >
> >> identical(PkgB::foo, PkgA::foo)
> > [1] TRUE
> >
> >
> > The warning on "replacing previous import by 'PkgA::foo'
when loading
> > 'PkgC'" that occurs due to import(PkgA, PkgB) is
generated in
> > base::namespaceImportFrom()
> > [http://svn.r-project.org/R/trunk/src/library/base/R/namespace.R]
> > Note how there is already code for avoiding "false" warnings
on S4
> > generic function.  This is what we'd like to have also for S3
generic
> > functions, but it's much harder to test for such since they're
not
> > formally defined.  However, I'd argue that it is safe to skip the
> > warning *when the variable to be imported does not actually exist in
> > the package being imported* (e.g. when just rexported), i.e.
> >