From hb at biostat.ucsf.edu  Fri Aug 30 21:47:27 2013
From: hb at biostat.ucsf.edu (Henrik Bengtsson)
Date: Fri, 30 Aug 2013 12:47:27 -0700
Subject: [Rd] "False" warning on "replacing previous import" when
 re-exporting identical object
In-Reply-To: <CAFDcVCTg6Sc91gDZwwrjJnTHxXwuqk45GwckLSYVUT2FQ9GJLg@mail.gmail.com>
References: <b0soje9u9ai23iirnopichs6.1377871104139@email.android.com>
	<CAFDcVCTg6Sc91gDZwwrjJnTHxXwuqk45GwckLSYVUT2FQ9GJLg@mail.gmail.com>
Message-ID: <CAFDcVCSsd0KcZCCRv0f-MzUU__PJE9ZkrGF4jxy7dZS9Ci1Wyg@mail.gmail.com>

On Fri, Aug 30, 2013 at 11:51 AM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
> Hi.
>
> On Fri, Aug 30, 2013 at 6:58 AM, Paul Gilbert <pgilbert902 at gmail.com> wrote:
>> 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.)
>
> 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],
> simply because it detects that "foo" (=n) has already been imported to
> PkgC' namespace (=impenv):
>
> if (exists(n, envir = impenv, inherits = FALSE)) {
>     if (.isMethodsDispatchOn() && methods:::isGeneric(n, ns)) {
>         ## warn only if generic overwrites a function which
>         ## it was not derived from
>         ...
>     }
>     warning(sprintf(msg, sQuote(paste(nsname, n, sep = "::")),
> sQuote(from)), call. = FALSE, domain = NA)
> }
>
> 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.
>
>>svn diff namespace.R
> Index: namespace.R
> ===================================================================
> --- namespace.R (revision 63776)
> +++ namespace.R (working copy)
> @@ -871,6 +871,10 @@
>      }
>      for (n in impnames)
>         if (exists(n, envir = impenv, inherits = FALSE)) {
> +            ## warn only if imported variable actually exists in the
> +            ## namespace imported from, which is not the case if
> +            ## the variable is rexported from another namespace
> +            if (!exists(n, envir = ns, inherits = FALSE)) next
>             if (.isMethodsDispatchOn() && methods:::isGeneric(n, ns)) {
>                 ## warn only if generic overwrites a function which
>                 ## it was not derived from

Ok, if import(PkgA, PkgB) and PkgB reexports a *different* foo() than
PkgA::foo(), say PkgZ::foo so identical(PkgB::foo, PkgA::foo) is
FALSE, then there is indeed a conflict.  An alternative patch:

>svn diff namespace.R
Index: namespace.R
===================================================================
--- namespace.R (revision 63776)
+++ namespace.R (working copy)
@@ -871,6 +871,11 @@
     }
     for (n in impnames)
        if (exists(n, envir = impenv, inherits = FALSE)) {
+            ## warn only if imported variable is non-identical to
+            ## the one already imported
+            getImp <- get(n, envir = impenv)
+            obj <- get(n, envir = ns)
+            if (identical(obj, getImp)) next
            if (.isMethodsDispatchOn() && methods:::isGeneric(n, ns)) {
                ## warn only if generic overwrites a function which
                ## it was not derived from

/Henrik

>
> I'm planning to propose ("wishlist / enhancement"; it may even be a
> bug) this over at https://bugs.r-project.org/.
>
> Comments, anyone?
>
> /Henrik
>
>
>> 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



[Rd] "False" warning on "replacing previous import" when re-exporting identical object
Henrik Bengtsson