From jmc at r-project.org  Tue Jun  7 19:06:03 2011
From: jmc at r-project.org (John Chambers)
Date: Tue, 07 Jun 2011 10:06:03 -0700
Subject: [Rd] Overloading S4 methods
In-Reply-To: <alpine.DEB.2.00.1106070812100.1796@luke-inspiron>
References: <BANLkTi=KwUzxy+3YA+HWmP-PPozD-g7zkg@mail.gmail.com>
	<4DE6631A.9010104@fhcrc.org>
	<BANLkTimCFhkqPq=3XowmiZVKDtwXhM4V3g@mail.gmail.com>
	<4DED467F.1080006@r-project.org>
	<alpine.DEB.2.00.1106070812100.1796@luke-inspiron>
Message-ID: <4DEE5A7B.8030903@r-project.org>

Yes, Dylan is in many ways more authoritarian than R!  Possibly also 
with fewer users to be annoyed.

We might go to a warning as Iago suggests.  If we did add a warning, it 
would be likely be more useful in the setMethod() call than at CMD check 
time, after the package has been designed and implemented.

John

On 6/7/11 6:15 AM, luke-tierney at uiowa.edu wrote:
> On Mon, 6 Jun 2011, John Chambers wrote:
>
>> This is a bug, medium-subtle, but also raises an interesting software
>> design point.
>>
>> The Bug:
>>
>> Nothing specific about "ANY" and "missing", but the issue is whether
>> the method was inherited (the "ANY" case) or defined directly (the
>> "missing" case).
>>
>> Generic functions keep a cached table of dispatched methods, to save
>> determining inherited methods repeatedly for calls with the same
>> signature. When pkg B is loaded, the inherited methods are reset, but
>> apparently the directly defined ones were not (but should have been if
>> pkg B overrides the method).
>>
>> It's interesting that this bug seems not to have been reported before,
>> which leads to:
>>
>> The Software Design Point:
>>
>> When a package (B) extends the class/method software in another
>> package (A), typically B adds new classes and perhaps new generic
>> functions with methods for previous classes in A as well as classes in
>> B. It might also extend the behavior for classes in A to other generic
>> functions.
>>
>> What is less usual is to directly override an existing method for a
>> class that belongs to A. Notice that there can be side-effects, such
>> as behavior of examples or tests in package A depending on whether B
>> has been loaded or not. And objects created entirely from A could have
>> their computations change after B was loaded.
>
> Dylan is simliar in using a generic funciton model. One of the Dylan
> books -- I forget which one -- strongly recomends that a library only
> define a method if either it also defines the generic or if it defines
> one of the classes the method is specialized on. THis isn't an enforced
> requirement but a strong recommendation.
>
> Best,
>
> luke
>
>>
>> Nothing at all illegal here, and we'll make it work. But a more
>> predictable implementation for most applications would, say, define a
>> new class in B that extended the class in A. In your example (very
>> helpful, by the way) one might have a class "mynumB", perhaps with the
>> same slots as "mynum" but with modified behavior.
>>
>> If you want to keep the current implementation, though, a workaround
>> until the bug is fixed would be something like:
>>
>> setMethod("plot", c("mynum", "missing"), getMethod("plot", c("mynum",
>> "missing")))
>>
>> executed after B is attached (I think it could be in the .onLoad
>> function for B, but have not tested that).
>>
>> John
>>
>>
>> On 6/6/11 4:11 AM, Iago Mosqueira wrote:
>>> On Wed, Jun 1, 2011 at 6:04 PM, Martin Morgan<mtmorgan at fhcrc.org> wrote:
>>>> On 06/01/2011 04:39 AM, Iago Mosqueira wrote:
>>>>>
>>>>> Dear all,
>>>>>
>>>>> I am experiencing some problems with S4 method overloading. I have
>>>>> defined a generic for graphics:plot, using
>>>>>
>>>>> setGeneric("plot", useAsDefault = plot)
>>>>>
>>>>> and with
>>>>>
>>>>> importFrom('graphics', 'plot') and
>>>>>
>>>>> exportMethods('plot') in the NAMESPACE file of pkg A.
>>>>
>>>> I'd guess you were creating two generics (explicitly in pkgA,
>>>> implicitly in
>>>> pkgB). Maybe
>>>>
>>>> export(plot)
>>>>
>>>> in NAMESPACE of pkg A,
>>>>
>>>> importFrom('pkgA', plot)
>>>> exportMethods(plot)
>>>>
>>>> in pkg B. Feel free to post to the list if that's helpful.
>>>>
>>>> Martin
>>>>
>>>>>
>>>>> I then proceed to define a method for signature c('myS4class',
>>>>> 'missing'). This works as expected: selectMethod('plot',
>>>>> c('myS4class', 'missing')) returns the newly defined method, and the
>>>>> method gets called when invoked.
>>>>>
>>>>> Another pkg, B, wishes to overload this and redefines the method for
>>>>> the same signature. A method is defined for c('myS4class', 'missing'),
>>>>> and exported on the NAMESPACE. The new method is shown by
>>>>> selectMethod() after pkg B has been loaded, but a call to
>>>>>
>>>>> plot(anobjectofmyS4class)
>>>>>
>>>>> comes up with the result of running the first method, from pkg A. I
>>>>> have tried importing 'plot' in B's NAMESPACE from both graphics or A,
>>>>> but the end result is the same.
>>>>>
>>>>> Package B does the same thing for a method created by pkg A, myMethod,
>>>>> and that works fine.
>>>>>
>>>>> Any pointers or where this might be going wrong? How is it that a
>>>>> different method than the one shown by selectMethod() is being run?
>>>>> Something to do with the 'missing' part of the signature?
>>>>>
>>>>> Many thanks,
>>>>>
>>>>>
>>>>>
>>>>> Iago Mosqueira
>>>
>>> Dear all,
>>>
>>> I have tried Martin's suggestion, but the problem persists. It seems
>>> to be related to having 'missing' in the signature, as doing the same
>>> kind of overloading for c('myclass', 'ANY') work as expected.
>>>
>>> I am attaching 2 simple packages where I attempt this repeated
>>> overloading of plot for the same class. Script below, also found in
>>> Bpkg/tests.test.R, shows what I have encountered so far:
>>> plot('myclass', 'ANY') can be re-overloaded, but plot('myclass',
>>> 'missing') cannot in the same way. If I run
>>>
>>> trace("plot", browser, exit=browser, signature = c("mynum", "missing"))
>>>
>>> the new method is actually called.
>>>
>>> Any hint on what I am doing wrong or where to look for an explanation
>>> will be much appreciated.
>>>
>>> Best regards,
>>>
>>>
>>> Iago Mosqueira
>>>
>>>
>>>
>>> ______________________________________________
>>> 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
>>
>



[Rd] Overloading S4 methods
John Chambers