From simon.urbanek at r-project.org  Thu Aug 26 18:46:33 2010
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Thu, 26 Aug 2010 12:46:33 -0400
Subject: [Rd] RCMD CHECK and non-methods
In-Reply-To: <19574.35318.774118.197785@lynne.math.ethz.ch>
References: <62C82B39B8A85E4B95A18F7F7B852F870576DBBB76@exvic-mbx03.nexus.csiro.au>
	<19574.35318.774118.197785@lynne.math.ethz.ch>
Message-ID: <80CFAA95-BC98-47AE-8A16-9CB753880E7D@r-project.org>


On Aug 26, 2010, at 11:36 AM, Martin Maechler wrote:

>>>>>>  <Mark.Bravington at csiro.au>
>>>>>>    on Wed, 25 Aug 2010 14:06:07 +1000 writes:
> 
>> I recently moved a function 'subset.with.warning' into the 'mvbutils' package (a version not yet on CRAN). When I tried RCMD CHECK, I got this warning:
>> * checking S3 generic/method consistency ... WARNING
>> subset:
>> function(x, ...)
>> subset.with.warning:
>> function(x, cond, mess.head, mess.cond, row.info, sub)
> 
>> See section 'Generic functions and methods' of the 'Writing R Extensions'
>> manual.
> 
>> I know that S3 method arguments need to be compatible with arguments of the generic. However, 'subset.with.warning' is deliberately not a registered S3 method, 
> 
> I think that's your real trouble ... and then your users' if you
> really insist.
> Short answer:  "Don't do that!"
> 
> There have been a few exceptions of "100 years old" R functions
> which validated this rule,
> the most notable probably  t() and t.test(),
> and we (R core) have explicitly listed them in the code base
> as "yes, looks like a method for an S3 generic, but not it ain't!",
> but have basically "forbidden" to commit more such crimes.
> {Also, if you are interested: I think both  t() and t.test()
> pre-dated S3}
> 

However, one would hope that S3 will be replaced by S4 (or R5? ;)) eventually so requiring such an arcane rule seems little strong. Personally, I prefer the use of . to that of camelCase [I find it more readable and faster to type] and thus I'm with Mark on this one. IMHO it is perfectly legal and clean to declare a symbol as a function and not an S3 method.

Cheers,
Simon



> 
>> and its USAGE section doesn't include a \method{generic}{class} statement. I couldn't see anything in "R Extensions" that says "don't do this", so I'm wondering: 
> 
> Yes, we should add a such "don't do this" somewhere.
> 
> Can you propose a good place to put it in there?
> 
>> - should this really be a NOTE not a WARNING (or nothing at all)?
> 
> {from the above: definitely a warning, if not "worse"}....
> 
> Best regards,
> Martin 
> 
> Martin Maechler, ETH Zurich
> 
>> - if not, shouldn't there be a more explicit statement to the effect that "if R decides it's a method, then it damned well is a method, whether you think it is or not"?
> 
>> - and if so, should there also be a check for functions that look like methods but aren't registered and declared as such?
> 
>> My preference would be for the first, FWIW. Admittedly, just because I didn't register 'subset.with.warning' as an S3 method, that won't stop 'subset' from trying to use it if it ever encounters an object of class "with.warning". It's a risk that I'm happy to take, though CRAN might not be...
> 
>> I made the warning go away by adding a '...' argument to the end of 'subset.with.warning', but that's not pretty.
> 
>> Mark Bravington
>> CSIRO
>> Hobart
>> Australia
> 
>>> sessionInfo()
>> R version 2.11.1 Patched (2010-06-30 r52418) 
>> i386-pc-mingw32 
> 
>> locale:
>> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
>> [5] LC_TIME=English_Australia.1252    
> 
>> attached base packages:
>> [1] grDevices tools     tcltk     stats     graphics  utils     methods   base     
> 
>> other attached packages:
>> [1] ad_1.0         chstuff_1.0    handy2_1.2     tweedie_2.0.2  statmod_1.4.1  handy_1.1      debug_1.2.3    mvbutils_2.5.2
>>> 
> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> ______________________________________________
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> 
> 



[Rd] RCMD CHECK and non-methods
Simon Urbanek