[R-pkg-devel] "apparent S3 methods" note in R CMD check

[Roebuck,Paul L]

Actually, between this and other things coming from 'R CMD check' these
days,
I disagree that this is reasonable at all - it's a hack at best that only
fixes
this particular issue. Better would be to introduce lint-like directives
that
turn off certain R CMD check notes/warnings at different scopes
(e.g., #pylint: disable=some-message,another-one) rather than introduce
individual workarounds. Would give us an extensible version of the
"--no-nanny"
option Kevin wants.


On 6/12/15 5:38 AM, "John Fox" <jfox at mcmaster.ca> wrote:

>Dear Martin,
>
>Thank you for addressing this issue. Introducing a nonS3method()
>directive in NAMESPACE
>seems a reasonable solution. It could replace export() for functions with
>"."s in their names.
>
>Best,
> John
>
>On Fri, 12 Jun 2015 09:55:18 +0200
> Martin Maechler <maechler at stat.math.ethz.ch> wrote:
>> >>>>> John Fox <jfox at mcmaster.ca>
>> >>>>>     on Wed, 10 Jun 2015 10:12:46 -0400 writes:
>> 
>>     > Dear list members,
>>     > One of the packages I maintain, effects, generates the following
>>note in R
>>     > CMD check:
>> 
>>     > * checking S3 generic/method consistency ... NOTE
>>     > Found the following apparent S3 methods exported but not
>>registered:
>>     > all.effects
>> 
>>     > The offending function, all.effects(), is deprecated in favour of
>>     > allEffects(), but I'd rather not get rid of it for backwards
>>compatibility.
>>     > Is there any way to suppress the note without removing
>>all.effects()? 
>> 
>>     > To be clear, all.effects() is *not* a method of all(), and is
>>defined as
>> 
>>     >> effects::all.effects
>>     > function (...)
>>     > {
>>     >  .Deprecated("allEffects")
>>     >  allEffects(...)
>>     > }
>> 
>> Dear John,
>> this is a good question without an obvious answer for the
>> moment.
>> 
>> The check producing it is relatively new *and* has helped to
>> detect problems in many packages and places,  but I would agree
>> is a "False Positive" in this case.
>> 
>> One reason for such a check is the following output {in R >= 3.2.0},
>> 
>>  > require("effects")
>>  Loading required package: effects
>>  > methods(all)
>>  [1] all,ddiMatrix-method     all,ldiMatrix-method
>>all,lsparseMatrix-method
>>  [4] all,Matrix-method        all,nsparseMatrix-method all.effects
>>       
>>  see '?methods' for accessing help and source code
>>  >
>> 
>> which wrongly does list your all.effects() among the all
>> methods.... and indeed (even worse), it *is* taken as S3 method
>> for all():
>>  
>>  > ex <- structure(FALSE, class="effects")
>>  > all(ex)
>>  Error: $ operator is invalid for atomic vectors
>>  In addition: Warning message:
>>  'all.effects' is deprecated.
>>  Use 'allEffects' instead.
>>  See help("Deprecated")
>>  > 
>> 
>> ---
>> 
>> Now I agree .. and have e-talked about this with another R core
>> member .. that it would be desirable for the package author to
>> effectively declare the fact that such a function is not an S3
>> method even though it "looks like it" at least if looked from far.
>> 
>> So, ideally, you could have something like
>> 
>>  nonS3method("all.effects")
>> 
>> somewhere in your package source ( in NAMESPACE or R/*.R )
>> which would tell the package-checking code -- but *ALSO* all the other
>>S3
>> method code that  all.effects should be treated as a regular R
>> function.
>> 
>> I would very much like such a feature in R, and for that reason,
>> I'm cross posting this (as one of the famous exceptions that
>> accompany real-life rules!!) to R-devel.
>> 
>> There is one current work-around -- some would say "hack" -- in the R
>>sources
>> for exceptions on a per package basis, and I will now activate
>> that workaround for you.
>> 
>> Martin
>>
>
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