[Rd] Should '@" now be listed in tools:::.get_internal_S3_generics() ?

[Karolis Koncevičius]

Ah, you are correct, my bad and apologies. I forgot that table is only for available methods, not for available generics.

KK.

> On Apr 30, 2023, at 4:49 PM, Kurt Hornik <Kurt.Hornik using wu.ac.at> wrote:
> 
>>>>>> Karolis Koncevičius writes:
> 
>> But this might require a more detailed investigation. For example I
>> just noticed that even with the patch `@` is still not listed in
>> .S3_methods_table().
> 
> Afaict base does not register any methods for @ or @<- ?
> 
> -k
> 
>> KK.
> 
>>> On Apr 29, 2023, at 4:44 PM, Karolis Koncevičius <karolis.koncevicius using gmail.com> wrote:
>>> 
>>> Hello Kurt,
>>> 
>>> With r84341 it now works on my side.
>>> 
>>> Warm regards,
>>> Karolis K.
>>> 
>>>> On Apr 29, 2023, at 1:24 PM, Kurt Hornik <Kurt.Hornik using wu.ac.at> wrote:
>>>> 
>>>>>>>>> Karolis Koncevičius writes:
>>>> 
>>>> Can you pls try again with r84341 or later?
>>>> 
>>>> Best
>>>> -k
>>>> 
>>>>> A more concrete example in order to correct my vague messages below.
>>>>> Writing an R package that uses `@` and `@<-` as S3 generics. Line from manual pages in .Rd files:
>>>> 
>>>>> \method{@}{newclass}(object, name) <- value
>>>> 
>>>>> Throws this error during R CMD check —as-cran
>>>> 
>>>>> Bad \usage lines found in documentation object ’code’:
>>>>> <unescaped bksl>method{@}{newclass}(object, name) <- value
>>>> 
>>>>> This error is due to tools::checkDocFiles eventually calling tools:::.S3_method_markup_regexp and not finding `@` as a valid for S3.
>>>>> This error is gone if we adjust tools:::.S3_method_markup_regexp to pass for ‘@‘ by adding ‘\\@‘ to regexp.
>>>> 
>>>>> Please note that this now is not dependant on using or not using roxygen2
>>>>> KK.
>>>> 
>>>>>> On Apr 29, 2023, at 12:53 AM, Karolis Koncevičius <karolis.koncevicius using gmail.com> wrote:
>>>>>> 
>>>>>> Thank you for such a quick reply, Gabriel,
>>>>>> 
>>>>>> I am not too familiar with the package tools, so cannot speak too confidently, but below is how I see the issue currently.
>>>>>> 
>>>>>> The issue is not for external packages to rely on unexported functions from tools::, rather the issue is that 'R CMD check —as-cran' runs those functions from tools:: in order to check the validity of Rd files (from any package). R 4.3.0 added @ as internal S3 generic. However, package tools does not recognise it as valid in Rd files and throws errors when it sees S3 method declared for @ in the Rd usage lines.
>>>>>> 
>>>>>> So any package that will try to use @ generic will run into the issue, without attempting to use internal S3 functions in their code, but during the R CMD check step.
>>>>>> 
>>>>>> Hope I am being clearer now, and not missing something important (all these things: both @ as generic and tools:: package are quite new to me),
>>>>>> Karolis K.
>>>>>> 
>>>>>> On Apr 29, 2023, at 12:38 AM, Gabriel Becker <gabembecker using gmail.com> wrote:
>>>>>> 
>>>>>> Karolis,
>>>>>> 
>>>>>> It seems likely, without having looked myself, that you could be correct about the issue, but it does seem worth noting that both of the functions you have mentioned are not exported, and thus not part of the API that extension packages are allowed to use and rely on.
>>>>>> 
>>>>>> If retrieving the list of "internal S3 generics" is something package and user code is allowed to do, the real fix seems to go beyond what you're suggesting, to actually providing an API entry point that gives the relevant information (maybe in an identical form to how those internal functions do so, maybe not). If it's not, for some principled reason, something R-core wants to support package and user code doing, then the fact that the new thing doesn't work automatically with roxygen2 would become the roxygen maintainers' job to fix or document. 
>>>>>> 
>>>>>> I do not know whether R-core feels this is something packages/users should be able to do; both decisions strike me as possible, to be honest, depending on details I don't know and/or am not privy to.
>>>>>> 
>>>>>> Best,
>>>>>> ~G 
>>>>>> 
>>>>>> On Fri, Apr 28, 2023 at 1:49 PM Karolis Koncevičius <karolis.koncevicius using gmail.com <mailto:karolis.koncevicius using gmail.com> <mailto:karolis.koncevicius using gmail.com>> wrote:
>>>>>>>> This issue might go deeper - I was not successful in passing R CMD checks for the usage files. R CMD check kept showing errors for `@` declarations, even thou they were identical to `$` declarations (which passed fine).
>>>>>>>> 
>>>>>>>> Seems like the usage check functions are not prepared for `@` - also in tools:::.S3_method_markup_regexp
>>>>>>>> 
>>>>>>>>> On Apr 28, 2023, at 10:34 PM, Karolis Koncevičius <karolis.koncevicius using gmail.com <mailto:karolis.koncevicius using gmail.com> <mailto:karolis.koncevicius using gmail.com>> wrote:
>>>>>>>>> 
>>>>>>>>> I was building a package that uses the new generic @ and kept having errors with “roxygen2” documentation. “roxygen2” generated NAMESPACE added `@.newclass` as a newly exported function, not as a S3method.
>>>>>>>>> 
>>>>>>>>> At first I thought this must be a bug in roxygen2 and they lag behind the new developments in R. But after some investigation I found that “roxygen2” is using tools:::.get_internal_S3_generis() to decide if the method should be exported as S3method or not. For some reason “@<-“ is listed in there, but “@“ is not.
>>>>>>>>> 
>>>>>>>>> Am I missing some context, or is this an oversight?
>>>>>>>>> 
>>>>>>>>> Kind regards,
>>>>>>>>> Karolis Koncevicius
>>>>>>>> 
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