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.hor...@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.koncevic...@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.hor...@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.koncevic...@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 <gabembec...@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.koncevic...@gmail.com <mailto:karolis.koncevic...@gmail.com>
>>>>>> <mailto:karolis.koncevic...@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.koncevic...@gmail.com <mailto:karolis.koncevic...@gmail.com>
>>>>>>>>> <mailto:karolis.koncevic...@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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>>>>>>>> <mailto:R-devel@r-project.org> mailing list
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>>>>>>
>>>>
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