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().
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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>>>>
>>
>>
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