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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