>>>>> 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
>> <[email protected]> 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 <[email protected]> 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
>>> <[email protected] <mailto:[email protected]>>
>>> 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
>>>> > <[email protected] <mailto:[email protected]>>
>>>> > 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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>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
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