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