[R-pkg-devel] Recent dev version of R CMD check fails when a package function named X also has a parameter named X

[Deepayan Sarkar]

On Mon, 30 Oct 2023 at 12:48, Markus Jochim
<markusjochim using phonetik.uni-muenchen.de> wrote:
>
> Hi R people,
>
> I am the maintainer of the emuR package and I am having a problem with
> recent versions of R CMD check.
>
> CRAN‘s r-devel test suites [1] have started to emit a NOTE about the
> HTML version of the manual:
>
> > Version: 2.4.1
> > Check: HTML version of manual
> > Result: NOTE
> >     Found the following HTML validation problems:
> >     query.html:50:9 (query.Rd:22): Warning: <code> anchor "query"
> > already defined
> > Flavors: r-devel-linux-x86_64-debian-clang,
> > r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang,
> > r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
> >
> This is caused by one of my package’s functions that is named query and
> also has a parameter named query.
>
> I think I have tracked this down to SVN revision r85407 of R. With
> earlier versions:
>
> R CMD Rdconv -t html query.Rd
>
> would output (line 50, as referenced by the NOTE):
>
> <tr><td><code id="query_:_query">query</code></td>
>
> But newer versions output:
>
> <tr><td><code id="query">query</code></td>

Yes, sorry, my bad.

r85440 (just committed) should have a temporary fix by omitting the id
from the <h2> title. Please let me know if problems still persist.

Best,
-Deepayan

> Notice the difference in id. The id "query" appears both here and
> further up in the file, specifically in the h2 heading. This triggers
> the HTML validation problem. I suppose this is a bug in the experimental
> table of contents feature? As such, should I rather post this to R-devel?
>
> Unfortunately, this also prevents me from uploading a new version of my
> package, since it does not get past CRAN’s automatic pretest. Can I
> resubmit my new version and simply state in the comments that I cannot
> fix the NOTE from r-devel at this point? Or should I rather wait until
> this is changed upstream? (the described NOTE is the only complaint from
> the pretest). Changing the function or parameter name is not an option,
> they have been used in this package ever since it was released a couple
> of years ago.
>
> This NOTE can also be reproduced with a minimal R package that has
> nothing but a hello function with a parameter named hello.
>
> Thanks for reading this. I appreciate any help.
>
> Markus
>
>
> Institute for Phonetics and Speech Processing
>
> Ludwig-Maximilians-Universität München
>
> https://www.phonetik.uni-muenchen.de
>
>
> [1] https://cran.rstudio.com//web/checks/check_results_emuR.html
>
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