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

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>

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-Universit?t M?nchen

https://www.phonetik.uni-muenchen.de


[1] https://cran.rstudio.com//web/checks/check_results_emuR.html