[Rd] R CMD INSTALL warning for S4 replacement functions on R 4.1.0-alpha

[Sebastian Meyer]

I can confirm this Rd warning in R-devel (2021-04-23 r80216), but not in
R 4.0.5. It happens when installing the static help (INSTALL option --html).

The following R code reproduces the warning by creating a tiny test
package and then calling relevant internal functions from 'tools':

```R

## create test package
dir.create(pkgdir <- tempfile())
tools:::.write_description(  # need a DESCRIPTION
    unlist(head(packageDescription("tools"), -1)),
    file.path(pkgdir, "DESCRIPTION"))
dir.create(file.path(pkgdir, "man"))
cat(r"(\name{test-package}
\title{Test Package}
\alias{\%/\%}
\description{Test alias.}
)", file = file.path(pkgdir, "man", "test-package.Rd"))

## build HTML help
dir.create(outDir <- tempfile())
tools:::.install_package_description(pkgdir, outDir)
tools:::.writePkgIndices(pkgdir, outDir)
tools:::.convertRdfiles(pkgdir, outDir, types = "html")


```

The output is

  converting help for package ‘tools’
    finding HTML links ... done
    test-package                            html
REDIRECT:topic	 %/% -> test-package.html [ FAIL ]
REDIRECT:file	 test-package.html -> test-package.html [ SUCCESS ]
Rd warning: cannot open file
'/tmp/RtmpasTPyq/fileb3d72f4ea1cf/help/%/%.html': No such file or directory


A workaround (if needed) is to set the environment variable
_R_HELP_LINKS_TO_TOPICS_ to a false value.

Best regards,

	Sebastian


Am 23.04.21 um 19:01 schrieb Felix Ernst:
> Hi all,
> 
> Since R 4.1, R CMD INSTALL throws warning during building the man pages, when installing from source.
> 
> We noticed this first on Windows for man pages involving S4 replacement function:
> 
>   *   http://bioconductor.org/checkResults/devel/bioc-LATEST/Modstrings/riesling1-checksrc.html
>   *   http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicAlignments/riesling1-checksrc.html
> 
> However, it's also showing up on linux with a slight twist (file not found instead of invalid argument) for other functions:
> 
>   *   https://cran.r-project.org/web/checks/check_results_Matrix.html (right at the end)
> 
> From the messages and the involved offending filenames, we hypothesize that this is triggered by invalid filenames specific to the OS.
> Please note, that the warning is not issued during R CMD CHECK for a given package.
> 
> Can anyone comment on this? Is more information needed? If it is a bug, I am happy to post on the bug tracker.
> 
> Thanks for any advice.
> 
> Best regards,
> Felix
> 
> 	[[alternative HTML version deleted]]
> 
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