[Bioc-devel] R CMD check WARNING file link 'x' in package 'y' does not exist and so has been treated as a topic

Leif Wigge |e||@w|gge @end|ng |rom ch@|mer@@@e
Fri Apr 26 13:53:34 CEST 2019

Dear all,

I’ve had some trouble clearing the WARNING from R CMD check on tokay2 for my package piano (http://bioconductor.org/checkResults/3.9/bioc-LATEST/piano/tokay2-checksrc.html
). As an example, I get this warning:

Rd warning in diffExp.Rd:75: “file link '01.Introduction' in package 'limma' does not exist and so has been treated as a topic”

I have been trying to fix this over the last week but I cannot reproduce the warning on my system and therefore had to rely on iterating fixes and waiting for the check report on Bioconductor.org, which has been a bit slow for obvious reasons. I hope this WARNING will not prevent piano from being included in the next release, as it is “only” a documentation issue?

I have followed the solution provided here: https://stackoverflow.com/questions/48430093/how-do-i-resolve-rd-warning-missing-file-link-when-building-packages-in-rstudi
This basically involves making cross-links in the Rd-files like this: \link[pkg:foo]{bar}, where foo is the ‘file’, pkg is the package and bar is the link text. As an example, I have in diffExp.Rd:75: \link[limma:01.Introduction]{limma}. This link works fine on my system and shows the limma package introduction page if one clicks the link.

In addition, in my R console, commands: ?limma, ?`01.Introduction` and ?limma::`01.Introduction` all show the same help page, at the top displaying “01.Introduction {limma}”.

Does anyone have any pointers as how to properly format these links in Rd files to avoid the WARNING mentioned above?

Thanks for any help!

Kind regards

Leif Väremo Wigge

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