[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
Mon Apr 29 08:30:33 CEST 2019

Dear Benjamin,

Thanks for the pointers! I adopted your solution and it now passes the check on tokay2 as well! Thanks!

All the best


On 2019-04-26, 15:51, "Benjamin Tremblay" <b2trembl using uwaterloo.ca> wrote:

    I’ve actually had the exact same problem. The solution for me was to change \link[pkg:foo]{bar} where foo is the actual .Rd filename in the original package. Downloading the limma source reveals there is an Rd file named 01Introduction.Rd, without the dot as you had it. So it would look like:
    Hopefully this works for you.
    Benjamin Tremblay
    > Le 26 avr. 2019 à 07:53, Leif Wigge <leif.wigge using chalmers.se> a écrit :
    > 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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