Manuals generated by bioconductor includes internal functions

[oganm]

This was discussed in the bioc-devel mailing list this month under "Excluding internal functions from package manual".

I was trying to find a way to exclude documenting package internals in the reference files created by bioconductor and was told that R CMD check that bioconductor runs in the build procedure deliberately (?) runs Rd2pdf with --internals option. I am unsure if this behaviour is actually desirable or just an artefact of history but it does cause quite a bit of clutter in the reference pdfs if one elects to document internal functions and it would be nice to have a way not having that.

In contrast, reference pdfs built by CRAN does not include internal functions.

[hpages]

See https://stat.ethz.ch/pipermail/bioc-devel/2025-February/020835.html for my attempt at describing what's going on.

[oganm]

I should add that one reason we document internal functions, apart from ease of development is inheritance. We have several functions that use the same internal functions to process an output. To avoid keeping multiple copies of the same information that we'd have to manually update, we inherit the return documentation from these internal functions which would make it quite disruptive to remove internal documentation

[jwokaty]

@oganm Thanks for your comment and opening this issue. I plan to address it but may not get to it until after the release.