Hi Burak,
AFAIK 'R CMD build' doesn't generate the PDF of the reference manual but
'R CMD check' does (it puts the manual in the <pkg>.Rcheck folder). This
is the manual that we propagate to the package landing pages, and it
seems that it does indeed include the man pages of the internal
functionality, that is, the man pages that contain \keyword{internal}.
I investigated this and here is what I found:
- The reference manual can also be generated with 'R CMD Rd2pdf'.
- The Rd2pdf command does NOT include the man pages of the internal
functionality by default. To include them, one needs to specify the
--internals option. See 'R CMD Rd2pdf --help'.
- 'R CMD check' actually uses the Rd2pdf command internally to generate
the manual but for some reason it calls it with the --internals option.
Propagation of the PDF manuals generated by 'R CMD check' was
implemented a long time ago as part of our build system. I guess the
reason for doing it that way was because it was the simplest way to go.
Maybe at the time 'R CMD check' was NOT calling Rd2pdf with the
--internals option, so everything was fine, and the option was added
later in more recent versions of R, I don't know (I didn't search R NEWS
file for that).
I don't know if there's an easy fix besides refactoring slightly the
build system to include our own Rd2pdf step to generate the PDFs. Maybe
you want to open an issue at https://github.com/Bioconductor/BBS/issues
to discuss this further with the BBS maintainers.
Best,
H.
On 13/02/2025 16:48, Burak Ogan Mancarci wrote:
I maintain gemma.R in bioconductor, a package with quite a few internal
functions with documentation. In CRAN, functions that are not exported are
not included in the reference pdf that is generated, however in
Bioconductor, we seem to have all documented functions included. I have
been trying to see if there's a difference I can identify but from the
build logs in bioconductor I see that packages are built using
R CMD build --keep-empty-dirs --no-resave-data --md5 gemma.R
which generates a reference pdf without internal functions.
I am wondering what I am missing here and if there is a way to exclude
these internal functions from the reference. I have checked a few other
packages to see how they are handling the issue but I could only see the
internals being left undocumented entirely
Cheers,
Ogan
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