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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