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 .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
functiona
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 s
