Thank you, the reproducible example helps one think through things.
For what it's worth the warning can be generated via
> tools:::.check_Rd_xrefs(dir = "~/Downloads/Tester")
Looking at the code and reflecting on the issue, since limma is in the
Suggests: field, it is not guaranteed to be installed on a system where
the Tester package is installed. So in general the help system cannot
resolve the link to a file; it requires additional hints on where the
documentation will be. Hence the need for \link[limma]{lmFit}.
I think the phrase "not-yet-installed packages" in section 2.5 of
Writing R Extensions is to be interpreted as 'not-yet-installed by
Tester and its implied dependencies".
As with the earlier discussion of \link[]{}
https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
it seems like in this case the WARNING is a non-issue -- my
understanding is that the link will resolve dynamically at run time (if
limma is installed) or not at all (if limma is not installed) regardless
of use of [limma]. If one wanted to follow up further the best place
would probably be
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Hope that helps
Marti
On 05/12/2018 02:00 AM, Dario Strbenac wrote:
Good day,
I created a minimalist package that demonstrates the issue and it is attached
to this letter. After using R CMD build, the subsequent R CMD check process
emits one warning.
--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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