[Bioc-devel] Unexpected Warning About Cross-Reference Without Package Specification

[Martin Morgan]

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
> 
> 
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 


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