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

Martin Morgan m@rtin@morg@n @ending from ro@wellp@rk@org
Sat May 12 15:11:27 CEST 2018

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[]{}


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


Hope that helps


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

This email message may contain legally privileged and/or...{{dropped:2}}

More information about the Bioc-devel mailing list