[Bioc-devel] Warnings on R CMD check on Mac OS and Linux

[Hervé Pagès]

Hi,

I don't see that you have aliases for these symbols, hence the warning:

   hpages using spectre:~/cyanoFilter/man$ grep 'alias{PhytoFilter}' *.Rd
   hpages using spectre:~/cyanoFilter/man$ grep 'alias{clusterExtract}' *.Rd
   etc...

Note that even though you have aliases for some PhytoFilter **methods**:

   hpages using spectre:~/cyanoFilter/man$ grep -w PhytoFilter *.Rd | grep 
alias | grep method
 
fullFlowframe-PhytoFilter-method.Rd:\alias{fullFlowframe,PhytoFilter-method}
   plot-PhytoFilter-ANY-method.Rd:\alias{plot,PhytoFilter,ANY-method}
 
reducedFlowframe-PhytoFilter-method.Rd:\alias{reducedFlowframe,PhytoFilter-method}


here 'R CMD check' is complaining about the lack of an alias for the 
PhytoFilter **object** (which turns out to be a function). Since you 
export this symbol (via the export(PhytoFilter) directive in your 
NAMESPACE file), you need to provide an alias for it in one of your man 
pages.

Hope this helps,

H.


On 3/8/21 2:45 PM, Oluwafemi OLUSOJI via Bioc-devel wrote:
> Dear All,
> 
> I get this warning on the latest update of my package. The warning occurs
> only with Mac and Linux. I am a bit at loss here. These errors don't
> actually exist because these functions and methods are properly documented.
> The missing link doesn't even exist anymore.
> 
> I have rebuilt both the documentation and rebuilt the source. R CMD check
> and R CMS check --as.cran doesn't report either on my system as well. I
> will appreciate any heads-up here.
> 
> Regards,
> Daniel
> 
> 
> Missing link or links in documentation object 'oneDgate.Rd':
>    getChannel
> 
> See section 'Cross-references' in the 'Writing R Extensions' manual.
> * checking for missing documentation entries ... WARNING
> Undocumented code objects:
>    PhytoFilter clusterExtract clusterExtractp debrisNc
>    getChannel newFlowframe newFlowframe2 pairsPlot pigmentGate
>    reducedFlowframe rowNumbers summaries
> Undocumented S4 methods:
>    generic 'summaries' and siglist 'DebrisFilter'
>    generic 'summaries' and siglist 'MarginEvents'
>    generic 'summaries' and siglist 'PhytoFilter'
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
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> 

-- 
Hervé Pagès

Bioconductor Core Team
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