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

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Thu Mar 11 03:10:54 CET 2021


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

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

   hpages using spectre:~/cyanoFilter/man$ grep -w PhytoFilter *.Rd | grep 
alias | grep 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 

Hope this helps,


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
hpages.on.github using gmail.com

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