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

[Oluwafemi OLUSOJI]

Hello Herve,

Thank you for the insight, but after rewriting the man pages by hand. I
still get the same error after the latest commit. I am really at a loss
here because this builds perfectly on my system.

Regards,
Daniel

Op do 11 mrt. 2021 om 03:11 schreef Hervé Pagès <hpages.on.github using gmail.com
>:

> 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]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>

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