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

[Hervé Pagès]

On 3/11/21 7:45 AM, Oluwafemi OLUSOJI wrote:
> Hello Herves,
> 
> I finally solved this. It had more to do with my commits than the 
> package itself.
> 
> There is this error message when the package is built on a Windows 
> server. What am I to do about this?

The flowCore package cannot currently be installed because it requires 
cytolib >= 2.3.4 which doesn't compile on Windows at the moment. The 
cytolib maintainers are aware of the situation and working on it.

Not much we can do so let's ignore for now.

Thanks,
H.

> 
> Regards,
> Daniel
> 
> ===============================
> 
>   R CMD BUILD
> 
> ===============================
> 
> * checking for file 'cyanoFilter/DESCRIPTION' ... OK
> * preparing 'cyanoFilter':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
>        -----------------------------------
> ERROR: dependency 'flowCore' is not available for package 'cyanoFilter'
> * removing 'C:/Users/pkgbuild/AppData/Local/Temp/RtmpYhB4xB/Rinst1ce0655031d2/cyanoFilter'
>        -----------------------------------
> ERROR: package installation failed
> 
> 
> Op do 11 mrt. 2021 om 15:54 schreef Oluwafemi OLUSOJI 
> <oluwafemi.olusoji using uhasselt.be <mailto:oluwafemi.olusoji using uhasselt.be>>:
> 
>     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 <mailto: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 <mailto:Bioc-devel using r-project.org>
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>          >
> 
>         -- 
>         Hervé Pagès
> 
>         Bioconductor Core Team
>         hpages.on.github using gmail.com <mailto:hpages.on.github using gmail.com>
> 

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com