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

[Oluwafemi OLUSOJI]

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?

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>:

> 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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