[Bioc-devel] Warnings on R CMD check on Mac OS and Linux
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 at uhasselt.be <mailto:oluwafemi.olusoji at 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 Herv? Pag?s
<hpages.on.github at gmail.com <mailto:hpages.on.github at gmail.com>>:
Hi,
I don't see that you have aliases for these symbols, hence the
warning:
? ?hpages at spectre:~/cyanoFilter/man$ grep 'alias{PhytoFilter}' *.Rd
? ?hpages at spectre:~/cyanoFilter/man$ grep
'alias{clusterExtract}' *.Rd
? ?etc...
Note that even though you have aliases for some PhytoFilter
**methods**:
? ?hpages at 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 at r-project.org <mailto:Bioc-devel at r-project.org>
mailing list
>
--
Herv? Pag?s
Bioconductor Core Team
hpages.on.github at gmail.com <mailto:hpages.on.github at gmail.com>
Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com