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.olus...@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.git...@gmail.com>: > >> Hi, >> >> I don't see that you have aliases for these symbols, hence the warning: >> >> hpages@spectre:~/cyanoFilter/man$ grep 'alias{PhytoFilter}' *.Rd >> hpages@spectre:~/cyanoFilter/man$ grep 'alias{clusterExtract}' *.Rd >> etc... >> >> Note that even though you have aliases for some PhytoFilter **methods**: >> >> hpages@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@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > >> >> -- >> Hervé Pagès >> >> Bioconductor Core Team >> hpages.on.git...@gmail.com >> > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel