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]]
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Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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