[Bioc-devel] Check warning: Undocumented code objects:, ‘summary’

Martin Morgan mtmorgan at fhcrc.org
Fri Feb 3 18:29:58 CET 2012

On 02/03/2012 01:36 AM, rcaloger wrote:
> Hi,
> I am the maintainer of oneChannelGUI, I am getting a strange warning
> from the devel version of the package:
> Undocumented code objects:
> ‘summary’
> As far as I could understand it seems that a function called summary was
> never described in as man page.
> However, I check for the presence of "summary" function in my package
> and I have never defined it.
> I use summary methods from GOstats, siggenes DyDoc, and IRanges.
> I am expecting that this problem depend on the configuration of NAMESPACE
> Therefore I modified NAME adding explicitly all packages from which I am
> importing summary:
> oneChannelGUI NAMESPACE is the following:
> importMethodsFrom(GOstats, summary)
> importMethodsFrom(siggenes, summary)
> importMethodsFrom(DynDoc, summary)
> importMethodsFrom(IRanges, sapply, as.data.frame, summary)
> # All functions exported other than those starting with "."
> exportPattern("^[^\\.]")
> exportMethods(summary, sapply, as.data.frame)
> However, the warning remains.
> Could somebody help me in understanding this warning?

In principle, if you don't define the generic you don't have to document 
it, so the warning could be a bug in R. On the other hand in the version 
of the NAMESPACE that is reported on the Bioc build page and in your 
current svn you export(summary), but this shouldn't be necessary -- just 


> Cheers
> Raffaele

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