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

[rcaloger]

Many thanks!
I modified the NAMESPACE
changing
export(summary)
with
exportMethods(summary)

and the warning disappeared

Cheers
Raf



On 2/3/12 6:29 PM, Martin Morgan wrote:
> 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 exportMethods(summary).
>
> Martin
>
>> Cheers
>> Raffaele
>>
>>
>>
>
>


-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
MBC Centro di Biotecnologie Molecolari
Via Nizza 52, Torino 10126
tel.   ++39 0116706457
Fax    ++39 0112366457
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
        raffaele[dot]calogero[at]gmail[dot]com
www:   http://www.bioinformatica.unito.it