[Bioc-devel] Version not updated on bioconductor site

[Tim Yates]

Hi Kasper,

They are not S3 methods, but they do have a dot in the name;

  all.transcripts
  all.genes

Etc...  What I don't understand, is I have other methods, eg;

  gene.details

Which also contain dots in the name, but are not flagged up by this warning.

Does it just flag the first occurrence? Is this 'dot in the name' rule a
recent change?  As I said, I don't get warned by checking the package under
R2.13.1 on our systems.

Cheers,

Tim


On 09/08/2011 15:31, "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
wrote:

> 2011/8/9 Tim Yates <tyates at picr.man.ac.uk>:
>> Ahhh, I hadn't seen the error for 1.7.8. That's me writing a stupid unit
>> test that works locally as I have MySQL on localhost.  I'll fix that now.
>> 
>> Not sure what the warnings:
>> 
>>> S3 methods shown with full name in documentation object 'xmapcore.all':
>>>   Oall.arrays¹ Oall.chromosomes¹ Oall.domains¹ Oall.est_exons¹
>>>   Oall.est_genes¹ Oall.est_transcripts¹ Oall.exons¹ Oall.genes¹
>>>   Oall.prediction_transcripts¹ Oall.probes¹ Oall.probesets¹
>>>   Oall.proteins¹ Oall.symbols¹ Oall.synonyms¹ Oall.transcripts¹
>>> 
>>> The \usage entries for S3 methods should use the \method markup and not
>>> their full name.
>> 
>> Are though...  I guess something has changed in the dev version of R as I'm
>> not seeing thm here...
> 
> I would recommend reading the (perhaps too short) section in R-exts on
> how to document S3 methods (or is this a wrong warning where you have
> a '.' in the name without it being an S3 method).  In general they
> want something like this
>   \S3method{print}{chisqGoodnessOfFit}(x, \ldots)
> in the usage section (this is for print.chisqGoodnessOfFit)
> 
> Kasper
> 
> 
> 
> 
> 
>> 
>> Time for some searchng and reading ;-)
>> 
>> Thanks again!
>> 
>> Tim
>> 
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