[Bioc-devel] Version not updated on bioconductor site

[Kasper Daniel Hansen]

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
>
> On 08/08/2011 20:19, "Hervé Pagès" <hpages at fhcrc.org> wrote:
>
>> Hi Tim, Vince,
>>
>> Again some build system turbulences. The build report for devel is now
>> updated:
>>
>>    http://bioconductor.org/checkResults/2.9/bioc-LATEST/
>>
>> but xmapcore 1.7.8 won't propagate to our public repo because it didn't
>> pass check.
>>
>> For the release version (1.6.2), it should propagate tonight around
>> midnight (Seattle time).
>>
>> Let me know if you have further questions.
>>
>> Cheers,
>> H.
>>
>>
>> On 11-08-08 05:36 AM, Vincent Carey wrote:
>>> the build-check reports seem to date back to 4 august, so perhaps this is a
>>> vacation related pause.  i did an svn up on my archive and i saw 1.7.8, so i
>>> think the archive is where you want it to be, just want the build system to
>>> catch up
>>>
>>> see
>>>
>>> http://bioconductor.org/checkResults/
>>>
>>>
>>>
>>> On Mon, Aug 8, 2011 at 4:26 AM, Tim Yates<tyates at picr.man.ac.uk>  wrote:
>>>
>>>> Hi all!
>>>>
>>>> I have fixed a bug in xmapcore release (which is now up to v1.6.2) and
>>>> added
>>>> some functionality to devel (now up to v1.7.8), but the bioconductor site
>>>> seems to have not picked up the changes...
>>>>
>>>> Could it be that I am using git-svn?  Is this a known issue?
>>>>
>>>> Cheers,
>>>>
>>>> Tim
>>>> --------------------------------------------------------
>>>> This email is confidential and intended solely for the...{{dropped:10}}
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
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