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[Bioc-devel] Version not updated on bioconductor site

8 messages · Vincent Carey, Hervé Pagès, Tim Yates +2 more

Original
Hervé Pagès
# 
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:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Tim Yates
    

    

      
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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:

            

      
      
      
    

        
Are though...  I guess something has changed in the dev version of R as I'm
not seeing thm here...

Time for some searchng and reading ;-)

Thanks again!

Tim

        
On 08/08/2011 20:19, "Herv? Pag?s" <hpages at fhcrc.org> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
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      Kasper Daniel Hansen
    

    

      
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2011/8/9 Tim Yates <tyates at picr.man.ac.uk>:

            

      
      
      
    

        
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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Tim Yates
    

    

      
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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:

            

      
      
      
    

        
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      Martin Morgan
    

    

      
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On 08/09/2011 07:57 AM, Tim Yates wrote:

            

      
      
      
    

        
'all' is a generic function (see ?all) whereas 'gene' is not.

The function all.genes is a method on all, whether you like it or not. 
Objects of class 'genes' get dispatched to all.genes

 > all.genes = function(...) "all.genes"
 > g = structure(list(), class="genes")
 > all(g)
[1] "all.genes"
 > all(unclass(g))
[1] TRUE

So the advice is to avoid dots in function names.

Martin

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Tim Yates
    

    

      
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Hi Martin,

Ahhh, I see...  I hadn't come across that code convention before... Just
goes to show, there's always stuff to learn!

I guess the only proper solution would be to rename all the methods in our
package to not contain dots.

I'll have a think and see if I can come up with a nice way of doing this, as
this would break anyone's code that uses our package.

Sometimes seemingly (at the time) arbitrary decisions from 4+ years ago can
come back to haunt you ;-)

Thanks for the explanation!

Tim

        
On 09/08/2011 16:57, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:

        

            

      
      
      
    

        
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