[Bioc-devel] Version not updated on bioconductor site

[Tim Yates]

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:

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