[Bioc-devel] Candidates for BiocGenerics

[Benilton Carvalho]

Thanks, Herve, for everything.. I'll fix oligoClasses so you dont' get
the warning on BiocGenerics.

Additionally, for a second round of inclusions, could you [please
consider adding 'weights' to BiocGenerics as well?

Thank you very much,

benilton

2012/3/2 Hervé Pagès <hpages at fhcrc.org>:
> Done in BiocGenerics 0.1.10.
>
> Summary:
>
>  - Removed plot and summary generics (already defined in stats4).
>
>  - Added nrow, ncol, NROW, NCOL, boxplot, image and residuals generics.
>
>  - Didn't add coef (already defined in stats4).
>
>  - Didn't add dim either because it's an "internal generic primitive"
>    function (like length(), dimnames(), `dim<-`, `dimnames<-`, etc...,
>    see ?InternalMethods for the complete list) so it's not needed.
>
>  - Added a note in ?BiocGenerics about how to request addition of a
>    new generic to the package.
>
> Benilton, 'R CMD check BiocGenerics' will produce a warning because I
> put the following invalid link in the man pages for boxplot and image:
>
>  \link[oligoClasses]{FeatureSet}
>
> (please do ?BiocGenerics::image so see the context).
>
> The reason I put this link is that, for every generic, I'm trying to
> provide a link to one of the existing methods and also a link to the
> class for which this method is defined. In the case of boxplot and
> image, the man page points to the method for FeatureSet and this
> class is defined in the oligoClasses package, hence the link.
> However, for this link to be valid, the FeatureSet alias would need
> to be added somewhere in the man pages of the oligoClasses package
> (in FeatureSetExtensions-class.Rd it seems).
> Can you please take care of this?
>
> I know I could use something like \link[oligoClasses]{FeatureSet-class}
> and that link would be valid but...
>
> More generally speaking I'd like to encourage developers to make
> ?SomeClass work for their class. Many beginners have no idea they need
> to do class?SomeClass or ?`SomeClass-class` in order to get to
> the man page for a class and ?SomeClass is less typing anyway.
> You could argue that class?SomeClass should be for the class and
> ?SomeClass for the SomeClass() function but this function, if defined,
> should be the constructor for that class and it's probably a good idea
> to document it in the same man page as the class. So, to summarize,
> putting
>
> \alias{SomeClass-class}
> \alias{SomeClass}
>
> in the man page for the SomeClass class makes its documentation a little
> bit easier to access for a very small extra cost.
>
> Cheers,
> H.
>
>
>
> On 03/01/2012 10:24 AM, Benilton Carvalho wrote:
>>
>> Thank you very much Herve! cheers, b
>>
>> 2012/3/1 Hervé Pagès<hpages at fhcrc.org>:
>>>
>>> Hi Benilton, Sean,
>>>
>>>
>>> On 03/01/2012 08:18 AM, Sean Davis wrote:
>>>>
>>>>
>>>> On Thu, Mar 1, 2012 at 7:57 AM, Benilton Carvalho
>>>> <beniltoncarvalho at gmail.com>    wrote:
>>>>>
>>>>>
>>>>> Hi,
>>>>>
>>>>> I'm implementing a few things in oligo and I wonder if it'd make sense
>>>>> to
>>>>> have
>>>>>
>>>>> boxplot/coef/image/ncol/residuals
>>>>>
>>>>> defined in BiocGenerics?
>>>>>
>>>>> If it's only me using them, I'm happy to have everything in oligo.
>>>>>
>>>>> Thoughts?
>>>>
>>>>
>>>>
>>>> It seems that if someone is proposing a generic for functionality
>>>> already in base R, that generic is by definition a good candidate for
>>>> inclusion in BiocGenerics.
>>>
>>>
>>>
>>> I agree.
>>>
>>>
>>>> Are there downsides to having this be a
>>>> criterion for inclusion?
>>>
>>>
>>>
>>> Not that I know of.
>>>
>>> I'll add boxplot, coef, image, ncol and residuals to BiocGenerics today.
>>> I'll also add nrow, NROW, NCOL and dim, which are all interconnected
>>> with ncol.
>>>
>>> Cheers,
>>> H.
>>>
>>>
>>>>
>>>> Sean
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>>
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpages at fhcrc.org
>>> Phone:  (206) 667-5791
>>> Fax:    (206) 667-1319
>
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319