[Bioc-devel] Candidates for BiocGenerics

Wed Mar 7 19:27:08 CET 2012

On 03/07/2012 12:33 AM, Benilton Carvalho wrote:
> Hi Herve,
>
> thanks again for this!
>
> Both affyPLM and oligo have methods for weights().

Thanks! Link added in ?BiocGenerics::weights.

Note that both packages would need to be modified to import the
weights() generic from BiocGenerics and to export the "weights"
methods they implement.

Cheers,
H.

>
> b
>
> 2012/3/7 Hervé Pagès<hpages at fhcrc.org>:
>> Hi Benilton,
>>
>>
>> On 03/05/2012 08:13 AM, Benilton Carvalho wrote:
>>>
>>> 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?
>>
>>
>> Done in BiocGenerics 0.1.13.
>>
>> Note that there doesn't seem to be any method defined in Bioconductor
>> for weights() yet. Please let me know when you add one so I can provide
>> a link to it in the man page for the generic. Thanks!
>>
>> H.
>>
>>
>>>
>>> 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
>>
>>
>>
>> --
>> 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