[Bioc-devel] Webpage spring cleaning - Package submission
mtmorgan at fhcrc.org
Fri Feb 22 17:27:45 CET 2013
On 02/22/2013 07:08 AM, Wolfgang Huber wrote:
> I would like to suggest clarification of the information in the "Package
> Guidelines"  and the "Package Submission"  pages.
> 1. Information that is actually of type "guideline" is (only) stated on the
> submission page, which is confusing. Shouldn't one page describe the applied
> criteria, and the other the submission procedure?
> 2. We state: "Packages should also conform to the following: • Use S4 classes
> and methods.". This is vague and confusing. I think what it should say is
> that *existing* S4 classes and generic functions, and existing methods,
> should be re-used. What many developers seem to interpret this as is that
> they should come up with lots of their own, new, ideosyncratic S4 classes and
> methods. Which mostly only adds overhead and complexity, and rarely any
> benefit. I would like to suggest removing that statement, or clarifying it.
I addressed this specific issue by changing the package-submission text to
Use existing S4 classes and generic functions; see the Package Guidelines for
details on appropriate use.
and the package-guideline text to
Re-use existing S4 classes and generics where possible. This encourages
interoperability and simplifies your own package development. If your data
requires a new representation or function, carefully design an S4 class or
generic so that other package developers with similar needs will be able to
re-use your hard work, and so that users of related packages will be able to
seamlessly use your data structures. Do not hesitate to ask on the Bioc-devel
mailing list for advice.
We will revisit the submission / guideline pages over the next several days, but
additional specific issues are certainly welcome from you or others...
> Best wishes Wolfgang
>  http://www.bioconductor.org/developers/package-guidelines/ 
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