[Bioc-devel] Webpage spring cleaning - Package submission
On 02/22/2013 07:08 AM, Wolfgang Huber wrote:
I would like to suggest clarification of the information in the "Package Guidelines" [1] and the "Package Submission" [2] 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... Martin
Best wishes Wolfgang [1] http://www.bioconductor.org/developers/package-guidelines/ [2] http://www.bioconductor.org/developers/package-submission/
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