[Bioc-devel] Webpage spring cleaning - Package submission

Martin Morgan 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" [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...


> Best wishes Wolfgang
> [1] http://www.bioconductor.org/developers/package-guidelines/ [2]
> http://www.bioconductor.org/developers/package-submission/
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