[Bioc-devel] Why should Bioconductor developers re-use core classes?

Vincent Carey stvjc at channing.harvard.edu
Wed Oct 18 02:16:50 CEST 2017

I found it a very congenial presentation.

One related issue -- perhaps -- a new HDF5 interface package, that is
based on R6!


Core class consciousness is surely worthy of promotion.  But what about OOP
methodology?  I personally am happy with S4.  I believe there are some
that use setRefClass ... any guidance on this?

On Tue, Oct 17, 2017 at 7:54 PM, Levi Waldron <lwaldron.research at gmail.com>

> I'm putting together a presentation with a demo on why Bioconductor
> developers should re-use and extend core classes whenever possible. It
> includes a demo of some real-life consequences from two packages I use a
> lot, metagenomeSeq and phyloseq. These are far from the only examples, many
> Bioconductor packages have created new classes from scratch, and I think as
> a community we should greatly reduce that practice. I would welcome any
> feedback:
> https://www.slideshare.net/LeviWaldron/why-reuse-core-classes
> (sorry the slides are a little Frankenstein - in the interest of speed I
> made part of it in Powerpoint and part in Beamer, and used pdftk to
> concatenate these! In practice I would do the Beamer part as a live-demo,
> and take advantage of some animations in PPT)
> --
> Levi Waldron
> http://www.waldronlab.org
> Assistant Professor of Biostatistics     CUNY School of Public Health
> US: +1 646-364-9616                                           Skype:
> levi.waldron
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