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

If Biocondutor integration is important, then reference classes
(setRefClass) are preferable, since they fully integrate with the rest of
S4, including class hierarchies and method dispatch. It's important not to
be confused by the R6 branding. It's (sort of) an alternative to S4, not an
evolution of it.

Does R now have more HDF5 interfaces or more OOP frameworks?

Michael

On Tue, Oct 17, 2017 at 5:16 PM, Vincent Carey <stvjc at channing.harvard.edu>
wrote:

I found it a very congenial presentation.

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

https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hhoeflin_hdf5r&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=7p6EBgpmq8k2A5GFXnzr1xAeSglBWSTiCKL7PRFVWZ4&s=vmpy2qtzBGi5DFekbDE1qkhGv0M7xO2rWFLc0QhcKno&e=

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

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

wrote:

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://urldefense.proofpoint.com/v2/url?u=https-3A__www.slideshare.net_LeviWaldron_why-2Dreuse-2Dcore-2Dclasses&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=7p6EBgpmq8k2A5GFXnzr1xAeSglBWSTiCKL7PRFVWZ4&s=yHRWnacXXrnqXO4MhBRdET7vTRtXXqUyttaU7pb-hjQ&e=

(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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.waldronlab.org&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=7p6EBgpmq8k2A5GFXnzr1xAeSglBWSTiCKL7PRFVWZ4&s=Cme7IjGc4Z0ZBhjX5BXbB8rmp7Jz9igM5hzVrYZTk3A&e=
Assistant Professor of Biostatistics     CUNY School of Public Health
US: +1 646-364-9616                                           Skype:
levi.waldron

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