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

[Hervé Pagès]

It should also be pointed out that reference classes classes are rarely
needed and can easily be used for the wrong reasons (e.g. performance?).
The pass-by-reference semantic they provide can fire back. Most of the
time objects don't need and should not have pass-by-reference semantic,
only *some* of their slots.

Nice slides Levi!

H.

On 10/17/2017 10:04 PM, Michael Lawrence wrote:
> 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
>>>
>>>          [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>>>
>>
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>>
>
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>
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-- 
Hervé Pagès

Program in Computational Biology
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