[Bioc-devel] Why bioconductor?

[Turaga, Nitesh]

As far as Levi’s comment about PEP8. It’s possible to design something similar with Jim Hester’s “lintr” package, which purely defines a style guide for code. 

https://github.com/jimhester/lintr

> On Oct 10, 2018, at 3:16 PM, Levi Waldron <lwaldron.research using gmail.com> wrote:
> 
> A related comment came up in a conversation I recently had with a potential
> Bioconductor developer I met recently, who commented that even as an
> experienced Python or CRAN developer, it is difficult to orient oneself to
> the Bioconductor "style" and infrastructure for developers. He gave the
> example of wishing there were something like
> https://www.python.org/dev/peps/pep-0008/ available. One specific that we
> discussed was how to orient oneself to the hierarchy of Bioconductor S4
> classes and how to choose classes to develop from, something that
> http://bioconductor.org/developers/how-to/commonMethodsAndClasses/ falls
> short on because it only gives the biological contexts of some important
> classes.
> 
> 
> On Wed, Oct 10, 2018 at 11:52 AM Ludwig Geistlinger <
> Ludwig.Geistlinger using sph.cuny.edu> wrote:
> 
>> While this might be obvious to most of us, it seems to be less clear to
>> others.
>> 
>> In particular, those who worked out their first package and wonder what's
>> the difference between having a package available on Github, CRAN, or
>> Bioconductor.
>> 
>> 
>> I wonder whether it would be helpful for the Bioc webpage to pick up on
>> the benefits of submitting to CRAN by Hadley
>> 
>> 
>> http://r-pkgs.had.co.nz/release.html
>> 
>> 
>> and several considerations with respect to Bioconductor
>> 
>> 
>> https://bioinformatics.stackexchange.com/questions/639/why-bioconductor
>> 
>> 
>> (Maybe FAQ?)
>> 
>> 
>> Just a thought.
>> 
>> 
>>        [[alternative HTML version deleted]]
>> 
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
> 
> -- 
> Levi Waldron
> http://www.waldronlab.io
> Associate Professor of Biostatistics    CUNY School of Public Health
> US: +1 646-364-9616                                           Skype:
> levi.waldron
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.