[Bioc-devel] Short URLs for packages?

[Wolfgang Huber]

Before we start a religious war, can we make progress on the pragmatic goal of making it possible to provide such URLs to people?

There are two concepts
- ‘the package' - a specific version, running in a specific environment, ‘frozen’, etc. (Gabe)
- ‘the package’ - as a concept and a living artifact (me, Bernd, Tim)
Both are useful. And having URLs for both would also be useful.

Wolfgang







> On Mar 23, 2015, at 18:43 GMT+1, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
> 
> I just meant that the mnemonic link
> 
> http://www.bioconductor.org/limma/  (SEO version of limma ;-))
> 
> could dump people at something like
> 
> http://www.bioconductor.org/release/limma/3.22.7/   (I'd prefer this)
> 
> or if need be for backwards compatibility,
> 
> http://www.bioconductor.org/packages/3.0/limma/3.22.7/  (seems less good)
> 
> instead of
> 
> http://www.bioconductor.org/packages/3.0/bioc/html/limma.html  (current)
> 
> and furthermore the specific version page could note more prominently that
> the build of limma being referenced at that particular instance in time may
> or may not be the same as was cited in a paper, used in an analysis,
> available for download the previous evening, etc. thus citation("limma") is
> a Very Good Idea when writing up results that depend upon it.  Because even
> the WEHI guys could theoretically have a bug that impacted someone's
> results (as opposed to the usual case of Didn't Read The Fine Limma Manual)
> 
> Does that make more sense?  (Probably not, but worth a try)
> 
> Statistics is the grammar of science.
> Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>
> 
> On Mon, Mar 23, 2015 at 9:29 AM, Dan Tenenbaum <dtenenba at fredhutch.org>
> wrote:
> 
>> 
>> 
>> On March 23, 2015 9:18:57 AM PDT, "Tim Triche, Jr." <tim.triche at gmail.com>
>> wrote:
>>> 
>>>> Packages are (read: should be, IMHO) published, citable pieces of
>>> research, though. Imagine if a paper you cite were silently updated
>>> without the doi/citation changing. That wouldn't be good
>>> 
>>> I don't disagree, but the existing setup does nothing to address that.
>>> Citation('limma'), for example, does.
>>> 
>>> .../release/... and .../devel/... can change at any time, potentially
>>> overnight (with or without a new BioC release).  The only real way to
>>> cite an exact version is to cite that exact version, which is already
>>> the proper way to do things and would remain unaffected by this, at
>>> least AFAIK.
>>> 
>>> Perhaps a useful addendum would be for the mnemonic
>>> 
>>> http://bioconductor.org/limma
>>> 
>>> To redirect to
>>> 
>>> 
>> http://bioconductor.org/packages/limma/whateverTheMostRecentStableVersionMayBe/
>>> 
>>> And then everything is explicit.
>>> 
>>> Does that address the competing issues discussed herein?
>> 
>> 
>> Note that 'release' and 'devel' are just symlinks to the current release
>> and devel versions. I.e. currently 3.0 and 3.1 respectively. So you can
>> always link directly to a specific version.
>> 
>> Dan
>> 
>>> 
>>> Best,
>>> 
>>> --t
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
>> 
> 
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