[Bioc-devel] Short URLs for packages?

Tim Triche, Jr. tim.triche at gmail.com
Mon Mar 23 18:43:44 CET 2015

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>

> 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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