[Bioc-devel] Short URLs for packages?
On Mon, Mar 23, 2015 at 9:00 AM, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
.../release/... silently changes every six months or so, as does .../devel/..., so I don't see how this changes anything beyond that. It does make finding the
packages a lot easier in general, and more mnemonic.
It makes finding whatever the package is at the time you read the publication easier, yes. Finding the software discussed or used in the publication ... not really. 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
If you want to document the versions of packages used in an analysis, there's always sessionInfo() and/or a dockerfile, rite?
I guess my problem is that there is even an "if" at the beginning of that sentence. That's not an attack on you, I know that the above reflects the current state of affairs, I'm simply saying that perhaps Bioconductor, as a project, can help/encourage people to do better. ~G
--t
On Mar 23, 2015, at 8:38 AM, Gabe Becker <becker.gabe at gene.com> wrote: On Mon, Mar 23, 2015 at 8:05 AM, Fischer, Bernd < b.fischer at dkfz-heidelberg.de> wrote:
During the production process of the paper we want to link to the accompanying BioC package that is in devel, but not yet in release. Before the first release, the link (e.g. www.bioconductor.org/<packagename>) should go to the devel version (maybe with an additional warning that it is only available in devel), before the first release of the package and should go to release afterwards.
I understand the appeal of this, but decoupling publications from the actual, exact versions they discuss or use seems like a relatively large step backwards in terms of reproducibility. At the very least, I think there is some nuance here that warrants careful consideration before we adopt a single-silently-changing-link-per-package paradigm. ~G
Bernd
On 23.03.2015, at 11:45, Sean Davis <seandavi at gmail.com> wrote: Just so we don't lose the thoughts that have come before, here is a
link
to
a similar proposal from last year. https://stat.ethz.ch/pipermail/bioc-devel/2014-February/005292.html Sean
On Mon, Mar 23, 2015 at 6:17 AM, Wolfgang Huber <whuber at embl.de>
wrote:
I wonder whether it?d possible to have the website understand URLs
like
http://www.bioconductor.org/<pkgname> This could resolve to http://www.bioconductor.org/packages/release/bioc/html/<pkgname>.html or http://www.bioconductor.org/packages/devel/bioc/html/<pkgname>.html depending on whether the package was yet released. This could be handy in papers or grants that mention packages. Wolfgang ---- Wolfgang Huber Principal Investigator, EMBL Senior Scientist Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg, Germany T +49-6221-3878823 wolfgang.huber at embl.de http://www.huber.embl.de
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