[Bioc-devel] Short URLs for packages?

[Gabe Becker]

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
> >>>>
> >>>> _______________________________________________
> >>>> Bioc-devel at r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>>      [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> >
> > --
> > Gabriel Becker, Ph.D
> > Computational Biologist
> > Genentech Research
> >
> >    [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Gabriel Becker, Ph.D
Computational Biologist
Genentech Research

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