On Mon, Mar 23, 2015 at 9:00 AM, Tim Triche, Jr. <tim.tri...@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.g...@gene.com> wrote: > > > > On Mon, Mar 23, 2015 at 8:05 AM, Fischer, Bernd < > > b.fisc...@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 <seand...@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 <whu...@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.hu...@embl.de > >>>> http://www.huber.embl.de > >>>> > >>>> _______________________________________________ > >>>> Bioc-devel@r-project.org mailing list > >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> Bioc-devel@r-project.org mailing list > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > >> _______________________________________________ > >> Bioc-devel@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@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel