[R-pkg-devel] DOI for archived package?

Sean Davis @e@nd@v| @end|ng |rom gm@||@com
Thu Sep 10 18:51:04 CEST 2020

I have found reminding editors of this editorial to be useful:


Community repositories that carry out testing are ideal for commonly used
> programs (for example, those used in statistical analysis), and a fair
> proportion of the genetics community is fortunately familiar with the
> Comprehensive R Archive Network (http://cran.r-project.org/) and the
> principles of stewardship of modular software embodied in the Bioconductor
> suite (http://www.bioconductor.org/). The journal has sufficient
> experience with these resources to endorse their use by authors. We do not
> yet provide any endorsement for the suitability or usefulness of other
> solutions but will work with our authors and readers, as well as with other
> journals, to arrive at a set of principles and recommendations.

As a tangential but informational comment, Bioconductor started minting
minimalist DOIs for packages a couple years ago. I do not think DOIs have
seen broad uptake as a citation mechanism for Bioc packages (I states
without evidence), but the opportunity arose to do so and we took it.



On Thu, Sep 10, 2020 at 12:36 PM Iñaki Ucar <iucar using fedoraproject.org> wrote:

> If you proposed
> https://cran.r-project.org/src/contrib/Archive/
> <pkg>/<pkg>_<version>.tar.gz
> and the editor is suspicious about the "src/contrib/Archive" stuff, you
> could propose instead
> https://cran.r-project.org/package=<pkg>&version=<version>,
> which *looks* more permanent I guess.
> Iñaki
> On Thu, 10 Sep 2020 at 18:14, Kevin R. Coombes <kevin.r.coombes using gmail.com>
> wrote:
> > Hi,
> >
> > I am in the process of submitting a "workflow" article about an R
> > package (which is onCRAN) to F1000Research. The associate editor that I
> > am dealing with wants a "DOI" for the source code of the package being
> > described in the manuscript.  I have already explained that CRAN
> > archives all versions of packages, and I sent him the URL to the archive
> > page for the package, However, he still seems to believe that a DOI
> > needs to be assigned by some site like Zenodo.
> >
> > I haven't yet responded by pointing out that CRAN has been archiving all
> > versions of packages since at least the year 2000, it has mirrors all
> > over the world, and the URL/URI used here is likely to be far more
> > permanent than the DOI from Zenodo. Nor have I pointed out that there
> > are more than 15,000 packages at CRAN, nor that not a single R user
> > would ever think to go look on Zenodo for an R package.
> >
> > Does anyone have other suggestions for how to respond? (I know;  I could
> > just put the [expletive] thing into Zenodo and move on, but creating a
> > permanent identifier for something that will *never *be accessed just
> > seems stupid.)
> >
> > Thanks,
> >    Kevin
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-package-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
> --
> Iñaki Úcar
>         [[alternative HTML version deleted]]
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892

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