[Bioc-devel] Package name

Laurent Gatto |@urent@g@tto @end|ng |rom uc|ouv@|n@be
Sun Oct 24 21:15:56 CEST 2021

My specific example falls in Henrik's category.

I am working on a package that handles peptide-spectrum matches, commonly called PSMs in proteomics. I realised, to my great dismay, that there used to be a PSM package on CRAN (https://cran.r-project.org/web/packages/PSM/index.html) for non-linear mixed-effects modelling using stochastic differential equations for population stochastic modelling. As you might imagine, that name is very far fetched in my view.

I renamed my package.

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Henrik Bengtsson <henrik.bengtsson using gmail.com>
Sent: 22 October 2021 14:02
To: Wolfgang Huber
Cc: bioc-devel using r-project.org
Subject: Re: [Bioc-devel] Package name

For CRAN packages it's easy. Packages on CRAN are eternal. They may be
archived, but they are never removed, so in a sense they're always
"currently on CRAN". Archived packages may still be installed, but only
with some efforts of the user. Some packages go in an out of "archived"
status depending how quick the maintainer fixes issues. Because of this, I
cannot really see how a CRAN package name can be "reused" by anyone else
without a formal handover agreement between old and new maintainers. Even
so, I think CRAN needs to approve on the "update" in order to unarchive it.

Personally, I'd argue the same should apply to Bioconductor packages.
Reusing package names for other purposes/different APIs is just asking for
troubles, e.g. when it comes to future scientists trying to reproduce
legacy results.


On Fri, Oct 22, 2021, 03:02 Wolfgang Huber <wolfgang.huber using embl.org> wrote:

> This is probably a niche concern, but  I’d find it a pity if a good
> package name (*) became unavailable forever, esp. if it refers to a
> real-world concept not owned by the authors of the original package.
> Perhaps we could allow re-using a name after a grace period (say 1 or 2
> years)?
> To be extra safe, one could also require the first version number of the
> new package be much higher than the last version of the old (dead) package.
> (*) One example I have in mind where we re-used the name of an extinct
> project is rhdf5.
> Kind regards
> Wolfgang
> > Il giorno 21ott2021, alle ore 13:39, Kern, Lori
> <Lori.Shepherd using RoswellPark.org> ha scritto:
> >
> > Good point.  I'll open an issue on the github to fix.
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Comprehensive Cancer Center
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> > ________________________________
> > From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of
> Laurent Gatto <laurent.gatto using uclouvain.be>
> > Sent: Thursday, October 21, 2021 12:53 AM
> > To: bioc-devel using r-project.org <bioc-devel using r-project.org>
> > Subject: [Bioc-devel] Package name
> >
> > The Package Guidelines for Developers and Reviewers say that:
> >
> > A package name should be descriptive and should not already exist as a
> current package (case-insensitive) in Bioconductor nor CRAN.
> >
> > The sentences says current packages - does that imply that names of
> packages that have been archived (on CRAN) or deprecated (on Bioconductor)
> are available? This is likely to lead to serious confusion.
> >
> > Laurent
> >
> > _______________________________________________
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