[Bioc-devel] Package name

[Wolfgang Huber]

A more specific name seems appropriate here anyway, when I https://www.google.com/search?q=PSM or https://en.wikipedia.org/wiki/PSM neither your nor Mortensen and Klim’s expansion of this abbreviation would seem to be the most obvious to most people.

Kind regards
Wolfgang




> Il giorno 24ott2021, alle ore 21:15, Laurent Gatto <laurent.gatto using uclouvain.be> ha scritto:
> 
> 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.
> 
> /Henrik
> 
> 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
>>> 
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
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