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.ga...@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-boun...@r-project.org> on behalf of Henrik > Bengtsson <henrik.bengts...@gmail.com> > Sent: 22 October 2021 14:02 > To: Wolfgang Huber > Cc: bioc-devel@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.hu...@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.sheph...@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-boun...@r-project.org> on behalf of >> Laurent Gatto <laurent.ga...@uclouvain.be> >>> Sent: Thursday, October 21, 2021 12:53 AM >>> To: bioc-devel@r-project.org <bioc-devel@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@r-project.org mailing list >>> >> https://secure-web.cisco.com/18tLjfrOdSZ-K_8neKbEy5VWz_fgbNJthSRI3zRVyXXtc-p9kCgNhG51wWXnY7UGhy4yP_imTwLGoP4BCIicB_fqzg9U937WF_IJiOPJh7NnfQXFLeEV-SiiJJ1eCyN2vaJFacWPvahAlN135mDHZNw_peW0Yl4BOq8m2QBMh4i952Nt6oghMQpSWSjaP_2bN4VKIBT2ZP-A7pDqddlOSeCCaMEKJZp_6w1WthdY69MB6lAbsF-i9uX3JVNSCmAlXW3YMNOfVEBijto4EJaGIUJMJwGX_vec9kTf9gtFiYztotSHNfquFZ4GlaHmXeHwPaBEtazOY5fPiuzLjzDK52Q/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel >>> >>> >>> >>> This email message may contain legally privileged and/or confidential >> information. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-mail and delete this email message from your computer. Thank you. >>> [[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 >> > > [[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
