[Bioc-devel] Package naming

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Sun Apr 23 23:32:58 CEST 2023

Bioconductor and CRAN are closely tied and it is impossible to use a package name that already exists on one of them.  I would say the change suggested something like SpectreSC is appropriate and would be permitted.

Lori Shepherd - Kern

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 Thomas Ashhurst via Bioc-devel <bioc-devel using r-project.org>
Sent: Friday, April 21, 2023 8:54 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Package naming

Hi there,

We have an R package we would like to upload to Bioconductor. The package is named Spectre, currently on Github (https://secure-web.cisco.com/1hiTPoFuWsEvN2LI48qk0VQtz2KNqPxBVNh4snEwDNJir1HB-zOnnPAQ4TEJN9EM9IlcFM7J5t51wNVCKUE7elt-6jAKO05PEy9XW4SpnmkNzAbh38Jm6DC8qSvXuY6AR2hnLlr9op4WHVwd75-GDEem7Q1nGrEbpx-Yn5cviasggY9zYftN5UaJg5AFIptL_7G_RXH672IPRvdRvsZe219AINZiWpTLaE3juMhaA8McsfoSXYTntetfDxkpIT_u1ha5tddGwR9AhrSI1ntMznp7vf8TwSng7wsjKryJWl4Vjyc0ZzlKoWr7eInZb6bzi/https%3A%2F%2Fgithub.com%2FImmuneDynamics%2Fspectre). There is no other package on Bioconductor with this name, but one (not ours) was uploaded to CRAN before we managed to get ours to Bioconductor (https://secure-web.cisco.com/1jQY3ladfzNOhhCdzkgJQ6Xbal854KIyqNSRZ6FttGQE907q9WfqjzY98L7Sl8CNdf26eTHzKE08h2hPFj2GNrvItAo93T0IPud8xdpxtvNwcccRktDzGnIGXzIwkuzMkRV1N0B7RHQ3ZGyKNHSGd7FWPA6A1OrPIDggxf_wNKUaYSLocMrvrd97KXMiYZWP0UGgLDtWKrpZkbM52CK8pRw0jA5lfjpN873tumKZ6vXa4Omjwdmh19sXEyDaVw2yWkc8ioar50x4rUArNCFBJG2_KheqOrDc6sOJtFuBRYfn5NNChwXRStuL0W9PI6-ao/https%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2Fspectre%2Findex.html).

We are revisiting this now, to find a way to put our package into Bioconductor. As I understand it, the policy indicates that we cannot use a package name that is already on CRAN, even if it is not in Bioconductor. Ideally we would like to stick with our existing package name -- our package is well known at this stage, and widely used in the cytometry and single-cell communities, so we are reluctant to change it substantially. However, we could make a small names change -- SpectreSC or something along these lines. Would that be acceptable? I am aware the policy discourages names that imply a temporal relationship (e.g. Spectre2 or SpectrePlus), but SpectreSC to me seems distinct enough. Would something like this be suitable

Thanks so much for your help!


Thomas Ashhurst, Ph.D

Senior Cytometry Scientist
Sydney Cytometry Core Research Facility

Honorary Research Fellow
Infection, Immunity, and Inflammation
School of Medical Sciences
Faculty of Medicine and Health

The University of Sydney
Charles Perkins Centre D17
E thomas.ashhurst using sydney.edu.au<mailto:thomas.ashhurst using sydney.edu.au>
M +61401050583

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