[Bioc-devel] Request to rename devel-only package BamScale to BamScaleR before the 3.24 release

[Kern, Lori]

Thank you for your inquiry.

I agree there is no need to deprecate and we can handle the renaming.

I would however recommend still submitting onto BiocContributions as the renamed package including all internal references and having it added via the automatic process to make sure everything is changed on our system completely.   Since they are different names we can then wait until its on the system to remove the old version in devel.   Once submitted and policies accepted, please tag me (@lshep) and I will handle the expediated process and make sure it stays on my queue to remove the old.

Thank you




Lori 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 Chirag Parsania <chirag.parsania using gmail.com>
Sent: Thursday, September 3, 2026 10:52 PM
To: maintainer using bioconductor.org <maintainer using bioconductor.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Request to rename devel-only package BamScale to BamScaleR before the 3.24 release

Dear Bioconductor core team,

I maintain BamScale, which was accepted on 4 May 2026 (Bioconductor/Contributions issue #4128) and is currently in the 3.24 devel nightly builds at version 0.99.14. The package has never been part of a Bioconductor release.

I would like to rename it to BamScaleR before the 3.24 release. The reason is [REASON, e.g. to avoid confusion with the existing BAMscale command-line tool from NCBI (github.com/ncbi/BAMscale), which does something different]. I have checked that BamScaleR does not exist on CRAN or in Bioconductor (BiocManager::install("BamScaleR") fails and the name is absent from the 3.24 manifest).

I am aware that the guidelines describe renaming as deprecating the old package and resubmitting the new one for review. Since BamScale has not been in any release, there are no users to protect with a deprecation cycle. I noticed the same situation was handled by renaming the repository directly for SingleRBookWrapper -> SingleRBook (Contributions #1609) and scTypeR -> scClassifR (Contributions #1798), and I hope the same is possible here.

Concretely, could you:

  1. rename packages/BamScale to packages/BamScaleR on git.bioconductor.org,
  2. update the entry in the 3.24 software manifest,
  3. update the push-access configuration so my SSH key maps to the new repository,
  4. let me know whether I should push the renamed DESCRIPTION before or after
     your change.

On my side I will rename the GitHub repository (cparsania/BamScale -> cparsania/BamScaleR), change the Package field and all internal references (useDynLib, native routine registration, vignette, documentation, URLs), bump to  0.99.15, and push to the renamed upstream to trigger a build. The version will stay in the 0.99.x pre-release series.

I would like to complete this well before the release branch for 3.24 is created, so the renamed package gets clean nightly builds first. If you would rather I go through the deprecate-and-resubmit route via BiocContributions instead, I will do that, though I would hope to avoid missing the 3.24 release.

Thank you very much for your help.

Best regards,
Dr. Chirag Parsania
Maintainer, BamScale
https://secure-web.cisco.com/11Jzh2zczghQiMddnUkanvzcn5n2dtqZOnyNN2oM4D_9Aftgk9B8hac0NXOUyZodvm48WTbnpt-PR3jITb6O52N8ewOjsE2XZQ29t8LSYPvSaubA3EVRUlyfDdwEAcQpbIIF49ZCLnDjwvnY65UlG0v0HTXwMxxvMf9kNJtdP48wgHu3JEMBIEbqnM-x1TPE11rJ6POHNmEWMuAalIeeHlUjJiHFsfyd-h33dJdqnGVeruDcLJlSll_UE3Q2qtkKff2dWQ52FdUxDyaTvGV42Dhe6tf0oEtywUxKyNstQ6xv2JG_lvjNRi4-M03KI462d/https%3A%2F%2Fgithub.com%2Fcparsania%2FBamScale
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