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

[CoreTeam Bioconductor]

Wanted to follow up on this and the recommendation to submit to the new
submission queue?

On Fri, Sep 4, 2026 at 7:17 AM Kern, Lori <Lori.Shepherd using roswellpark.org>
wrote:

> 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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