[Bioc-devel] Important Bioconductor Release 3.22

[Martin Morgan]

Hi Lori et al., I think AlphaMissenseR is failing because of files downloaded to BiocFileCache; the cache needs to be cleaned (on all machines) by removing all rname starting with 'AF-P35557’. The underlying problem was fixed in a previous commit

commit 822e44e1491d02126e4a2c652f4357f21a9bc527
Author: Martin Morgan <mtmorgan.xyz using gmail.com>
Date:   Sat Oct 11 18:08:27 2025 -0400

    ensure AlphaFold prediction returns exact match to query
    
    - apparently asking for uniprot xxx also returns xxx-1, etc


Let me know how to proceed.

Thanks,

Martin

> On Oct 20, 2025, at 11:59 AM, Kern, Lori via Bioc-devel <bioc-devel using r-project.org> wrote:
> 
> The deadline for fixing packages in preparation for the release is this Friday October 24th. All packages should be installing, building, and checking without ERROR in the Bioconductor devel build report.  While you can continue to push changes past this date, this ensures all changes are reflected in at least one build report before the code freeze for release.  Packages that continue to show ERRORs in the build report after the release will be consideration for deprecation. We are on schedule to release Wednesday October 29th.
> 
> Please also remember to update your NEWS files for any information about changes to your packages during this last development cycle.  Bioconductor collates all package news files as part of the release announcement. If your NEWS file is not formatted correctly and not updated by this weekend, it will not be included in the release announcement.
> 
> For clarification:
> The release 3.22 branch has not yet been created.  Please continue to update the devel branch.
> Next week when the release occurs the core team will automatically create the RELEASE_3_22 branch on git.bioconductor.org but until that time the only branch accessible is devel.  Do NOT try to create a RELEASE_3_22 branch on your own; the core team will do this for you.  Bioconductor will also handle bumping the y of a package version x.y.z  on release day.
> 
> Cheers,
> 
> 
> 
> Lori Kern
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
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