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[Bioc-devel] Important Bioconductor Release 3.22

5 messages · Shepherd, Lori, Ulrich Bodenhofer, Martin Morgan +1 more

Shepherd, Lori
# 
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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Ulrich Bodenhofer
# 
Dear Lori,

Thanks for the information regarding the upcoming 3.22 freeze and release! Please note that there is a pending issue of my ?podkat? package on the taishan server (Linux openEuler 24.03 LTS) / aarch64). The check does not work because a package needed for building the vignette is missing on taishan. I have reported it on Oct 3 (https://stat.ethz.ch/pipermail/bioc-devel/2025-October/021144.html) and it seems it is still pending. I do not see a way how I could fix this (instead of making my package worse by removing the example in the vignette that depends on a BSgenome-based package that is not available on taishan) and I do not see it as my responsibility. So I hope that either the maintainers of taishan fix this or that the maintainers of the relevant packages fix their packages such that they work on taishan.

Regards,
Ulrich


From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Kern, Lori via Bioc-devel <bioc-devel at r-project.org>
Date: Monday, 20. October 2025 at 17:59
To: Bioc-devel <bioc-devel at r-project.org>
Subject: [Bioc-devel] Important Bioconductor Release 3.22

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


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.

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Shepherd, Lori
# 
Thank you for your reply.  We have been noticing some issues with Taishan builds and as long as the package is clean on the other OS,  it will not affect your package being included in the upcoming release.
We agree it seems an issue with the builder and not your package specifically, we will follow up with the maintainers of Taishan for a status update.


Lori Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
2 days later
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 at 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

  
  


  


      

    

    

      
      

        


  

        

      Lori Shepherd
    

    

      
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Removing entries hopefully this will clear up.


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center


On Thu, Oct 23, 2025 at 3:48?PM Martin Morgan <mtmorgan.xyz at gmail.com>
wrote: