[Bioc-devel] Important Bioconductor Release 3.22

[Lori Shepherd]

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 using gmail.com>
wrote:

> 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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