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 <[email protected]> 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 <[email protected]> > 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 < > [email protected]> 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 > > > > > > 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. > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > [email protected] mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > [[alternative HTML version deleted]] > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
