Hi Lori, There is some documentation <https://contributions.bioconductor.org/package-end-of-life-policy.html#criteria-for-package-deprecation-by-core-team> about how to keep a package on Bioconductor (and when they are archived). Among other conditions it mentions that they shouldn't be failing checks.
There are currently two packages on Bioconductor 3.20 that depend on a package no longer available, as a consequence they fail some checks. One dependency is a software package on CRAN and the other an experimental data package. These packages do not have the dependency removed on the devel branch as far as I can tell or the maintainers are aware of the situation ( no activity on their issue tracker). However, I don't see these packages on this list. Are these cases handled differently? Best, Lluís On Thu, 27 Mar 2025 at 15:56, Kern, Lori via Bioc-devel < bioc-devel@r-project.org> wrote: > The Bioconductor Team is continuing to identify packages that will be > deprecated in the next release to allow for the Bioconductor community to > respond accordingly. This is the current list of deprecated packages for > Bioc 3.21. > > It should be noted, we did try to reach out to these package maintainers > multiple times and they were either unresponsive or had emails bounce. We > encourage anyone that is familiar with a package maintainer on this list to > reach out to them and notify them directly. Packages can be un-deprecated > if a maintainer fixes the package to build/check cleanly before the next > release and requests un-deprecation on the bioc-devel@r-project.org > mailing list > > Do not un-deprecate a package yourself. You must request un-deprecation > from the Bioconductor core team at bioc-devel@r-project.org. We will not > recognize a self un-deprecation > > Software User Requested: > - Director > - erma > - girafe > - RBioinf > - Rtreemix > - synapter > - zlibbioc > > Software Unresponsive: > > - AneuFinder > - BEARscc > - CBEA > - chromstaR > - coMET > - crossmeta > - dce > - DeProViR > - DIAlignR > - GeneGeneInteR > - genoCN > - gespeR > - GraphPAC > - HTSeqGenie > - iPAC > - MAGeCKFlute > - netDx > - NeuCA > - PanViz > - pareg > - paxtoolsr > - PICS > - PING > - QuartPAC > - ReactomeContentService4R > - RGMQL > - SpacePAC > - staRank > - STdeconvolve > - supraHex > - trigger > - TypeInfo > > Experiment Data Requested > > - parathyroidSE > - benchmarkfdrData2019 > - synapterdata > > Workflow Requested > > - BiocMetaWorkflow > > Annotation Data Requested > > - mirbase.db > - targetscan.Hs.eg.db > - targetscan.Mm.eg.db > > > > > Lori Shepherd - 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]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
