Hi Lori, There is no need to flush libraries or reinstall R versions to check packages available on repositories. Comparing available packages with dependencies of current (or devel) Bioconductor dependencies generates that list.
Checking this more often will give package maintainers more time to adjust and update their packages. It could also strengthen the collaboration between packages as they can work with upstream developers to get the packages back to the repository (Bioconductor or CRAN). If there is interest I could write a small script to do it on the Bioconductor checks or outside and report back to the community. (I already have this in a package to be published in a repository once R 4.5 is released. It doesn't take longer than 3 seconds on my computer. ) Best, Lluís On Mon, 31 Mar 2025 at 13:14, Kern, Lori <lori.sheph...@roswellpark.org> wrote: > Because of the way the builders are set up we only see CRAN dependency > disappear when we do a new install of R or manually flush the repository. > Therefore there can be a delay in seeing these failures/ERROR's. If it is > due to a Bioconductor package, we normally notify reverse dependencies > once a package is listed as deprecated (not necessarily only failing). > > We try to be very fair to package maintainers so depending on when we (and > they) are aware of the failure, we may give them extra time moving into a > release as we realize package maintenance is not everyone's top priority > (even tho we would like it to be) > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* Lluís Revilla <lluis.revi...@gmail.com> > *Sent:* Saturday, March 29, 2025 4:05 AM > *To:* Kern, Lori <lori.sheph...@roswellpark.org> > *Cc:* bioc-devel <bioc-devel@r-project.org> > *Subject:* Re: [Bioc-devel] List of Deprecated Packages for Bioc3.21 > > Hi Lori, > > There is some documentation > <https://secure-web.cisco.com/1CaaN3K9FoTk2Yod51sOa073f3kslapZhz7-LVKYRBmE93Yq1qBXI4SRYWldRJEjARLQRUbqtbWxUO8xJrGXFZs6h3-B6ge0M7EdxtpwKgJAVFhA8R2zE7GkKmWorRq7eQ7UvSZFnj-hPRzxJw8nmGAqsJx_bjDQBVuUEIjD_mDmplcj1IgsAVBbzdD8Kkjzfetcxv4eR_9zCQfnpb0DgFOvThpu6M7zp6rZ8djT-_4SyjfCX-Wu5yVL6Qt-lnAIt03FWlt3zJakrcdbCo0KdTYN8iBqm7Hwi0ICpEa8W1gp7wR7yl0d_uQMCSoRShNGo/https%3A%2F%2Fcontributions.bioconductor.org%2Fpackage-end-of-life-policy.html%23criteria-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 > <https://secure-web.cisco.com/1klVmodPT2uSBoyCBt8nZ3B_MKZx_zEGzrINROOkFGKz6HcmOvF4GYfab5n1Pe4TaBSfyhP2kxz4GrecCJRZ4T008p2EbPvR-WbhYsehE7BT0-reNauTwJC5fIV6k05W5isBfT5ErLVrdYyCXI2NV0-2m9reFDmyR5rODIMs7WBwM-jB1YaJ2zju2xTimmu5i5YQXIbOTrIVnG6wv8-JDtiWe7XYSNnFg2E2gh531hY_l9Ivrohq4JuyqJQR4JY0dqqV9wNIC9K3pr42W69TIbw_FDkvg-L4e5kGBktZRd-T7qNIN9h2XAoYaObseC8-z/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel> > > > 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
