Thanks Lori, I see this is handled differently (not sure how frequently). I hope that developers have enough time so that users aren't impacted (much).
On Wed, 2 Apr 2025 at 13:20, Kern, Lori <lori.sheph...@roswellpark.org> wrote: > This is already implemented in BiocCheck; but BiocCheck is not run on > accepted packages currently. So people have the opportunity to check it > whenever they like > > We flush libraries so then they are picked up on the Bioconductor Build > System and maintainers will get the automatic build notifications. > > > > > > 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:* Tuesday, April 1, 2025 6:14 PM > *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 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. > > > 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
