[Bioc-devel] List of Deprecated Packages for Bioc3.21
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: Llu?s Revilla <lluis.revilla at gmail.com>
Sent: Tuesday, April 1, 2025 6:14 PM
To: Kern, Lori <Lori.Shepherd at RoswellPark.org>
Cc: bioc-devel <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] List of Deprecated Packages for Bioc3.21
Sent: Tuesday, April 1, 2025 6:14 PM
To: Kern, Lori <Lori.Shepherd at RoswellPark.org>
Cc: bioc-devel <bioc-devel at 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, Llu?s On Mon, 31 Mar 2025 at 13:14, Kern, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at 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: Llu?s Revilla <lluis.revilla at gmail.com<mailto:lluis.revilla at gmail.com>> Sent: Saturday, March 29, 2025 4:05 AM To: Kern, Lori <Lori.Shepherd at RoswellPark.org> Cc: bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at 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, Llu?s On Thu, 27 Mar 2025 at 15:56, Kern, Lori via Bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at 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 at r-project.org<mailto:bioc-devel at 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 at r-project.org<mailto:bioc-devel at 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. 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