Software package: DChIPRep and Workflow package: maEndToEnd User requested deprecation. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Shepherd, Lori
Sent: Monday, March 30, 2020 11:36 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Final List of Deprecated Packages for Bioc3.11
Sent: Monday, March 30, 2020 11:36 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Final List of Deprecated Packages for Bioc3.11
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. The list will be updated monthly. This is the current list of deprecated packages for Bioc 3.11 : Maintainer requested deprecation: Software: QUALIFIER motifRG triform CVE proteoQC affypdnn splicegear Genominator IdMappingAnalysis IdMappingRetrieval manta RefNet AnalysisPageServer scfind kimod plw cn.mops cobindR LMGene sRAP gCMAP gCMAPWeb DESeq Annotation: org.At.tair.db hom.At.inp.db hom.Ce.inp.db hom.Dm.inp.db hom.Dr.inp.db hom.Hs.inp.db hom.Mm.inp.db hom.Rn.inp.db hom.Sc.inp.db KEGG.db (use KEGGREST instead) Unresponsive/not-maintained packages: Software: SELEX CTDquerier MTseeker readat anamiR MEAL BiSeq CALIB cellGrowth chroGPS DEDS LVSmiRNA MANOR MCRestimate nem PAPi pcaGoPromoter pint RIPSeeker SANTA waveTiling BayesPeak bgafun lol M3D MergeMaid IPPD biosvd birta DupChecker FEM geecc MaxContrastProjection mitoODE MoPS PowerExplorer Vega ExpermentData: MTseekerData RIPSeekerData The follow Annotation packages were deprecated in 3.10 and removed from 3.11 but not previously announced. MafDb.ESP6500SI.V2.SSA137.hs37d5 MafDb.EXP6500SI.V2.SSA137.GRCh38 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 mailing list. We will be sending emails out to packages that have been broken across all platforms for an extended period of time as those are packages that are up for immediate deprecation if not corrected in a timely fashion. We will still be keeping track of failing packages and compiling a list to deprecate immediately after the release. This could have been because the package has reverse dependencies or was identified to late to deprecate in 3.11. We encourage anyone that knows the maintainers of these packages to reach out to them to fix their package to avoid deprecation. The current list for immediate deprecation in 3.12 is: DESeq MotIV NOISeq omicade4 PGSEA Starr VanillaICE Thank you Lori Shepherd 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.