The (very popular) safe package breaks due the quite disruptive class(matrix) update in R-4.0.0 which I could easily fix if given access.
Marcel and I contacted the maintainer of the safe package (William T Barry), but received the following automatic notice. "AUTOMATIC NOTICE: Please note that as of March 17th, 2018, I am no longer employed at Dana-Farber Cancer Institute, nor affiliated with DF/HCC, HMS, B&CB and the Alliance Statistics and Data Center. Please contact individuals in each organization with urgent or new matters. For ongoing activities, I will receive and respond to this message as I am able. Cheers," Could you please advise how to proceed as breaking of safe (and the package not being available for bioc-devel) currently prevents me from building my enrichOmics workshop for Bioc2020, and I would thus be interested in resolving this asap. Many thanks, Ludwig ________________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Monday, June 8, 2020 11:50 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] List of Deprecated Packages for Bioc 3.12 ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** 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 3.12 : Maintainer requested deprecation: Software: CGEN DESeq: please see DESeq2 chimera flowFit flowSpy netReg metaseqR: please see metaseqR2 MPFE OGSA prada PWMEnrich rTANDEM scsR shinyTANDEM spotSegmentation Unresponsive/not-maintained packages: Software: adaptest ArrayTV BioNet BioSeqClass CHARGE CNVtools CorMut flowType flowVS focalCall FourCSeq gage GeneOverlap GenRank GOFunction ImpulseDE ImpulseDE2 joda JunctionSeq LINC Logolas MAIT Mirsynergy MotIV NarrowPeaks netbenchmark NOISeq omicade4 omicRexposome OmicsMarkeR pathprint PathwaySplice PGSEA plrs Prize reb Roleswitch safe sampleClassifier sigaR signet Starr Experiment Data Package: FunciSNP.data mitoODEdata Mulder2012 PWMEnrich.Dmelanogaster.background PWMEnrich.Hsapiens.background PWMEnrich.Mmusculus.background RNAinteractMAPK RnaSeqSampleSizeData 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. 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. 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. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel