Hi Lori, Is it possible to undeprecate the "PathNet" package? I just checked, the problem is a failing unit test, causing the otherwise well working package to fail R CMD check.
I fixed this here on a local clone of https://git.bioconductor.org/packages/PathNet and could push these minor changes if granted access. The PathNet package implements a solid network-based enrichment method and the corresponding paper has some 50 citations - it would thus be unfortunate to see it gone. Thanks, Ludwig ________________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Monday, October 7, 2019 9:41 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10 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 final list for the 3.10 release is as follows: Maintainer requested deprecation: Software: SNPchip GenomeGraphs HTSanalyzeR Rchemcpp charm Pbase Experiment Data Package: charmData Unresponsive/not-maintained packages: Software: dSimer flipflop exomePeak CNPBayes brainImageR plateCore rHVDM SEPA condcomp PathNet scone birte mlm4omics RnaSeqSampleSize Experiment Data Package: facopy.annot allenpvc Renaming The package CAMTHC is marked for deprecation. This package has been renamed to debCAM The following Annotation Packages have been user requested deprecated: MafDb.gnomADex.r2.0.1.GRCh38 MafDb.gnomAD.r2.0.1.GRCh38 MafDb.gnomADex.r2.0.1.hs37d5 MafDb.gnomAD.r2.0.1.hs37d5 They are replaced with MafDb.gnomADex.r2.1.GRCh38 MafDb.gnomAD.r2.1.GRCh38 MafDb.gnomADex.r2.1.hs37d5 MafDb.gnomAD.r2.1.hs37d5 The Bioconductor team will continue to send 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. Packages that are ERRORing and not fixed before the October 30th 3.10 release will immediately be marked as deprecated in devel 3.11. 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