We normally like to do a full round of a package in a deprecation state before removal completely (so deprecated in Bioc 3.19 and removed in Bioc 3.20) but since there are no reverse dependencies, I don't think this should be an issue to directly remove from 3.19 without deprecation.
Please confirm direct removal over standard deprecation processes and I can take care of this. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Charles Warden via Bioc-devel <bioc-devel@r-project.org> Sent: Monday, April 15, 2024 7:14 PM To: bioc-devel@r-project.org <bioc-devel@r-project.org> Cc: Xiwei Wu <x...@coh.org>; Yate-Ching Yuan <yy...@coh.org> Subject: [Bioc-devel] Request to Retire COHCAP Bioconductor Package Hi, I have greatly appreciated the assistance provided by Bioconductor support over several years! However, my requested end date to work in the Integrative Genomics Core at City of Hope is 4/30/2024. Later this year, I will be starting a PhD program at UC-Riverside. When I was previously in graduate school at the University of Michigan, I switched to using my personal e-mail address to support the COHCAP Bioconductor package. However, we would prefer to improve the transition this time that I am going to graduate school. So, after a number of discussions, we have decided to request to retire the COHCAP Bioconductor package (https://secure-web.cisco.com/18MW32Nmr7CBKJg3Ep7wXuI8t3lFqrL7diwmsQYI7dBiV2DnODHyT7MEKyQI_XbTm9SxFc-X59sAg_eJO5wjVcXo1_bK66HNtSdjt5vNojTo5hKNWi-Dl8DW2oDONNXjUjpvl9NTJOO3l5YjYsbzM3Nl2bQvljjnk3VZeY1qwvpf7cG1BJhQHY3RL7WpoFTiBYyCxK8HqpNz1dhxGBJOTBFDm0w-8leXCP7NCojJat40_hGb6YIofwnhi39okN_Clxzp0gzb8FQRap2AT3oyNiEZKelvaNxWXUmh2abcTYFawXskGOEAWZXfQv5BTmpkp/https%3A%2F%2Fwww.bioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FCOHCAP.html). We will instead request users to go to the source page on GitHub (https://secure-web.cisco.com/1j9Obf_O7HxIn__GrQM5CQS_vyKFobzQGg5-jot9RzFCjkUGpO1HaL4J4Adtt605Oq38PACHleEPSjAb5snp2drWgmWmB6FxuGzqlL9OWz2QFJxu1TKALIhHYujdQJS-2mP2a9XdUEB-_sp4ipEwnETlWLuOI9ExJulZ2LNOQ-fC7N1ZUTo29RGbD-fFRI-MXYemgl_nph8dRYz_1TOTLiIBSPeCu42J362tgxREQM3YrbFIkkjD88aM5CGs9UWNI7xNKWB2JucADbBq1n8bu9sec4G5raWiZ4r2zSF4quP3JtCRG8OpUgu_KBca9hWSQ61AXx0yfOKhXzb7mhejUog/https%3A%2F%2Fgithub.com%2Fcwarden45%2FCOHCAP), where we have made changes in the README file. I have cc'd Yate-Ching Yuan (the Bioinformatics Director, at the time of development of the original code) as well as Xiwei Wu (the Integrative Genomics Core Director, where I currently work and where I was working when the code was first converted to be provided through Bioconductor). Since we won't be making changes for future formatting requirements and we don't want to use a non-COH e-mail address as a support contact, can you please help with actively removing the COHCAP package from Bioconductor (before 4/30)? Thank you very much! Sincerely, Charles Charles Warden, Bioinformatics Specialist (He/Him) Integrative Genomics Core Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA 91016) Room 1086 Internal Ext: 80375 | Direct: (626) 218-0375 ---------------------------------------------------------------------- ------------------------------------------------------------ -SECURITY/CONFIDENTIALITY WARNING- This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). 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