[Bioc-devel] Request to Retire COHCAP Bioconductor Package

[Kern, Lori]

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-bounces using r-project.org> on behalf of Charles Warden via Bioc-devel <bioc-devel using r-project.org>
Sent: Monday, April 15, 2024 7:14 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Cc: Xiwei Wu <XWu using coh.org>; Yate-Ching Yuan <YYuan using 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


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