Hello, I was wondering whether someone from the Bioconductor core team might reply to this e-mail and/or to this GitHub issue [1] to confirm Bioconductor's hotfix policy. Specifically, the web server that JASPAR2024 relies on has changed and the old server SSL certificate expired on 2024-08-31 that breaks the package. It would be great if someone could confirm it's okay to apply the bug fix outside of the typical release cycle to the current release branch. I don't see this hotfix edge case in the general contributor guidelines [2] though of course I may have overlooked it mentioned elsewhere. Thank you for any help, Pariksheet [1] https://github.com/da-bar/JASPAR2024/issues/3 [2] https://contributions.bioconductor.org/versionnum.html
[Bioc-devel] Okay to push a hotfix for an existing release?
4 messages · Nanda, Pariksheet, Shepherd, Lori, Marcel Ramos
Yes if it is a bug fix and required for the package to function properly, It is okay to push to the RELEASE_3_20 branch. 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 at r-project.org> on behalf of Nanda, Pariksheet via Bioc-devel <bioc-devel at r-project.org>
Sent: Monday, December 2, 2024 10:07 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Okay to push a hotfix for an existing release?
Sent: Monday, December 2, 2024 10:07 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Okay to push a hotfix for an existing release?
Hello, I was wondering whether someone from the Bioconductor core team might reply to this e-mail and/or to this GitHub issue [1] to confirm Bioconductor's hotfix policy. Specifically, the web server that JASPAR2024 relies on has changed and the old server SSL certificate expired on 2024-08-31 that breaks the package. It would be great if someone could confirm it's okay to apply the bug fix outside of the typical release cycle to the current release branch. I don't see this hotfix edge case in the general contributor guidelines [2] though of course I may have overlooked it mentioned elsewhere. Thank you for any help, Pariksheet [1] https://secure-web.cisco.com/1r-1Bb_j0rBv39qrUiH6pPD-fDppwdQpQYr750SR7HK8lYIEkV9zmmllntm3dKRc-nLuiZUXkaLcKfbaD06_wUxdzgxW7k3gPrThxGYG2JktA-0JasgdK7oXJirGWL7fUFis0FxoM4KiH5MTxzGH48YES3sGlR3bDBeR-m1ywMXFCubt6c_QdZECUvAhKzvt_c2luqcIOpe_qS1CFKOvUKn4O-1kDXZuNDmRCzU_9gi7XghmIM2cfMeFw8zthmGRgN8JzkFA7YjsFbNfqCpqmP7LXW58WBo8Z3VP018E6RxNF1hoiwv6aksiGuEnE88Iv/https%3A%2F%2Fgithub.com%2Fda-bar%2FJASPAR2024%2Fissues%2F3 [2] https://secure-web.cisco.com/105co6aPz2-HGmzZOxgVDcq2qihyztP1WcbTPGmzT1AtL4Rdf5YREtGssnaRrk7gE2i_JhbVYnCgW5E5LR0SHTwOp4Tx6NumarctO60TvdeC7T3B1O2GKC_zdIuJYCqOXMFgAEDirFoDea9fUpGpzR6O1a-n1HrkQ9JvMZ-XX2_j0mQJxqCJvrCsiz3pZbeNlH3zDUsjtn97vtIeV5qzpXzqo_J5Yk6GaBwoJNWpeWqxdsaqNhwoRxPLs8gwccflARsSBeT1hLuEXKFGaXCxmCac0RJ7qBUKpEGEcvzyuQ-STQSNbH_ULRGEHeBN0yC0r/https%3A%2F%2Fcontributions.bioconductor.org%2Fversionnum.html _______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/1emYlbxE5qdBfyOINzGXCmGDDZ3cJ5b26ckk3XDmmKHrTw1J9edHyzUZY0l23Mk5R4AwSt4mbMbnfg6NQZHrZiKfTp8dWk_gEbHe7B0UWP_GCBjg775H6W8-j2_FQtqMUClKgdb7gBHg0UArhL32uarR60mKVVuDQD0Dxymf4m5kDmEwepSHP5sbyqucweu7qu_2yZhCpqSef_fKpwZEXAPYChFSeeRa0yHBCjfyX2uJfyWK_gaM-5oWckOf82mQTyUUlE0b_TNM5mMDEyCpdnb3T6JIjeKnUppnclVZRWuwiP0jgf9HJtQKPAwaKSeaR/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel 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.
1 day later
Hi Pariksheet, Thanks for pointing this out. I have created an issue regarding this scenario here: https://github.com/Bioconductor/pkgrevdocs/issues/130 and we will add more details at https://contributions.bioconductor.org To answer your question, yes, the package should be updated in the release and devel branches so that it remains functional. Best regards, Marcel
On 12/2/24 10:07 AM, Nanda, Pariksheet via Bioc-devel wrote:
* This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hello, I was wondering whether someone from the Bioconductor core team might reply to this e-mail and/or to this GitHub issue [1] to confirm Bioconductor's hotfix policy. Specifically, the web server that JASPAR2024 relies on has changed and the old server SSL certificate expired on 2024-08-31 that breaks the package. It would be great if someone could confirm it's okay to apply the bug fix outside of the typical release cycle to the current release branch. I don't see this hotfix edge case in the general contributor guidelines [2] though of course I may have overlooked it mentioned elsewhere. Thank you for any help, Pariksheet [1]https://urldefense.com/v3/__https://github.com/da-bar/JASPAR2024/issues/3__;!!LRXxDv2l!R1UBbqc4BHJec6ZHNELX8IUi15Kbh_AubbZAfATDL6GXHAx_0JPPkdwBP017w0_6_roNAS1s0HU-6nhdnP3MBxqWLM_2BA$ [2]https://urldefense.com/v3/__https://contributions.bioconductor.org/versionnum.html__;!!LRXxDv2l!R1UBbqc4BHJec6ZHNELX8IUi15Kbh_AubbZAfATDL6GXHAx_0JPPkdwBP017w0_6_roNAS1s0HU-6nhdnP3MBxpFbAmIZw$
_______________________________________________ Bioc-devel at r-project.org mailing list https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!LRXxDv2l!R1UBbqc4BHJec6ZHNELX8IUi15Kbh_AubbZAfATDL6GXHAx_0JPPkdwBP017w0_6_roNAS1s0HU-6nhdnP3MBxp76WNcIw$
____ *Marcel Ramos, MPH* Sr. Data Scientist CUNY Graduate School of Public Health & Health Policy 55 W. 125th Street, 6th Fl.| New York, NY 10027 marcel.ramos at sph.cuny.edu <mailto:marcel.ramos at sph.cuny.edu> | (646) 364-9585 sph.cuny.edu <https://sph.cuny.edu>
Thank you, Lori and Marcel! Pariksheet