Great, thanks a lot Nitesh. Do I need to push again? Many thanks, Mikhail
From: Nitesh Turaga <nturaga.b...@gmail.com> Date: Tuesday, 8 September 2020 at 16:34 To: "Shepherd, Lori" <lori.sheph...@roswellpark.org> Cc: "Spivakov, Mikhail" <mikhail.spiva...@lms.mrc.ac.uk>, "bioc-devel@r-project.org" <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] Hotfix rejected by git This email from nturaga.b...@gmail.com originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. Hi Mikhail, The RSS issue should be fixed now. Best regards, Nitesh On Sep 8, 2020, at 7:45 AM, Shepherd, Lori <lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>> wrote: Yes I can see the updates 1.17.1 on the master branch on git.bioconductor.org<http://git.bioconductor.org/>. We are looking into the RSS git ERROR. We only allow corrections to the current release (RELEASE_3_11) and devel (master) branches. We do not allow updates to past releases for legacy and reproducibility. Cheers, Lori Shepherd 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<mailto:bioc-devel-boun...@r-project.org>> on behalf of Spivakov, Mikhail <mikhail.spiva...@lms.mrc.ac.uk<mailto:mikhail.spiva...@lms.mrc.ac.uk>> Sent: Tuesday, September 8, 2020 7:22 AM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> Subject: [Bioc-devel] Hotfix rejected by git Hello! We�ve identified a small bug in our Chicago package that we�ve updated on the master branch and now wanted to update retrospectively in releases 3.9, 3.10 and 3.11. I initially updated and pushed just the master branch, and got this: $ git push remote: fatal: this operation must be run in a work tree remote: ERROR:root:Exception: Command '['git', 'rev-parse', '--show-toplevel']' returned non-zero exit status 128 remote: ERROR:root:local variable 'package_name' referenced before assignment remote: Note: failed to update RSS feed;git repository updated successfully. To g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>:packages/Chicago 05d4c19..73223a0 master -> master From the above I presumed that the issues with RSS update were not critical, and that the git repo itself was updated successfully. Please correct me if I�m wrong� I then switched to the corresponding release branches, backpropagated the changes from master using $ git cherry-pick and, after some initial rejects due to illegal version numbering, managed to push RELEASE_3_11 successfully. However, I�m still getting the changes into RELEASE_3_9 and RELEASE_3_10 rejected for reasons that do not seem to be related to version numbering: remote: FATAL: W refs/heads/RELEASE_3_10 packages/Chicago m.spivakov DENIED by fallthru remote: error: hook declined to update refs/heads/RELEASE_3_10 remote: FATAL: W refs/heads/RELEASE_3_9 packages/Chicago m.spivakov DENIED by fallthru remote: error: hook declined to update refs/heads/RELEASE_3_9 remote: fatal: this operation must be run in a work tree remote: ERROR:root:Exception: Command '['git', 'rev-parse', '--show-toplevel']' returned non-zero exit status 128 remote: ERROR:root:local variable 'package_name' referenced before assignment remote: Note: failed to update RSS feed;git repository updated successfully. To g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>:packages/Chicago 9658bab..73bfc0a RELEASE_3_11 -> RELEASE_3_11 ! [remote rejected] RELEASE_3_10 -> RELEASE_3_10 (hook declined) ! [remote rejected] RELEASE_3_9 -> RELEASE_3_9 (hook declined) error: failed to push some refs to 'g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>:packages/Chicago' I would very much appreciate any advice on how to fix this. Thanks so much, Mikhail -- Mikhail Spivakov, PhD Group Leader and Honorary Senior Lecturer (Associate Professor) MRC London Institute of Clinical Sciences Imperial College Faculty of Medicine Hammersmith Hospital Campus Du Cane Road London W12 0NN http://secure-web.cisco.com/1U822-uvoL9om08hwQO041V4JXFHowXUFi7YivT8ac5MmHwuMQ9e1Q_dzOj_KxgfdBUW5rtuFYCsadFAQ3RDO1s-AF2X6Gte7-lOuT4sTKbcfLHPm1ZdUtj0hQonw3kKtHRRSMsOmP9kmAXiyLus_lsUgfBn4BNrRtlxWAiwLTSj1YZO3MNRj1PfIheRS00LWVoko5gxhXFycg4YpReoX1KSvlC9qXYbxcCOq05HOmVHsvwSNifKqp0VpuEcxb7YVUPYTNazSqz52SbXEhM2JZgnfmOBHEyCUdBA_8oFxO3i4426E1oG5nlT9vm1JIZf8/http%3A%2F%2Fwww.FunctionalGeneControl.group [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://secure-web.cisco.com/1vB6suqSvUY3x_ju9SwX0QaXzGUN_e5pY5o-gc0dZArjaO6MeGpNNUJzSrL6fQV5dAJYmPNPynepXImGuId4424d_TCNooXUeW6hSsj3OUfvV4DpFCVxSRixzgUq93jhnDa3xts6dmjfa4L0lqo7N-i9wkAKY2mgro1P0jiR6iZZ8oayjcFCGyYoGGNDrh7_KoAllpWkVpjfdSWUMAL42Iy8cKskKOFKT0M1xo-bwbh-Ei2D1hojDuoR9O1qzX2vkx2bfrk0OqLcVu5iF6hAAl8hOaBzm9CP4kcbEwgeOtEF7M1mHN_Nflhe93VBTkfFI/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. 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