Hi Herv� I'll come up with a bugfix for this.
You are right about the regex, I'll have to fix it. I'll disable for the time being. Best Nitesh Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: Pages, Herve <[email protected]> Sent: Saturday, May 11, 2019 4:49:22 PM To: Turaga, Nitesh; [email protected]; Bioc-devel Subject: Re: Pre-receive hook on git.bioconductor.org to prevent merge conflict markers enabled I worked around this by replacing my ===== lines with -------- lines. Note that you cannot exclude the possibility that legit code contains things like ======= or <<<<<<< so whatever regex the hook is using at the moment should probably be made more stringent in order to avoid these false positives. Thanks, H. On 5/11/19 13:37, Pages, Herve wrote: Hi Nitesh, I'm running into some problems today when trying to push a commit to BiocGenerics: hpages@spectre:~/git.bioconductor.org/software/BiocGenerics$<mailto:hpages@spectre:~/git.bioconductor.org/software/BiocGenerics$> git remote -v origin [email protected]:packages/BiocGenerics.git<mailto:[email protected]:packages/BiocGenerics.git> (fetch) origin [email protected]:packages/BiocGenerics.git<mailto:[email protected]:packages/BiocGenerics.git> (push) hpages@spectre:~/git.bioconductor.org/software/BiocGenerics$<mailto:hpages@spectre:~/git.bioconductor.org/software/BiocGenerics$> git status On branch master Your branch is ahead of 'origin/master' by 1 commit. (use "git push" to publish your local commits) nothing to commit, working directory clean hpages@spectre:~/git.bioconductor.org/software/BiocGenerics$<mailto:hpages@spectre:~/git.bioconductor.org/software/BiocGenerics$> git push Counting objects: 12, done. Delta compression using up to 8 threads. Compressing objects: 100% (12/12), done. Writing objects: 100% (12/12), 2.69 KiB | 0 bytes/s, done. Total 12 (delta 7), reused 1 (delta 0) remote: Error: You cannot commit without resolving merge conflicts. remote: Unresolved merge conflicts in these files: remote: R/mean.R, R/t.R To [email protected]:packages/BiocGenerics.git<mailto:[email protected]:packages/BiocGenerics.git> ! [remote rejected] master -> master (pre-receive hook declined) error: failed to push some refs to '[email protected]:packages/BiocGenerics.git<mailto:[email protected]:packages/BiocGenerics.git>' I don't see merge conflicts in these files though: hpages@spectre:~/git.bioconductor.org/software/BiocGenerics$<mailto:hpages@spectre:~/git.bioconductor.org/software/BiocGenerics$> cat R/mean.R ### ========================================================================= ### The mean() generic ### ------------------------------------------------------------------------- ### setGeneric("mean") hpages@spectre:~/git.bioconductor.org/software/BiocGenerics$<mailto:hpages@spectre:~/git.bioconductor.org/software/BiocGenerics$> cat R/t.R ### ========================================================================= ### The t() generic ### ------------------------------------------------------------------------- ### setGeneric("t") Can you help? Thanks! H. On 5/10/19 09:03, Turaga, Nitesh wrote: Dear Maintainers, A new "pre-receive hook" on git.bioconductor.org server has been enabled to keep the repositories in good shape. The new hook prevents "merge conflict markers". Please note that the hook is now enabled as of 11:45 AM May 10th 2019. Git merges sometimes result in conflicts within files which lead to markers like � <<<<<<< HEAD � ======= � >>>>>>> new_branch These cause issues for the repository and leave it in a bad state. We've noticed a few repositories with such issues over the last release. If any of you notice issues/errors in your "push" to the bioconductor git server as a result of this hook, please let me know. Note that, the hook acts as the first defense against bad commits, before our other hooks come into play. The hook will allow all commits to go through if there are no merge conflict markers. For more information on this, check our documentation on our website, https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_git_resolve-2Dconflicts_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qid2ArsLYpg_q85nYw_AMhLvNlH5eFEfOJwfF2x2FF0&s=PsdZ3g55BPew_TUsGI7pZ2lo47yYEeQuw_AnVrgDrfo&e=. Other resources, 1. What are merge conflicts - https://urldefense.proofpoint.com/v2/url?u=https-3A__www.atlassian.com_git_tutorials_using-2Dbranches_merge-2Dconflicts&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qid2ArsLYpg_q85nYw_AMhLvNlH5eFEfOJwfF2x2FF0&s=Ihr5SU83Z1Qr9vfxTHhxE5Zdvn65rlMe-472crxPrb8&e= 2. Resolving merge conflicts - https://urldefense.proofpoint.com/v2/url?u=https-3A__help.github.com_en_articles_resolving-2Da-2Dmerge-2Dconflict-2Dusing-2Dthe-2Dcommand-2Dline&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qid2ArsLYpg_q85nYw_AMhLvNlH5eFEfOJwfF2x2FF0&s=8Wa9lQ_di5auvcBw1AwQsK4DgDODW6MBjvES5FO3vrk&e= Best, Nitesh Turaga Bioconductor Core Team 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. -- Herv� Pag�s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: [email protected]<mailto:[email protected]> Phone: (206) 667-5791 Fax: (206) 667-1319 -- Herv� Pag�s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: [email protected]<mailto:[email protected]> Phone: (206) 667-5791 Fax: (206) 667-1319 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]]
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