Hi Ulrich, Your problem looks like another problem of which the Bioc core team is aware but yours looks a bit different so it might be something new.
Last Friday another developer shared <https://community-bioc.slack.com/archives/C6MVC96AZ/p1676638521702469> this in the Slack #bioc_git channel: OSCA.basic % git push upstream RELEASE_3_16 Enumerating objects: 13, done. Counting objects: 100% (13/13), done. Delta compression using up to 4 threads Compressing objects: 100% (8/8), done. Writing objects: 100% (8/8), 829 bytes | 165.00 KiB/s, done. Total 8 (delta 5), reused 0 (delta 0) remote: Traceback (most recent call last): remote: File "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow", line 89, in <module> remote: apply_hooks(hooks_dict) remote: File "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow", line 71, in apply_hooks remote: if hooks_dict["pre-receive-hook-merge-markers"]: # enable hook remote: KeyError: 'pre-receive-hook-merge-markers' To git.bioconductor.org:packages/OSCA.basic ! [remote rejected] RELEASE_3_16 -> RELEASE_3_16 (pre-receive hook declined) error: failed to push some refs to 'g...@git.bioconductor.org:packages/OSCA.basic' and here is the answer of Lori Shepherd: Lori Shepherd 2:21 PM <https://community-bioc.slack.com/archives/C6MVC96AZ/p1676636473133529> sorry thats on me most likely -- I updated the hooks yesterday . I'll investigate (edited) I found the issue and am actively working on the remedy. This should not affect software packages but data experiment, workflows, and books are affected. I hope to have it remedied shortly. On Mon, Feb 20, 2023 at 5:33 PM Ulrich Bodenhofer <bodenho...@bioinf.jku.at> wrote: > Hi, > > I am the maintainer of the 'msa' package which has been in Bioconductor > for eight years now. The package is hosted on github and synchronized with > the BioC git repo. Today I merged a pull request that had been contributed > by a github user. I further updated the package's DESCRIPTION and inst/NEWS > file and wanted to push the latest version to the BioC git repo. No matter > what I did, I did not succeed. The error messages are attached below. I am > not a very skilled git user. Does anybody have an idea what I could/should > do? Any help is gratefully appreciated! > > Thanks, > Ulrich > > -- > > Enumerating objects: 22, done. > Counting objects: 100% (22/22), done. > Delta compression using up to 8 threads > Compressing objects: 100% (13/13), done. > Writing objects: 100% (13/13), 19.57 KiB | 1.96 MiB/s, done. > Total 13 (delta 9), reused 0 (delta 0), pack-reused 0 > remote: Traceback (most recent call last): > remote: File "hooks/pre-receive.h00-pre-receive-hook-software", line 93, > in <module> > remote: apply_hooks(hooks_dict) > remote: File "hooks/pre-receive.h00-pre-receive-hook-software", line 79, > in apply_hooks > remote: prevent_duplicate_commits(oldrev, newrev, refname) > remote: File > "/home/git/.gitolite/local/hooks/repo-specific/prevent_duplicate_commits.py", > line 67, in prevent_duplicate_commits > remote: rev2 = get_svn_revision(second) > remote: File > "/home/git/.gitolite/local/hooks/repo-specific/prevent_duplicate_commits.py", > line 43, in get_svn_revision > remote: revision = SVN_COMMIT_REGEX.match(body.decode()) > remote: UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa1 in > position 25709: invalid start byte > To git.bioconductor.org:packages/msa.git > ! [remote rejected] master -> master (pre-receive hook declined) > error: failed to push some refs to 'git.bioconductor.org:packages/msa.git' > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
