[Bioc-devel] Cannot push to BioC git repo

Ulrich Bodenhofer bodenho|er @end|ng |rom b|o|n|@jku@@t
Mon Feb 20 16:23:06 CET 2023


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!



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'

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