[Bioc-devel] Cannot push to BioC git repo

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Tue Feb 21 13:48:34 CET 2023

Thank you for the detailed messages.  We updated the hooks for packages last week and it appears I introduced a bug.  I will look into this immediately and hopefully should have it resolved shortly. Sorry for the inconvenience this has caused.

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 using r-project.org> on behalf of Ulrich Bodenhofer <bodenhofer using bioinf.jku.at>
Sent: Monday, February 20, 2023 10:22 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Cannot push to BioC git repo


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



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
line 67, in prevent_duplicate_commits
remote:     rev2 = get_svn_revision(second)
remote:   File
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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