[Bioc-devel] Cannot push to BioC git repo

[Martin Grigorov]

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
'git using 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 <bodenhofer using 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'
>
>
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>
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