[Bioc-devel] Cannot push to BioC git repo

Tue Feb 21 14:01:26 CET 2023

Re:  Making Pau Badia the maintainer of dorothea.  This has been taken care of. Please update the maintainer in the Description of the package.

In the future please create a new thread rather than replying to an unrelated thread for requests.

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 Daniel, Dimitrov <daniel.dimitrov using uni-heidelberg.de>
Sent: Tuesday, February 21, 2023 3:27 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Cannot push to BioC git repo

Dear all,

How can I make Pau Badia i Mompel (cc'd) the maintainer of DoRothEA
<https://secure-web.cisco.com/1ClpdjjJZOViiCJLwIv0tA2DEAqfkthQzDg5Qd4-o6WxpyWRdXl3HAZ4dOwZ9S3DxnrB4ZDHprwiEqtVkTnB8xuISf_IXGGmbhZIjc4E8TFJu-4vwsh-qnZfgrGDsjc_OxzSUVHWaMdKLDbR2IryRY1Pr502UdHWgyO-4f4iSzJ2VUeQQqECxrgHnT3qpNAqIlOox4ZkRQMy9EbZ6iDfRlzNC7fFXTmeVtxGX0VRzni96yT0grx5Dewi1F0_M0eAklzG3Dvkei-NaazPfz2nlPxEVkFVXUjAXSJyhtBl8Q2O43vgxzMrwwNE1OAeG8Ki6ZV22XhhPesiTVNQDvnzRIA/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fdata%2Fexperiment%2Fhtml%2Fdorothea.html>?
He's already registered in BioC and is a maintainer of another package
(decoupleR).

Thanks in advance!

Best,

Daniel

On 21.02.23 07:58, Martin Grigorov wrote:
> 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://secure-web.cisco.com/1kNivHquhiGv-xnef5cUAzKZwy4LJjKnhHM6eUTS0jr6kUFz--n8Tyx8OnFDPaq26mT4oHol3kUDtgcbJL6HDngYAo3VEzZ5JPS9QfIQAtaOOYjiea1r8R0U839QBeeVNcPFIrAUBbWR6_G4Qa_ZirWH2swviwNbf7t0Y9P0NyZBVWMLztiAP_mhcruq4fAMbrJvdnCtU5XsWoZ6ovwdcC2wD_1_GRUg9xp04omiwOM667sbDnuuul2qrYsLNTaIRvsyhoLQPU508mqqciOWOtkmr5FTN5xXo1nR56PqNnsU0RIlWEx_22Wo8CE2Lv-BLItv0RgP_CkxD457TNp6Llg/https%3A%2F%2Fcommunity-bioc.slack.com%2Farchives%2FC6MVC96AZ%2Fp1676638521702469>
> 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://secure-web.cisco.com/1dIgBFl35sNpQytZ9b-aHJm8arPXRRuLebC6-YOiuye-oEHlZ7oINHHAm9vHz2sNirxFA4vWI3mbrUb_nizuJhS1Kgawif_2ECFsoVCWLp8Nq6DmZ9fT9tVIkJgAN0k_Go4rP6suushLGMHDJWWDlniW59Tjmj9oIm_RQRY0k3MONSTWljzqO1f-ZozDbNQZomV4Cuha6XgRDSva5Euekt0J8JWAJub-vfFfueXmfvstRoydR7Bb_SFlIaN1C90iXSdoVyMGNCkQfYEGjzjKN4IcFoDOYDXyOtlf4FyJ40qBGmle144zF_xVGgifaAS83BI0iPn17GTih9KsD88BFlQ/https%3A%2F%2Fcommunity-bioc.slack.com%2Farchives%2FC6MVC96AZ%2Fp1676636473133529>
> 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'
>>
>>
>>          [[alternative HTML version deleted]]
>>
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