[Bioc-devel] Cannot push to BioC git repo
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 at r-project.org> on behalf of Daniel, Dimitrov <daniel.dimitrov at uni-heidelberg.de>
Sent: Tuesday, February 21, 2023 3:27 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Cannot push to BioC git repo
Sent: Tuesday, February 21, 2023 3:27 AM
To: bioc-devel at r-project.org <bioc-devel at 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 at 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 at 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 at r-project.org mailing list >> https://secure-web.cisco.com/1AP_1NZc14kI4bvPlkEI1hv1GhoSpE4l4Z7TdqMlVjVEzTZ8gC1pb4OgviJFMIc7E65uipZIP_F1VPn5SBQDoKggieJP_9yarTbyZyA51IvSOU0vKnkvFDk6e-QdZWfqe2CjGZsSp328Vb4icTSghaENYpCwGb3nBbu_tKnwGkinrB9LinHGzuEq--asrFVlP96BIRGPuPyT9TRatSNWvUkTQohMICiSKR2IZ3jy9mG8U336ad9ApfAiTeY7MK1QFwubUzq9Q1Vx8WdviwzTCkeX3b9-WI51gn-fTjDLEPThkpZlN5vG2PYKLX8dyZdaoAy6Pllpgw7PM-eEUzFDYlg/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel >> > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://secure-web.cisco.com/1AP_1NZc14kI4bvPlkEI1hv1GhoSpE4l4Z7TdqMlVjVEzTZ8gC1pb4OgviJFMIc7E65uipZIP_F1VPn5SBQDoKggieJP_9yarTbyZyA51IvSOU0vKnkvFDk6e-QdZWfqe2CjGZsSp328Vb4icTSghaENYpCwGb3nBbu_tKnwGkinrB9LinHGzuEq--asrFVlP96BIRGPuPyT9TRatSNWvUkTQohMICiSKR2IZ3jy9mG8U336ad9ApfAiTeY7MK1QFwubUzq9Q1Vx8WdviwzTCkeX3b9-WI51gn-fTjDLEPThkpZlN5vG2PYKLX8dyZdaoAy6Pllpgw7PM-eEUzFDYlg/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/1AP_1NZc14kI4bvPlkEI1hv1GhoSpE4l4Z7TdqMlVjVEzTZ8gC1pb4OgviJFMIc7E65uipZIP_F1VPn5SBQDoKggieJP_9yarTbyZyA51IvSOU0vKnkvFDk6e-QdZWfqe2CjGZsSp328Vb4icTSghaENYpCwGb3nBbu_tKnwGkinrB9LinHGzuEq--asrFVlP96BIRGPuPyT9TRatSNWvUkTQohMICiSKR2IZ3jy9mG8U336ad9ApfAiTeY7MK1QFwubUzq9Q1Vx8WdviwzTCkeX3b9-WI51gn-fTjDLEPThkpZlN5vG2PYKLX8dyZdaoAy6Pllpgw7PM-eEUzFDYlg/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. 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