[Bioc-devel] Hotfix rejected by git

[Spivakov, Mikhail]

Great, thanks a lot Nitesh. Do I need to push again?

Many thanks,
Mikhail

From: Nitesh Turaga <nturaga.bioc using gmail.com>
Date: Tuesday, 8 September 2020 at 16:34
To: "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
Cc: "Spivakov, Mikhail" <mikhail.spivakov using lms.mrc.ac.uk>, "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Hotfix rejected by git

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Hi Mikhail,

The RSS issue should be fixed now.

Best regards,

Nitesh


On Sep 8, 2020, at 7:45 AM, Shepherd, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>> wrote:

Yes I can see the updates 1.17.1  on the master branch on git.bioconductor.org<http://git.bioconductor.org/>.  We are looking into the RSS git ERROR.

We only allow corrections to the current release (RELEASE_3_11) and devel (master) branches.  We do not allow updates to past releases for legacy and reproducibility.

Cheers,


Lori Shepherd

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<mailto:bioc-devel-bounces using r-project.org>> on behalf of Spivakov, Mikhail <mikhail.spivakov using lms.mrc.ac.uk<mailto:mikhail.spivakov using lms.mrc.ac.uk>>
Sent: Tuesday, September 8, 2020 7:22 AM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: [Bioc-devel] Hotfix rejected by git

Hello!

We�ve identified a small bug in our Chicago package that we�ve updated on the master branch and now wanted to update retrospectively in releases 3.9, 3.10 and 3.11.

I initially updated and pushed just the master branch, and got this:

$ git push


remote: fatal: this operation must be run in a work tree

remote: ERROR:root:Exception: Command '['git', 'rev-parse', '--show-toplevel']' returned non-zero exit status 128

remote: ERROR:root:local variable 'package_name' referenced before assignment

remote: Note: failed to update RSS feed;git repository updated successfully.

To git using git.bioconductor.org<mailto:git using git.bioconductor.org>:packages/Chicago

  05d4c19..73223a0  master -> master

From the above I presumed that the issues with RSS update were not critical, and that the git repo itself was updated successfully. Please correct me if I�m wrong�

I then switched to the corresponding release branches, backpropagated the changes from master using $ git cherry-pick and, after some initial rejects due to illegal version numbering, managed to push RELEASE_3_11 successfully. However, I�m still getting the changes into RELEASE_3_9 and RELEASE_3_10 rejected for reasons that do not seem to be related to version numbering:

remote: FATAL: W refs/heads/RELEASE_3_10 packages/Chicago m.spivakov DENIED by fallthru
remote: error: hook declined to update refs/heads/RELEASE_3_10
remote: FATAL: W refs/heads/RELEASE_3_9 packages/Chicago m.spivakov DENIED by fallthru
remote: error: hook declined to update refs/heads/RELEASE_3_9
remote: fatal: this operation must be run in a work tree
remote: ERROR:root:Exception: Command '['git', 'rev-parse', '--show-toplevel']' returned non-zero exit status 128
remote: ERROR:root:local variable 'package_name' referenced before assignment
remote: Note: failed to update RSS feed;git repository updated successfully.
To git using git.bioconductor.org<mailto:git using git.bioconductor.org>:packages/Chicago
  9658bab..73bfc0a  RELEASE_3_11 -> RELEASE_3_11
! [remote rejected] RELEASE_3_10 -> RELEASE_3_10 (hook declined)
! [remote rejected] RELEASE_3_9 -> RELEASE_3_9 (hook declined)
error: failed to push some refs to 'git using git.bioconductor.org<mailto:git using git.bioconductor.org>:packages/Chicago'

I would very much appreciate any advice on how to fix this.

Thanks so much,
Mikhail


--
Mikhail Spivakov, PhD
Group Leader and Honorary Senior Lecturer (Associate Professor)
MRC London Institute of Clinical Sciences
Imperial College Faculty of Medicine
Hammersmith Hospital Campus
Du Cane Road
London W12 0NN

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