[Bioc-devel] hook declined or non-fast-forward problem
Martin Morgan
martin.morgan at roswellpark.org
Wed Mar 28 18:51:54 CEST 2018
On 03/28/2018 11:51 AM, Hongxu Ding wrote:
> Thank you Martin!
>
> I made the updates according to reviewers' comments from Bioinformatics,
> so I would say these are "new features".
>
> So does this mean I'm all set and the updates will be available on
> Bioconducotr for the next release?
yes the changes committed today will be available in the next release.
Martin
>
> Best,
> Ding
>
> 2018-03-28 11:45 GMT-04:00 Martin Morgan <martin.morgan at roswellpark.org
> <mailto:martin.morgan at roswellpark.org>>:
>
>
>
> On 03/28/2018 11:19 AM, Hongxu Ding wrote:
>
> Thank you very much Morgan! I followed your suggestions and
> solved the problem.
>
> I think the problem is the version is 1.1.0 on Bioconductor, and
> the version of my new update is 1.0.1. I bumped the version to
> 1.1.1 and used *_git push
> git at git.bioconductor.org:packages/iterClust.git master_* for
> updating my package:
>
> *Counting objects: 47, done.
> Delta compression using up to 4 threads.
> Compressing objects: 100% (27/27), done.
> Writing objects: 100% (47/47), 10.24 KiB | 209.00 KiB/s, done.
> Total 47 (delta 30), reused 31 (delta 20)
> To git.bioconductor.org:packages/iterClust.git
> d0a36e4..429821b master -> master*
>
> Another question, what should I do to the release branch of my
> GitHub repository? Specifically, should I also push my updates
> to Bioconductor, and if so what version, e.g. 1.1.1 should I use?
>
>
> If your changes were 'bug fixes', then they would normally also be
> added to the release branch. If they were 'new features' then they
> would only be added to the master branch.
>
> The version scheme is outlined at
>
> http://bioconductor.org/developers/how-to/version-numbering/
> <http://bioconductor.org/developers/how-to/version-numbering/>
>
> for version number x.y.z, the rule is to increment z to z + 1. In
> release your package has version 1.0.0, so the release version will
> be 1.0.1, 1.0.2, ...
>
> There will be another release soon
>
> http://bioconductor.org/developers/release-schedule/
> <http://bioconductor.org/developers/release-schedule/>
>
> resulting in RELEASE_3_7 and version 1.2.0, and in master 1.3.0. We
> do the version bumps associated with the release.
>
> Martin
>
>
> Thank you very much!
> Ding
>
> 2018-03-28 4:05 GMT-04:00 Martin Morgan
> <martin.morgan at roswellpark.org
> <mailto:martin.morgan at roswellpark.org>
> <mailto:martin.morgan at roswellpark.org
> <mailto:martin.morgan at roswellpark.org>>>:
>
>
>
> On 03/27/2018 11:14 AM, Hongxu Ding wrote:
>
> Dear Nitesh,
>
> I think I have similar problem...
>
> I tried to push some updates to Bioconductor using *git
> push
> upstream
> master *and having the following problem*:*
>
>
>
>
>
>
>
>
> *To git.bioconductor.org:packages/iterClust.git !
> [rejected] master
> -> master (non-fast-forward)error: failed to push some
> refs to
> 'git at git.bioconductor.org:packages/iterClust.git'hint:
> Updates were
> rejected because the tip of your current branch is
> behindhint:
> its remote
> counterpart. Integrate the remote changes (e.g.hint:
> 'git pull
> ...') before
> pushing again.hint: See the 'Note about fast-forwards'
> in 'git
> push --help'
> for details.*
>
>
> This just looks like there is a change in the repository at
> git.bioconductor.org <http://git.bioconductor.org>
> <http://git.bioconductor.org> that is not
>
> present in your local repository. Did you try to
>
> git pull
>
> as suggested? Probably the issue is that the package has
> had its
> version 'bumped' for the last release
>
> iterClust master$ git log --oneline -n 3
> d0a36e4 bump x.y.z versions to odd y after creation of
> RELEASE_3_6
> branch
> d1b1afa bump x.y.z versions to even y prior to creation of
> RELEASE_3_6 branch
> 03daa79 20171005
>
>
> and you have not incorporated the version bump in your own
> repository. (consider also more informative commit messages).
>
> Martin
>
>
> My *git remote -v* output:
>
>
>
>
> *origin git at github.com:hd2326/iterClust.git (fetch)origin
> git at github.com:hd2326/iterClust.git (push)upstream
> git at git.bioconductor.org:packages/iterClust.git
> (fetch)upstream
> git at git.bioconductor.org:packages/iterClust.git (push)*
>
> and my *git log --oneline** output*:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *da9b838 (HEAD -> master, origin/master) Merge pull
> request #2 from
> hd2326/releasef0b0cab 1.0.2431f1a6 1.0.25b8334b
> 1.0.22adc1d6
> 1.0.2f9f9057
> Merge pull request #1 from hd2326/mastera36f952
> 2017120103daa79
> 20171005df8e1d9 201709255a6f49c 20170925a396510
> 20170925a1e3a9b
> 2017092553257c1 20170925bba0041 20170925d60f929
> 201709257639318
> 2017092523ed47b 20170908fe94a79 2017090854c939e
> 2017090881890f3
> 20170908feefc44 201709083905d52 2017090863a7b21
> 20170908e4bbdc5
> 20170908fcdc396 20170908406d29b vignettescbf66ea
> doca24d4d9 updated
> Detailed section2933f89 Initial commit*
>
>
> Would you please help me on the problem?
>
> Thank you very much!
>
> Ding
>
>
>
>
> 2018-03-26 10:40 GMT-04:00 Turaga, Nitesh
> <Nitesh.Turaga at roswellpark.org
> <mailto:Nitesh.Turaga at roswellpark.org>
> <mailto:Nitesh.Turaga at roswellpark.org
> <mailto:Nitesh.Turaga at roswellpark.org>>>:
>
> Hi Yuande,
>
> This is being blocked because you have completely
> unrelated
> histories from
> what you have on your Github to the Bioc-git repo. We
> deliberately don’t
> allow force pushing.
>
> Are you sure you want to merge the unrelated
> histories? This
> is important
> to consider, particularly because we’ve had this
> problem of
> packages having
> duplicate commits.Please make sure your Github Repo
> does not
> have any
> duplicate commits. (“git log --oneline”)
>
> If you think the Github repo is at a state where it
> needs to
> synced to the
> Bioc-git repo, let me know and I’ll take a look at
> it and
> sync it for you.
>
> Send me the link to your Github repo or just send
> me the
> output to “git
> remove -v”.
>
> Best,
>
> Nitesh
>
> On Mar 25, 2018, at 11:55 AM, Yuande Tan
> <tanyuande at gmail.com
> <mailto:tanyuande at gmail.com> <mailto:tanyuande at gmail.com
> <mailto:tanyuande at gmail.com>>> wrote:
>
> Dear All,
> I tried to git push upstream master but I met
> problem:
>
> To git.bioconductor.org:packages/MBttest.git
>
> ! [rejected] master -> master
> (non-fast-forward)
>
> error: failed to push some refs to
> 'git at git.bioconductor.org
> <mailto:git at git.bioconductor.org>
> <mailto:git at git.bioconductor.org <mailto:git at git.bioconductor.org>>:
>
> packages/MBttest.git'
>
> hint: Updates were rejected because the tip of your
> current branch is
>
> behind
>
>
> hint: its remote counterpart. Integrate the remote
> changes (e.g.
>
> hint: 'git pull ...') before pushing again.
>
>
> Actually fixed merge conflict by using git add
> . and git
> commit -m
> "Resolved merge conflict by incorporating both
> suggestions."
>
> and git add ../README.md and git commit -m "add
> README.md file."
>
> I used git pull --allow-unrelated-histories
> origin master
>
> and I got
>
>
> From https://github.com/Yuande/MBttest
> <https://github.com/Yuande/MBttest>
> <https://github.com/Yuande/MBttest
> <https://github.com/Yuande/MBttest>>
>
> * branch master -> FETCH_HEAD
>
> Already up to date.
>
> I still did *~/.ssh*$ git push upstream master
> and I got
> the same error
> (non-fast-forward).
>
>
> When I used *~/.ssh*$ git push -f upstream
> master, I got
> "error: hook
> declined to update refs/heads/master"
>
>
>
> So how do I address this "hook declined" error?
>
>
> Thanks
>
>
> Yuande Tan
>
> [[alternative HTML version deleted]]
>
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