[Bioc-devel] hook declined or non-fast-forward problem
Hongxu Ding
hd2326 at columbia.edu
Wed Mar 28 18:56:57 CEST 2018
Thank you very much Martin!
2018-03-28 12:51 GMT-04:00 Martin Morgan <martin.morgan at roswellpark.org>:
>
>
> 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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