[Bioc-devel] hook declined or non-fast-forward problem

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/

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/

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>>:



    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> 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>>:

            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>> 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.o
rg>:

                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>

                * 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

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