[Bioc-devel] GitHub and Bioc sync: issue with dup commit for the sva package

Hi Leo,

I?ll try to help you with this issue.

The duplicates commit you have on your package ?sva? come from the pre-git era of Bioconductor.  There are three ways we can fix this,

1,

You fix your GitHub repo by removing the duplicate commits. They happen only after this commit.

commit d12b53824915f0ff7b7906043c7fc9237521e8f3
Author: Kipper Fletez-Brant <cafletezbrant at gmail.com>
Date:   Sat Apr 22 10:42:29 2017 -0400

    actually did it


You can do the cherry-picking of the commits (only one from a set of duplicate commits, one after the other to construct your git history). It is outlined in this document here,

        http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/.

If you choose this method, I can help with any questions you may have.

        Some help if you decide to choose this route,

        A.

        You might face issues with this commit (7e4aa44 Merge pull request #26 from cafletezbrant/master) while doing the cherry-pick.
        You can ignore this, because the commits themselves will be in the git history.

        d12b538 actually did it
        7cedd49 needed to use tcrossprod(t(...)) a bunch


        B.

        If you hit a lot of merge conflicts while doing the cherry-pick, the best way I?ve gotten used to is by using

                `git mergetool`.

        (I personally use the option `git mergetool -t vimdiff`, but feel free to use whatever merge tool you?d like)

        C.

        Make sure you cherry-pick the RELEASE commits which come from the core team while doing the cherry-pick process.

2,

I can fix the bioconductor repo on my end to show no duplicate commits. Then you?d have to force your Github master branch to be the same as the Bioconductor repo and then put Claire?s commits on top of them. This is a slightly less optimal solution because I might make some mistakes resolving the conflicts, since I don?t know the details of code.

3,

Since the issue of duplicate commits was pre-git era, we can just ignore the duplicates. It is pretty straightforward to disable the duplicate commit check, but it should only be a worst case. I don?t recommend this for your repo because there are very few issues and it seems we can resolve them. I reserve this option for packages which have extensively fractured their git history.


Best regards,

Nitesh


=
Nitesh Turaga
Bioconductor Core Team

On Aug 24, 2018, at 11:29 PM, Leonardo Collado Torres <lcollado at jhu.edu> wrote:

Hi,

I'm having trouble with synching a github repo with Bioc.

At https://github.com/jtleek/sva-devel/commits/master we have 3 recent
commits by Claire that we want to sync with Bioc. I followed the
instructions at
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
and then had to do step #8 where I ran steps 1-4 from "force
Bioconductor master to Github master"
http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-.
On the optional step 4 I used git cherry-pick to pick the 3 commits by
Claire. That's how we got to the current state on the jtleek/sva-devel
repo (git added me as a co-author of the commits). However, "git push
upstream master" keeps failing as shown below:

$ git push upstream master
Counting objects: 15, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (7/7), done.
Writing objects: 100% (15/15), 2.76 KiB | 2.76 MiB/s, done.
Total 15 (delta 9), reused 11 (delta 8)
remote: Error: duplicate commits.
remote:
remote: There are duplicate commits in your commit history, These cannot be
remote: pushed to the Bioconductor git server. Please make sure that this is
remote: resolved.
remote:
remote: Take a look at the documentation to fix this,
remote: https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
remote: particularly, point #8 (force Bioconductor master to Github master).
remote:
remote: For more information, or help resolving this issue, contact
remote: <bioc-devel at r-project.org>. Provide the error, the package name and
remote: any other details we might need.
remote:
remote: Use
remote:
remote:     git show 812b53941d5ba3e70797e4ecfef8401b89fc4741
remote:     git show a3406ad11056cc5f1896f71c7864e2c3bd80b817
remote:
remote: to see body of commits.
remote:
To git.bioconductor.org:packages/sva.git
! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'git at git.bioconductor.org:packages/sva.git'


If I clone git at git.bioconductor.org:packages/sva.git I can see that
both 812b5394 and a3406ad1 already exist on the Bioc git. I see that
one of the notes at
http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
mentions that the step 1-4 solution won't work in this scenario. The
"Reset to a previous commit" section recommends using git reset
--hard. But that still fails.

$ git reset -- hard a3406ad11056c
13:58 sva-devel $ git status
On branch master
Your branch is ahead of 'upstream/master' by 3 commits.
 (use "git push" to publish your local commits)

nothing to commit, working tree clean
13:58 sva-devel $ git push -f upstream master
Counting objects: 15, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (7/7), done.
Writing objects: 100% (15/15), 2.76 KiB | 1.38 MiB/s, done.
Total 15 (delta 9), reused 11 (delta 8)
remote: Error: duplicate commits.
remote:
remote: There are duplicate commits in your commit history, These cannot be
remote: pushed to the Bioconductor git server. Please make sure that this is
remote: resolved.
remote:
remote: Take a look at the documentation to fix this,
remote: https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
remote: particularly, point #8 (force Bioconductor master to Github master).
remote:
remote: For more information, or help resolving this issue, contact
remote: <bioc-devel at r-project.org>. Provide the error, the package name and
remote: any other details we might need.
remote:
remote: Use
remote:
remote:     git show 812b53941d5ba3e70797e4ecfef8401b89fc4741
remote:     git show a3406ad11056cc5f1896f71c7864e2c3bd80b817
remote:
remote: to see body of commits.
remote:
To git.bioconductor.org:packages/sva.git
! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'git at git.bioconductor.org:packages/sva.git'

So hm... I have no idea how to fix this.

Best,
Leo

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