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

Leonardo Collado Torres lcoll@do @ending from jhu@edu
Mon Aug 27 17:41:59 CEST 2018


Thank you Nitesh!

I'll talk to Jeff and Claire.

Best,
Leo

On Sat, Aug 25, 2018 at 2:00 AM Turaga, Nitesh
<Nitesh.Turaga using roswellpark.org> wrote:
>
> 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 using 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 using 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 using 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 using git.bioconductor.org:packages/sva.git'
> >
> >
> > If I clone git using 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 using 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 using git.bioconductor.org:packages/sva.git'
> >
> > So hm... I have no idea how to fix this.
> >
> > Best,
> > Leo
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
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