Hi all,
Trying to resolve duplicate commits. Sorry, I feel like I have ignored
a recent email with the same problem as I am about to mention (but I can't find
it)... I am having trouble synchronizing with bioconductor remote server. I
keep getting permission errorL
g...@git.bioconductor.org: Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
What am I doing wrong?
Thanks!
Justin
> On Apr 30, 2018, at 1:34 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org>
> wrote:
>
> Hi Maintainers,
>
> We just concluded the bump in the RELEASE_3_7 branch and master. But, the
> following packages have a history of duplicate commits and we are leaving it
> up to the maintainers to fix these duplicate commits.
>
> There were 12 software packages that had duplicate commits. Please fix these
> packages, otherwise the duplicate commits will keep propagating.
>
> methylumi
> sva
> bumphunter
> compcodeR
> flowClean
> similaRpeak
> IONiseR
> rnaseqcomp
> iCOBRA
> PanVizGenerator
> nucleoSim
> philr
>
>
> We will set up a more detailed document on how to resolve duplicate commits,
> but there are many ways. I’m listing just one of them below.
>
> How to resolve duplicate commits
> ———————————————
>
> Sync your package to the existing version on Bioconductor now.
> (http://bioconductor.org/developers/how-to/git/pull-upstream-changes/)
>
> 1. Make a backup of the branch with duplicate commits, call this
> “master_backup” or “RELEASE_3_7_backup”.
>
> On master, (make sure you are on master by “ git checkout master”)
>
> git branch master_backup
>
> 2. Identify the commit from which the duplicates have originated. These
> commits are more often than not, “merge” commits.
>
> 3. Reset you branch to the commit *before* the merge commit.
>
> git reset —hard <commit_id>
>
> 4. Now cherry pick your commits from the master_backup branch.
>
> git cherry-pick <commit_id>
>
> 4a. The commits you cherry-pick should be only 1 version of the
> duplicate commit, i.e don’t cherry-pick the same commit twice.
>
> 4b. Include the branching and version bump commits in your cherry-pick.
> Make the package history look as normal as possible.
>
>
> These packages have duplicate commits which are just being discovered because
> there has been no update in the last development cycle.
>
> Best,
>
> Nitesh Turaga
> Bioconductor Core Team
>
>
>
>
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