[Bioc-devel] The following bioconductor packages have duplicate commits

Justin Silverman jsilve24 at gmail.com
Tue May 1 18:47:40 CEST 2018


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


git at 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.Turaga at 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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