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

[Turaga, Nitesh]

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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