[Bioc-devel] Issue when merging upstream current release branch

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Thu Nov 12 18:35:20 CET 2020

To recap:
It seem like you have created the RELEASE_3_12 branch that will track from upstream (Bioconductor's  RELEASE_3_12 branch) as the following you said worked:

git checkout -b RELEASE_3_12 upstream/RELEASE_3_12

So the following fails:

git merge origin/RELEASE_3_12
merge: origin/RELEASE_3_12 - not something we can merge

For understanding and clarification.  If you look at your remotes with
"git remote -v "  this will show you all active remotes. If you followed the instructions you referenced above you would probably see something like

origin git @ github .com:<your github username>/wpm.git (fetch)
origin git @ github .com:<your github username>/wpm.git (push)
upstream git @ git.bioconductor .org:packages/wpm.git (fetch)
upstream git @ git.bioconductor .org:packages/wpm.git (push)

So this means when you reference origin, you are referencing your github repository and when you reference upstream you are referencing the git.bioconductor.org repository.

So when you did
git checkout -b RELEASE_3_12 upstream/RELEASE_3_12

It basically means   git checkout,   -b RELEASE_3_12 means create a branch named RELEASE_3_12  and use the code at upstream (git Bioconductor from the remote)'s branch of RELEASE_3_12

So when you are saying
git merge origin/RELEASE_3_12

It is saying merge the origin (your github)'s branch of RELEASE_3_12.  So you were right to suspect that it is because there is no existing branch on your Github for RELEASE_3_12.
Please try the following when you are checked out on your locally RELEASE_3_12 branch:
git push origin RELEASE_3_12
It should create a RELEASE_3_12 branch on your github using the code on whatever branch you are currently on.
This step is to ensure that if you made any changes on the github branch that they would be merged into the existing branch.  In this case you didn't have one so you could safely ignore it.  If you create the branch on your github,  which is advisable for tracking and bug correcting, than in the future you would want to make sure to keep your github branches in sync with the Bioconductor branches.

Generally you want to push changes to the devel / "master"/main  branch of upstream/master for git.bioconductor.org.  We only encourage pushing to the RELEASE_X_Y  branch for bug corrections and not for enhancements or new features.  And you would also want to push any changes also to your gihub to make sure they stay in sync.

Please let us know if you still need any additional help or if anything is still unclear.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of H�l�ne Borges <borges.helene.sophie using gmail.com>
Sent: Thursday, November 12, 2020 12:05 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Issue when merging upstream current release branch

Dear Bioc developers,

I am the maintainer of the wpm package which has been released for the
first time on Bioconductor release 3.12.
After reviewers comments for the corresponding paper, I need to make some
changes on my package, including adding a test dataset.
Since I changed my machine, I followed the instructions of the links:

I have cloned the project (origin master) and I have the Bioconductor
$ git fetch --all
Fetching origin
Fetching upstream

But I got a git message when trying to follow this command line (step 10
from the sync tutorial):
~/Documents/wpm (master)
$ git checkout -b RELEASE_3_12 upstream/RELEASE_3_12
Switched to a new branch 'RELEASE_3_12'
Branch 'RELEASE_3_12' set up to track remote branch 'RELEASE_3_12' from
~/Documents/wpm (RELEASE_3_12)
$ git merge origin/RELEASE_3_12
merge: origin/RELEASE_3_12 - not something we can merge

So, I supposed this means there is no RELEASE_3_12 branch locally, but
actually it does exist (I can "checkout" it)... What I saw is that no
RELEASE_3_12 was created on my GitHub repo, so how do I add it and merge it?
I tried some things but it did not work. No problem with the upstream
branch, so I suppose that if I push changes it will work for the
Bioconductor upstream but not for origin/master (GitHub).

In addition, I wonder on which branches commit + push my changes. I suppose
origin/master branch (Github) and the upstream/release branch
(bioconductor)  but I do not know how to make my changes correctly since
the merges requested in the tutorial do not work...

Any help or suggestion would be appreciated,
Thanks in advance,

H�l�ne Borges

        [[alternative HTML version deleted]]

Bioc-devel using r-project.org mailing list

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list