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

Hélène Borges borge@@he|ene@@oph|e @end|ng |rom gm@||@com
Thu Nov 12 19:00:37 CET 2020

Yes, I have exactly the output you suggest for the command git remote -v.
Also, it worked making the command you suggested (git push origin
To make things about versioning clear to me:

   - I have to push only to *origin/master* and *upstream/master *for the
   reviewers suggestions (since they are only suggestions, not bugs to fix),
   new features or improvements. And wait for the next Bioc release.
   - I have to push to *origin/release_x_y* and *upstream/release_x_y* only
   if there are bugs to fix.

Is it correct? I am a little lost because of the cherry-pick command
examples in the tutorial
It seems that we need to push on both master branches and release branches
for bugs fixes?
In any case, thanks a lot for your reply,

Hélène Borges

Le jeu. 12 nov. 2020 à 18:35, Kern, Lori <Lori.Shepherd using roswellpark.org> a
écrit :

> 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.
> Cheers,
> 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 Hélène
> 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:
> https://secure-web.cisco.com/1zz_YtKjE0RURZXghqT-DFjUqFGvojZLd1OdbFodvKpPiy4JcSsIqxP_mljNd9DnvFGFYIgOqhxPwPHjAPXl0zvLyH_wIWejglOeSSSQoudthMAdLJbIXO1aHQiJgZ8Ms9xgXF3Wc2NJiCu2QYz6I3rqFC47YvAB8yOlrX8jBSCJIcpMj5-Y0_VRoYDDoqwq3I4MjRftVRLqLyviipWnkN4axLt9QVlzaYJhmCeztjhENWB3VpXDATlFhrbQwZcda4f58ou7i7uylNAxsLmJB7wNZhJYeIygGgF5NH2NKA5r6rwrLbiXJnO8yBrHqT0QLgD1gzDc57YDRrXPhVHVZTg/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F
>  and
> https://secure-web.cisco.com/1SDlBjzXboqzboUzZt3KHqBlNsRJEW-DCduD7xg3e-pyiVcskNgk50OyyHUf6l1pjtDR3-uonffz1h6Sk6hWFDqMYic4OZMMn4lfZzbiqNczTUNiO_bCti2dNzLWcn91hTgnIO0AsrwFCF1h0dYNhN0zyKeo9VSdwPBVilCrNS-U2oPCfue613U92b9wriV_YU6zSiBscAgQW6KcvWrFB7V8QZ0e3CKpLy-bKm1W-fOK3hH8iXw312nB2-1Xx-h0mXcAxGpmbCHmWGC4G4j4yOz8It2Vfywrj4_wm54ELWQdkAZmhF8cJDesAKECXATH7nbUyRYp0RJ5KoCgxzaDwjQ/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fbug-fix-in-release-and-devel%2F
> I have cloned the project (origin master) and I have the Bioconductor
> upstream:
> $ 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
> 'upstream'.
> ~/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,
> Hélène Borges
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