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

Thu Nov 12 19:06:43 CET 2020

  *   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.

Yes that is correct.  That is what we recommend and encourage but it is entirely up to you what you push to the relesae and devel branches.  We encourage this format to allow release to be more stable and for packages that rely on other packages, only making changes in devel to allow adequate time to adjust and make compatible if it has some cascading effects.

Bug Fixes should be done on both the release branches and the devel branch so that it can be applied in both locations.  This is where the cherry-pick command can be helpful so that you don't have to write all the code changes on each branch and can apply the changes on one branch and then move just those changes (cherry pick which you want) to the other branch.

Hope this helps.

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: H�l�ne Borges <borges.helene.sophie using gmail.com>
Sent: Thursday, November 12, 2020 1:00 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Issue when merging upstream current release branch

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 RELEASE_3_12).
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 https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/<https://secure-web.cisco.com/15ZhCIvztXXHqlbe267ey55oK9-x21aHmXNYOnvwfCHLH-GrhYV4Avfc-EFXK5DAwRSW3U55xAAecpb6ulTzTYJdPbd6Tqu3jL-L-x3WXSIntIg00ZYmfMN37CeIb5ZCFh4VnlBEp_q6AdCKVJGodUMUYoTqINpx31f5DA1offUldtkDrDUPxqy8Kkxm4Mh4H428IE2gi3jYezLGOU9nhTA45gQtg0MDzcvxHgS9RsuMMymPgsKplAGLiW97qC7H816L6UhpogLaaXBmnWNiWUPQia8po3LIPxWfoW5kDWp8VQZLQ6aQa0B742l3hIEkc/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fbug-fix-in-release-and-devel%2F>. 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,

H�l�ne Borges

Le jeu. 12 nov. 2020 � 18:35, Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> a �crit :
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<http://secure-web.cisco.com/1ihijSvcMHCuleAbnELN6RSpgE3Mc0OYvJhtoRwlisGvSe07GKv92w97DSDYoZkBC8pRH5OxCj7vhHZTUjcTmbencSEm2s7ZOVYzL2WHu_yRomqdcpGug4aQNscYDF8yP-6SmFtP0Lf8VCnwEhdtr-KdtIuBBRc8sO-eCl0VZp0k6_XiAf5kit9svnxuWwpK1-epHjO824R2Mi5tiXpj8T3m689UXh8lh8668Avn5Z7j-vZ1RU68DcaiqdGqVvp7F4EiHhapK1YiJWK7G1g9f2OsbYws_ZFv0FOpBjle_I4L_rRp5X0_SsqpDkQs3guiV/http%3A%2F%2Fgit.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<http://secure-web.cisco.com/1ihijSvcMHCuleAbnELN6RSpgE3Mc0OYvJhtoRwlisGvSe07GKv92w97DSDYoZkBC8pRH5OxCj7vhHZTUjcTmbencSEm2s7ZOVYzL2WHu_yRomqdcpGug4aQNscYDF8yP-6SmFtP0Lf8VCnwEhdtr-KdtIuBBRc8sO-eCl0VZp0k6_XiAf5kit9svnxuWwpK1-epHjO824R2Mi5tiXpj8T3m689UXh8lh8668Avn5Z7j-vZ1RU68DcaiqdGqVvp7F4EiHhapK1YiJWK7G1g9f2OsbYws_ZFv0FOpBjle_I4L_rRp5X0_SsqpDkQs3guiV/http%3A%2F%2Fgit.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<mailto:bioc-devel-bounces using r-project.org>> on behalf of H�l�ne Borges <borges.helene.sophie using gmail.com<mailto:borges.helene.sophie using gmail.com>>
Sent: Thursday, November 12, 2020 12:05 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto: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,

H�l�ne Borges

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