[Bioc-devel] Rebasing possible on bioconductor git ?

[Turaga, Nitesh]

Hi Alex,

The easiest way to do this is literally just "fetch and merge".

5371  git clone git using github.com<mailto:git using github.com>:al2na/methylKit.git
5372  cd methylKit
5377  git remote add upstream git using git.bioconductor.org<mailto:git using git.bioconductor.org>:packages/methylKit
5378  git fetch --all
5379  git merge upstream/master

> At this point there are merge conflicts in the DESCRIPTION file.

/t/methylKit ❯❯❯ git diff                                                                                           master:merge ✚ ═
diff --cc DESCRIPTION
index 0b97b4e,5f8b8a9..0000000
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@@ -2,7 -2,7 +2,11 @@@ Package: methylKi
  Type: Package
  Title: DNA methylation analysis from high-throughput
      bisulfite sequencing results
++<<<<<<< HEAD
 +Version: 1.11.1
++=======
+ Version: 1.13.0
++>>>>>>> upstream/master

You need the Version: 1.13.0. Once that is done, merge the issues.

5386  git commit

5392  git log --oneline

5d26fae (HEAD -> master) Merge remote-tracking branch 'upstream/master'
e55fb87 (origin/master, origin/HEAD) Update vignette
5c754b6 (upstream/master) bump x.y.z version to odd y after creation of RELEASE_3_10 branch
cc00762 (upstream/RELEASE_3_10) bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
d34d04d Adjust Makevars and Makevars.win<http://Makevars.win> to work with latest Rhtslib
a22fb81 update NEWS and version bump
f019367 update vignette
edd837f correct typo in readMethylDB example code
e95a635 make methRead be quiet
e447b6c update help pages
0c2de19 make readMethylDB stop when there is no header
e87d958 actually create man page for readMethylDB this time


That should be how your git log looks like.

Once that is done you should be able to push to the Bioconductor Git repo. Because the packages will be in sync, without any issues. Please note. If you are having issues on your end, DO NOT PUSH to bioc git repo. Just reply on this thread and I'll sort it out for you from my end.

Best,

Nitesh


On Dec 9, 2019, at 10:39 AM, Alexander Gosdschan <alex.gos90 using gmail.com<mailto:alex.gos90 using gmail.com>> wrote:

As you can see in the branch network https://github.com/al2na/methylKit/network ,
I already rebased all commits to a copy of bioc master and checked the build on travis, but I was wondering whether this is the best way to do it.
Because this way I am rebasing 50 commits from GitHub, while on the bioc side it could only be a cherry pick or patch for the release and devel version bumps.

Best,
Alex


On 9. Dec 2019, at 16:34, Alexander Gosdschan <alex.gos90 using gmail.com> wrote:



The package I am talking about is methylKit, (https://github.com/al2na/methylKit).


On 9. Dec 2019, at 16:29, Turaga, Nitesh <Nitesh.Turaga using RoswellPark.org> wrote:

Hi,

Please let me know which package you are talking about.

Also, give me your GitHub package name.

Nitesh


On Dec 9, 2019, at 7:24 AM, Alexander Gosdschan <alex.gos90 using gmail.com> wrote:

Hi,

Somehow I missed to push a large number of commits to the bloc git master branch before the latest release and now I have 50 commits on GitHub that happened before the release.

What would be the best way to get the git remotes in sync again?
Is it possible to rebase commits on the bioc master branch, or do I have to force push to GitHub to get them in sync?

Best,

Alex





Alexander Blume (Gosdschan)

PhD Student
Berlin Institute for
Medical Systems Biology (BIMSB)
at Max Delbrueck Center (MDC)
Hannoversche Str. 28
10115 Berlin, Germany
Phone: +49 30 9406 1422

Email: alexander.blume using mdc-berlin.de
Web: https://www.mdc-berlin.de/bioinformatics











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