Fix bugs in devel and release

Goal: Maintainers will have to fix bugs from time to time, and make sure the patch is available both in the master branch and the current release branch.


  1. Sync existing repositories.

     git fetch --all
     git checkout master
     git merge upstream/master
     git merge origin/master
     git checkout <RELEASE_X_Y>
     git merge upstream/<RELEASE_X_Y>
     git merge origin/<RELEASE_X_Y>
  2. On your local machine, be sure that you are on the master branch.

     git checkout master

    Make the changes you need to fix your bug. Add the modified files to the commit. Remember to edit the DESCRIPTION file to update the version number, and ensure that only bug-fix changes are introduced in the commit.

     git add <files changed>
     ## after version bump
     git add DESCRIPTION

    Commit the modified files. It is helpful to tag the commit as bug fix.

     git commit -m "bug fix: my bug fix"
  3. (Alternative) If the changes are non-trivial, create a new branch where you can easily abandon any false starts. Merge the final version onto master

     git checkout master
     git checkout -b bugfix-my-bug
     ## add and commit to this branch. When the bug fix is complete...
     git checkout master
     git merge bugfix-my-bug
  4. Switch to the release branch and cherry-pick the commits from master corresponding to the bug fix, e.g., reference the most recent commit on the master branch with master; see examples in git cherry-pick --help. Remember to edit the DESCRIPTION file to update the release version according to Bioconductor’s version numbering scheme.

     git checkout <RELEASE_X_Y>
     git cherry-pick master
     ## Fix version bump by editing 'Version:' field of DESCRIPTION, then
     git add DESCRIPTION
     git commit -m "update RELEASE version number"

    NOTE: If you are patching your release for the first time, you have to make a local copy of the RELEASE_X_Y branch, by

     git checkout -b <RELEASE_X_Y> upstream/<RELEASE_X_Y>

    Following this one time local checkout, you may switch between RELEASE_X_Y and master with git checkout <RELEASE_X_Y>. If you do not use the command to get a local copy of the release branch, you will get the message,

     (HEAD detached from origin/RELEASE_X_Y)
  5. Push your changes to both the GitHub and Bioconductor master and <RELEASE_X_Y> branches. Make sure you are on the correct branch on your local machine.

    For the master branch,

     git checkout master
     git push upstream master
     git push origin master

    For the release branch,

     git checkout <RELEASE_X_Y>
     git push upstream <RELEASE_X_Y>
     git push origin <RELEASE_X_Y>