Here I provide a brief description of using git to manage Bioconductor packages. A detailed description is provided here.

Create a new repository:


  • I have GitHub account with username haowulab.
  • I have an existing Bioconductor package called mypkg.
  1. Create a new repo on GitHub with the same name as the package (mypkg).

  2. Clone the empty repo to my local machine:
    git clone

    Note after this step, the GitHub repo is the origin of my local repo.

  3. Add a remote to the cloned (local) repository (needs to be done in mypkg directory):
    git remote add upstream

    This makes to be the upstream of my local repo.

  4. Fetch content from remote upstream.
    git fetch upstream
  5. Merge upstream with origin’s master branch,
    git merge upstream/master
  6. Push changes to your origin master (this updates the content on GitHub): git push origin master.

  7. Push changes to the upstream master (updates the content on Bioconductor): git push upstream master. In order for this step to be successful, Bioconductor must grant you the access. Need to submit public SSH key here.

View existing remote

In the local git repo, do git remote -v. I see following:

origin (fetch)
origin (push)
upstream (fetch)
upstream (push)

Make and commit changes to existing

  • After making changes, run git commit -a -m "some msg" to commit all changes at once.
  • git add adds a new file to the repo.
  • git rm removes an existing file in the repo.
  • After making changes, one needs to push the changes to the upstream and origin, by doing
git push -u origin master
git push -u upstream master

Resolve conflicts

Sometimes git push -u upstream master will fail with a warning message like

failed to push some refs to ''. 
Updates were rejected because the remote contains work that you do not have locally.

This is usually caused by conflicts in files between local and upstream (bioconductor). Most likely, in the DESCRIPTION file becasue bioconductor modify the version number in new release. To resolve this, first run

git pull upstream master

Then fix the file with confliction (such as DESCRIPTION), and commit/push.