3  Containerizing and Publishing against specific Bioconductor release versions

3.1 For a {BiocBook} package not currently in Bioconductor

One can build against older Bioconductor releases as follows:

  • Commit current changes before switching branches (should be in devel branch)
gert::git_commit_all("Commit current changes")
  • Create a new branch named RELEASE_X_Y and checkout
  • Push local RELEASE_X_Y to Github

3.2 For a {BiocBook} package accepted in Bioconductor > 6 months ago

Once your package is accepted in Bioconductor, your repository will have access to a new remote named upstream, pointing to git@git.bioconductor.org. When Bioconductor releases a new version, your package will change version on the upstream remote, in a dedicated release branch RELEASE_X_Y. All details are available here.

To generate a Docker image and a version of the BiocBook website built on new Bioconductor releases, you can:

  • Add the Bioconductor remote to your local repository (this might already be set up)
gert::git_remote_add(name = 'upstream', url = 'git@git.bioconductor.org:packages/<YOUR-REPOSITORY>.git')
  • Create a new local RELEASE_X_Y branch
  • Pull the upstream RELEASE_X_Y commits
gert::git_pull("RELEASE_3_15", remote = "upstream")
  • Push the local RELEASE_X_Y branch to origin remote (your own Github repository)
gert::git_push("RELEASE_3_15", remote = "origin")
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