[Bioc-devel] A little confuse about how to update accepted package

Martin Morgan mtmorg@n@bioc @ending from gm@il@com
Sat Nov 10 12:10:13 CET 2018

The steps below are correct, but perhaps not sufficient for what you want to do.

Bioconductor packages consist of release branches, which are meant to be stable for the end user, and the 'devel' branch where new features can be introduced.

There is a version numbering scheme, outlined at


to ensure that each published version of the package has a different version, that versions in release always increase, and that the devel version is always ahead of the release version. For your package, the release version is 1.0.0, and the devel version is 1.1.0.

If you intended to make a change to the devel version of your package, because you were introducing a new feature or perhaps testing a bug fix, then you have been successful; you have pushed your changes to the devel ('master') branch, and incremented the version to 1.1.1.

If you intend to make this change also in the release, then the extra steps in


are required -- check out the RELEASE_3_8 branch, port your changes from master, increment the release version to 1.0.1, and push.

During the submission process packages are built immediately, but in the devel and release branches they are built nightly, approximately (I think that last night in particular there were issues with network connectivity that might severely limit the success of the build). The build reports are available from


note the 'snapshot' time stamps and commit information for the overall build and for your individual package to see whether your commit was included in the nightly build.


On 11/10/18, 5:53 AM, "Bioc-devel on behalf of Tang, Wenhao" <bioc-devel-bounces using r-project.org on behalf of wenhao.tang15 using imperial.ac.uk> wrote:

    Dear Bioconductor team,
    My package bayNorm has recently been accepted, it now has version 1.0.0. Currently I would like to make some changes to it. I look through the tutorials online but I am still very confused. Below is what I have done:
    My local repository has version 0.99.19. So I  did the following in my local repository:
      1.  git remote add upstream git using git.bioconductor.org:packages/bayNorm
      2.  git fetch --all
      3.  git checkout master
      4.  git merge origin/master
      5.  git merge upstream/master
    Now the local version is 1.1.0 rather than 0.99.19.
    Then I just did a small change (in addition, I bump the version to 1.1.1) and then run the following command under the local repository:
      1.  git push upstream master
      2.  git push origin master
    Is the above procedure correct? Will I see the package building report like what I have received during the submission process?
    Your tutorials are very clear, and I am sorry if my question is too trivial.
    Thank you very much!
    Best wishes,
    	[[alternative HTML version deleted]]
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