[Bioc-devel] stuck in setting up Bioconductor GitHub

Leif Väremo leif.varemo at chalmers.se
Tue Nov 15 10:50:37 CET 2016


I am trying to setup up my pre-existing Bioconductor package piano in GitHub. I am following the steps listed on the Bioconductor website:

  1.  git clone https://github.com/USER/REPO to clone the repository to your machine.
  2.  cd REPO to switch to the REPO directory.
  3.  bash /path/to/update_remotes.sh to setup the git remotes.
  4.  Commit to git and push to GitHub as you normally would.
  5.  Each time you want to push git commits to svn:
     *   git checkout devel to switch to the devel branch. (use release-X.X for release branches)
     *   git svn rebase to get the latest SVN changes.
     *   git merge master --log to merge your changes from the master branch or skip this step and work directly on the current branch.
     *   git svn dcommit --add-author-from to sync and commit your changes to svn. You may be prompted here for your SVN username and password.

After step 3, I have a local devel branch that does not yet exist in my remote (which would be my own fork of the Bioconductor-mirror).
My interpretation of step 4 is that I can work on any local branch, say devel or release-3.4, and then commit+push those changes to GitHub. However, when I try to push (either from the devel branch or a release branch) I get this:

remote: Permission to Bioconductor-mirror/piano.git denied to varemo.
fatal: unable to access 'https://github.com/Bioconductor-mirror/piano.git/': The requested URL returned error: 403

So it seems like it is trying to push to Bioconductor-mirror/piano.git whereas I would like to push to varemo/piano.git, right?

I assumed it was intended like this at least. So when I would be happy with my changes, e.g. updates to the local devel branch and in sync with the devel branch on varemo/piano.git, then I would move on and go through step 5 to push my edits to svn. But maybe I am missing something here?

As a side note: I am able to edit the local master branch and push that to GitHub, i.e. the master on varemo/piano.git. Is the idea that one should only work on master, and just use the other branches when doing step 5?

Would be grateful if anyone could clarify the system for me.


/Leif Väremo

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