[Bioc-devel] stuck in setting up Bioconductor GitHub

Dan Tenenbaum dtenenba at fredhutch.org
Tue Nov 15 15:58:06 CET 2016

Did you fork the repository first?

----- Original Message -----
> From: "Leif Väremo" <leif.varemo at chalmers.se>
> To: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Tuesday, November 15, 2016 1:50:37 AM
> Subject: [Bioc-devel] stuck in setting up Bioconductor GitHub

> Hi,
> 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.
> Thanks
> /Leif Väremo
>	[[alternative HTML version deleted]]
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