[Bioc-devel] GitHub and svn

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Sat Oct 15 20:36:19 CEST 2016

Not at the moment.  We are in the (long) process of changing this, but
there is no ETA for it.

The complications we currently have, as soon as a package is accepted in
Bioconductor, is that the "true" repository then becomes Bioconductor SVN
and your Github repository is just a way for you to develop.  This is not
the case during package submission.


On Sat, Oct 15, 2016 at 12:19 PM, S Manimaran <manimaran_1975 at hotmail.com>

> Hi,
> I never understood the github mirror setup and the instructions below look
> unnecessarily complicated to me. I see that the current package submission
> process with the automatic hook added to github is the most easiest of all
> with every commit to github automatically triggering a build at
> Bioconductor. Now, my question is: Can't this same procedure be carried
> over once the Bioconductor 3.4 is released as well i.e commits to github
> automatically resulting in triggering a build at Bioconductor? The main use
> case that I am looking for is an easy way to commit directly from inside
> R-Studio. With R-Studio setup for GitHub project, it directly commits to
> GitHub, but now for having to commit to BioConductor, if the automatic
> trigger works well as is the case with the new package submission process,
> all is well and good. But if I have to do as what the page in git-mirror
> says, then it looks like that I have to get out of R-Studio to do some
> overly complicated process to achieve the s!
>  ame. It will be really helpful if I can continue to use the automatic
> trigger to automatically build after Bioconductor 3.4 release as well.
> http://bioconductor.org/developers/how-to/git-mirror/
> Scenario 2: Set Up Your Own GitHub Repository
> If you do not already have a public git repository for package REPO the
> simplest thing to do is navigate to https://github.com/
> Bioconductor-mirror/REPO and click the Fork button in the upper right.
> This will create a copy of the repository on your personal account. You may
> want to re-enable issue tracking in your repository (it's disabled in the
> read-only mirrors and forks inherit this setting). To do this, go to
> Settings and then click the Issues checkbox. Then perform the following
> steps in your terminal.
>   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.
> When you're done, be sure and merge any changes from svn back into the git
> master branch:
> git checkout master
> git merge devel
> Thanks,
> Mani
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