[Bioc-devel] GitHub and svn

S Manimaran manimaran_1975 at hotmail.com
Sat Oct 15 23:21:08 CEST 2016

Thanks, Gabe and Kasper, for the info.

Following up on Gabe's reply: That means, I need to setup two projects in R-Studio with one for the release pointing to the release repository in SVN and another for the development version pointing to the development repository in SVN, right? Now, suppose I make a bug fix and commit to the release repository and I want the same fix in the development repository as well, how exactly do I go about this: Do I just manually copy those files with the changes to the other development version project and commit it there as well? (Personally, I also like to keep the original GitHub repository in sync with the latest in BioConductor development, which would mean I need to maintain three projects in R-Studio, right?) Or is there any other way about this?



From: Gabe Becker [mailto:becker.gabe at gene.com]
Sent: Saturday, October 15, 2016 4:35 PM
To: Kasper Daniel Hansen
Cc: S Manimaran; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] GitHub and svn


Related to what Kasper said, one thing you can do is commit directly to the canonical repo for your package (which again is not on github once the package is accepted) from rstudio. It supports svn.


On Oct 15, 2016 11:38 AM, "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com<mailto:kasperdanielhansen at gmail.com>> wrote:
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<mailto: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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