[Bioc-devel] Bioconductor Git/GitHub Mirrors

Leonardo Collado Torres lcollado at jhu.edu
Wed Jun 17 03:01:40 CEST 2015

On Tue, Jun 16, 2015 at 8:55 PM, Leonardo Collado Torres
<lcollado at jhu.edu> wrote:
> Hi,
> This sounds great! Not having to setup all those bridges everytime a
> new BioC version is released should be a great feature, plus keeping
> the commit history tidy. And we can still use Travis or other things
> like Slack notifications on our own bridges.

I meant repos here

I guess that it'd be good
> to remind users to pull new content from the bioc remote before trying
> to commit to svn.
> Anyhow, great work!
> I'm having a few problems with this new setup which hopefully are easy
> to iron out. Basically, I am stuck at the "git svn rebase && git svn
> dcommit --add-author-from" step. See 2b) below.
> 1) My git was pointing to an older version even after updated with
> brew. This was because I still had MacPorts around.
> How to diagnose:
> $ which git
> Wrong version was pointing to /opt/local/bin/git instead of
> /usr/local/bin/git Can also see by running
> $ git --version ## if it doesn't match the version number you
> installed from brew
> Solution:
> * Uninstall all of MacPorts following instructions from
> https://guide.macports.org/chunked/installing.macports.uninstalling.html
> * Follow part of
> http://stackoverflow.com/questions/20648235/error-linking-git-to-homebrew
> $ sudo brew prune
> $ brew update
> $ brew install git
> $ brew unlink git && brew link git
> You might want to update subversion.
> http://blog.victorquinn.com/fix-git-svn-in-mountain-lion might be
> relevant for you.
> 2) Test case: derfinderHelper.
> Smallest and simplest package I have, which won't matter much if
> things break because it's stable.
> a) You might want to delete update_remotes.sh after using it.
> * I deleted the git-svn bridges to both
> https://github.com/leekgroup/derfinderHelper and
> https://github.com/leekgroup/derfinderHelper-release
> * On https://github.com/leekgroup/derfinderHelper I removed bioc as a
> collaborator and deleted the push-hook since it seems like we don't
> need this anymore
> * Download and ran update_remotes.sh as instructed. It doesn't seem
> like we need it anymore after that point. If you leave it there, it
> seems to give problems.
> Easy to solve, but might want to clarify in the instructions.
> b) Following the section "Use Git Locally And Publicly" I get stuck on
> the "git svn rebase && git svn dcommit --add-author-from" step as
> shown at https://gist.github.com/lcolladotor/ac8838b25955caeebcf1. The
> "CONFLICT (add/add): Merge conflict" message lead me to
> http://stackoverflow.com/questions/19475387/how-to-handle-fix-git-add-add-conflicts
> from where I could resolve the initial problem that I saw using "git
> diff". But was basically the changes between the very first version of
> README.md and the very latest version of it.
> There must be a way to not have to go through every single commit
> and/or file one by one. Using "git rebase --continue" doesn't help.
> c) Given the issue with b, the devel branch already has a merge
> commit. Using http://stackoverflow.com/questions/927358/how-to-undo-the-last-commit
> I cleaned things up. I don't think it's needed, but I don't want to
> run into more issues.
> $ git rebase --abort
> $ git reset HEAD~1
> As you can tell, I'm no "git rebase" expert. From
> http://git-scm.com/docs/git-rebase it seems like the "ours" option
> might be useful. But right now I prefer to get some pointers on how to
> proceed before playing around further :P
> Thanks,
> Leo
> PS At the "Unable to determine upstream SVN information" section, I
> believe that there is a typo. "git svn dcomit" should be "git svn
> dcommit"
> On Tue, Jun 16, 2015 at 3:20 PM, Ryan C. Thompson <rct at thompsonclan.org> wrote:
>> This is great to hear. I sometimes want to delve into the source code of a
>> package's internals, but doing so through the SVN web interface is clunky.
>> Being able to use Github's repo browsing functionality for Bioc packages is
>> great.
>> On 06/16/2015 12:00 PM, Dan Tenenbaum wrote:
>>> Dear Bioconductors,
>>> We're pleased to announce the availability of Bioconductor Git Mirrors.
>>> These are read-only GitHub repositories (available under
>>> https://github.com/Bioconductor-mirror)
>>> for every Bioconductor software package. These repositories are
>>> synchronized with our
>>> Subversion repository. Package maintainers (or anyone else) can fork these
>>> repositories
>>> and do their development on the fork. Complete documentation of the
>>> mirrors is at
>>> http://bioconductor.org/developers/how-to/git-mirror/
>>> These mirrors supersede the Git-SVN bridge, which is now deprecated.
>>> Creation of new bridges is disabled and maintainers who are using the
>>> bridge
>>> should migrate to the Git mirrors as soon as it's convenient, as the
>>> bridge
>>> will eventually go away. Instructions for migrating can be found at the
>>> above link.
>>> Some features of the new Git Mirrors, and why we feel they are a better
>>> solution than the Git-SVN bridge:
>>>   - The mirrors contain complete commit history.
>>>   - The mirrors contain release branches for Bioconductor 3.0 and 3.1, and
>>>     new releases will be added as they happen. You will no longer need
>>>     separate repositories for release and devel.
>>>   - Setup is easy and you no longer have to grant any permissions on your
>>>     repository to other users. You can commit directly to Subversion
>>>     using git-svn (https://git-scm.com/docs/git-svn).
>>>   - Each git commit appears in the SVN log as a distinct SVN commit;
>>> commits
>>>     are no longer grouped together as they were with the bridge. Each git
>>>     commit can be mapped to a specific svn commit, and vice versa.
>>>   - The Git mirrors are much more reliable.
>>>   - Use is flexible. You can use git locally (without GitHub) or you
>>>     can use GitHub as well, to take advantage of all its social coding
>>> features.
>>>   - Using GitHub's code search, you can search the entire Bioconductor
>>> codebase.
>>>     Here's a sample search: https://goo.gl/jI92Ys
>>>   - Subversion is fully supported and remains the cannonical repository;
>>> use
>>>     of Git and GitHub is optional.
>>> We are excited about these new mirrors (brought to you by the hard
>>> work of Jim Hester) and we hope you are too. Questions and comments are
>>> welcome on the bioc-devel mailing list.
>>> Dan
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> _______________________________________________
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