News: Bioconductor Git/GitHub Mirrors
gravatar for Dan Tenenbaum
4.1 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:

Dear Bioconductors,

We're pleased to announce the availability of Bioconductor Git Mirrors. 
These are read-only GitHub repositories (available under
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

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 (
  •  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:
  •  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.

ADD COMMENTlink modified 4.1 years ago by Guangchuang Yu1.1k • written 4.1 years ago by Dan Tenenbaum8.2k
Answer: Bioconductor Git/GitHub Mirrors
gravatar for Steve Lianoglou
4.1 years ago by
Steve Lianoglou12k wrote:

... and there was much rejoicing!

ADD COMMENTlink written 4.1 years ago by Steve Lianoglou12k
Answer: Bioconductor Git/GitHub Mirrors
gravatar for Guangchuang Yu
4.1 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

I only run:


  1. bash /path/to/ to setup the git remotes.
  2. Commit to git and push to GitHub as you normally would.
  3. Each time you want to push git commits to svn:
    1. git checkout devel to switch to the devel branch. (use release-X.X for release branches)

When you’re done, be sure and merge any changes from svn back into the git master branch:

git checkout master
git merge devel


without other sub-step in step 3 since I though I don't have new commit to push to svn.


After that, I am trying to test it with a new commit, but I got the following msg:

Unable to determine upstream SVN information from working tree history



ADD COMMENTlink written 4.1 years ago by Guangchuang Yu1.1k

As the post stated, questions about this should be posted to the bioc-devel list. Please repost this there and include the link to your repository, and please post all commands and their output. Thanks.

ADD REPLYlink written 4.1 years ago by Dan Tenenbaum8.2k

already sent, thanks.

ADD REPLYlink written 4.1 years ago by Guangchuang Yu1.1k

but what is in


ADD REPLYlink written 6 months ago by karl.stamm10

I suggest following the documentation on the current help pages, and posting questions for help to the bioc-devel mailing list with enough information for someone to understand where you are running into problems.

ADD REPLYlink written 6 months ago by Martin Morgan ♦♦ 23k
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