[Bioc-devel] Bioconductor Git/GitHub Mirrors

Jim Hester james.f.hester at gmail.com
Wed Jul 15 18:03:42 CEST 2015


I think you have characterized the main issue well, a number of people have
run into issues stemming from the same problem. (
https://stat.ethz.ch/pipermail/bioc-devel/2015-June/007730.html and a
number of off-list queries).

As you mentioned the problems stem from the fact the SVN repositories has
only truncated history compared to the git repositories. Because git-svn
only handles completely linear histories even if you merge the two
histories locally you can still run into problems when running git svn

I agree syncing the SVN history with the original GitHub history should in
theory fix this problem, however because you cannot rewrite history with
SVN I am not positive it is actually possible to accomplish.

I will investigate that stackoverflow answer to see if there is any
techniques we could apply here, thank you for the link I had not come
across that previously.

I am also separately investigating a SubGit <http://www.subgit.com/>
solution that I believe will address this issue and also allow users to
interact with Bioconductor repositories exactly how they would with any
other git remote.

Thank you reaching out, this is definitely a pain point I am aware of and
trying to actively address. The current solution is IMHO less than ideal. I
would be happy to talk at Bioc2015 next week if you want to discuss in


On Tue, Jul 14, 2015 at 4:34 PM, Siddhartha Bagaria <sidb at google.com> wrote:

[cc]: bioc-devel for discussion with wider community.
> Hello Jim!
> This is related to using the new git mirror setup with pre-existing github
> repos (not forks of the mirror).
> I tried following the thread on
> https://stat.ethz.ch/pipermail/bioc-devel/2015-June/007725.html but it
> looks like the problem was not clearly reproduced, and a solution was not
> reached. I will briefly describe the problem here but am inclined to
> discuss possible solutions further in person during the upcoming conference
> if you will be there.
> The problem with an already existing github repo in the new setup is that
> the master branch of that repo will have its own commit history, which will
> be different from the svn commit history (no common ancestor). As a result,
> merging the entire master branch into the newly created devel branch will
> try to merge all the commits from master since the beginning. Because there
> is no common ancestor, all the new edits will appear as merge-conflicts.
> One can manually resolve these conflicts but the process is cumbersome and
> error-prone.
> One way of skipping to manually resolve all the conflicts is merging the
> commits from devel into master first with strategy "ours", so that master
> gets the commit logs from devel but the content in master is unchanged (to
> avoid addressing conflicts). After this, a merge back into devel will work
> without conflicts. However, there is a problem with both these merge
> approaches.
> After a resolved merge (through manual resolution of conflicts, or through
> pre-merging histories), the commit histories between devel and master
> branches will be in sync, but the commit history in devel will now have
> extra entries from master interleaved with its previously existing entries.
> This would mean that now the devel branch and the svn repo do not have a
> common history. 'git svn' will get confused by these interleaved commits
> and will complain "Unable to determine upstream SVN information from HEAD
> history". So a merge does not work with this setup.
> The easiest solution so far is to cherry-pick the new commits from master
> and only merge those with the devel branch, so that svn and git continue to
> share a common history up until the cherry-picks. While this works
> smoothly, this is error-prone again as a commit can be missed when manually
> cherry-picking.
> It seems like one solution would be a one-time ability to sync the commit
> history of SVN repo with the commit history of the original github repo.
> This way, all three repos will have common ancestors. Other solutions which
> I have not studied in depth include:
> http://stackoverflow.com/questions/3864934/how-do-i-re-integrate-a-svn-and-git-repository-without-a-common-history
> Let me know if you would like a reproducible example. I am happy to
> discuss more.
> Cheers!
> Sid

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