[Bioc-devel] Bioconductor Git/GitHub Mirrors

From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
To: "Leonardo Collado Torres" <lcollado at jhu.edu>
Cc: "bioc-devel" <bioc-devel at r-project.org>, "Ryan C. Thompson" <rct at thompsonclan.org>
Sent: Tuesday, June 16, 2015 7:02:36 PM
Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors



----- Original Message -----

From: "Leonardo Collado Torres" <lcollado at jhu.edu>
To: "Ryan C. Thompson" <rct at thompsonclan.org>
Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel"
<bioc-devel at r-project.org>
Sent: Tuesday, June 16, 2015 5:55:05 PM
Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

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 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

Good to know. Things seem to work on the Macs I have tested with the
vanilla git-svn that ships with the OS.

You might want to update subversion.
http://blog.victorquinn.com/fix-git-svn-in-mountain-lion might be
relevant for you.

I haven't needed to update svn.

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

Yes, you can delete the push hook. Leaving it does no harm as long as
the bridge has been deleted (nobody will listen to the hook on the
other end once the bridge is deleted).

* 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.

Can you explain what problems?

Easy to solve, but might want to clarify in the instructions.

I do this in a separate directory:

git clone https://github.com/Bioconductor/mirror.git

and then I have a repos containing the script where I can run 'git
pull' if it ever changes. You could also symlink to it in
/usr/local/bin. We'll see about changing the docs for this.

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.

I didn't have this problem.