[Bioc-devel] Bioconductor Git/GitHub Mirrors

[Dan Tenenbaum]

----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> To: "Leonardo Collado Torres" <lcollado at jhu.edu>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Tuesday, June 16, 2015 8:05:37 PM
> Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors
> 
> 
> 
> ----- Original Message -----
> > 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.
> 
> 
> 
> Sorry, I wasn't following along correctly, I didn't start with your
> github repos (formerly bridged). What's the link to it?
> 

Answering my own question: https://github.com/leekgroup/derfinderHelper

I can reproduce the issue, this is the first time it has come up in all the formerly-bridged repos I have tested. Will get back to you.

Dan


> Dan
> 
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