----- Original Message ----- > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "Leonardo Collado Torres" <lcoll...@jhu.edu> > Cc: "bioc-devel" <bioc-devel@r-project.org>, "Ryan C. Thompson" > <r...@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" <lcoll...@jhu.edu> > > To: "Ryan C. Thompson" <r...@thompsonclan.org> > > Cc: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" > > <bioc-devel@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? Dan _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
