On Tue, Jun 16, 2015 at 8:55 PM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote: > 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 meant repos here 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 > > You might want to update subversion. > http://blog.victorquinn.com/fix-git-svn-in-mountain-lion might be > relevant for you. > > 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 > * 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. > Easy to solve, but might want to clarify in the instructions. > > 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. > > c) Given the issue with b, the devel branch already has a merge > commit. Using > http://stackoverflow.com/questions/927358/how-to-undo-the-last-commit > I cleaned things up. I don't think it's needed, but I don't want to > run into more issues. > $ git rebase --abort > $ git reset HEAD~1 > > > As you can tell, I'm no "git rebase" expert. From > http://git-scm.com/docs/git-rebase it seems like the "ours" option > might be useful. But right now I prefer to get some pointers on how to > proceed before playing around further :P > > Thanks, > Leo > > > PS At the "Unable to determine upstream SVN information" section, I > believe that there is a typo. "git svn dcomit" should be "git svn > dcommit" > > On Tue, Jun 16, 2015 at 3:20 PM, Ryan C. Thompson <r...@thompsonclan.org> > wrote: >> This is great to hear. I sometimes want to delve into the source code of a >> package's internals, but doing so through the SVN web interface is clunky. >> Being able to use Github's repo browsing functionality for Bioc packages is >> great. >> >> >> On 06/16/2015 12:00 PM, Dan Tenenbaum wrote: >>> >>> Dear Bioconductors, >>> >>> We're pleased to announce the availability of Bioconductor Git Mirrors. >>> These are read-only GitHub repositories (available under >>> https://github.com/Bioconductor-mirror) >>> 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 >>> >>> http://bioconductor.org/developers/how-to/git-mirror/ >>> >>> 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 (https://git-scm.com/docs/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: https://goo.gl/jI92Ys >>> - 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. >>> >>> Dan >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
