Hi, Dan previously said:
Try starting over again. Remove your local repository and do a fresh clone: git clone https://github.com/leekgroup/derfinderHelper.git cd derfinderHelper bash /path/to/update_remotes.sh git checkout devel git svn rebase git merge master --no-edit git svn dcommit --add-author-from So I went and did that. Note that if you have local branches, like I did, make sure that you push them to GitHub first. 1) I first encountered an authentification error. I solved it below by deleting any previous SVN auth info I had (I only use SVN for Bioc). $ git svn dcommit --add-author-from --username=l.collado-torres Committing to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/derfinderHelper ... ERROR from SVN: URL access forbidden for unknown reason: Access to '/bioconductor/!svn/me' forbidden No changes between ef1c7dc3236ba31adace8c2205d30cc76e913032 and refs/remotes/git-svn-devel Resetting to the latest refs/remotes/git-svn-devel ERROR: Not all changes have been committed into SVN, however the committed ones (if any) seem to be successfully integrated into the working tree. Please see the above messages for details. Solution: ## Check what auth files I had $ ls ~/.subversion/auth/svn.simple/* ## Was my username in any of them? Nope $ grep -l l.collado-torres ~/.subversion/auth/svn.simple/* ## Clear them. If you use SVN for multiple repos, you don't want to do this. $ rm ~/.subversion/auth/svn.simple/* ## Yup, it's empty. $ ls ~/.subversion/auth/svn.simple/* ## Start over and use this line on the first git svn rebase $ git svn rebase --username=l.collado-torres ## Now my SVN auth info is there $ ls ~/.subversion/auth/svn.simple/* $ grep -l l.collado-torres ~/.subversion/auth/svn.simple/* 2) The commands Dan posted before worked just like he described. That is, it didn't commit anything back to SVN (since there's nothing new). I'm re-posting them for clarity. ## Remove local repository and do a fresh clone git clone https://github.com/leekgroup/derfinderHelper.git cd derfinderHelper bash /path/to/update_remotes.sh git checkout devel git svn rebase git merge master --no-edit git svn dcommit --add-author-from ## Output from last command Committing to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/derfinderHelper ... No changes 4a21725268e160061103dadb063d0f382235d7e6~1 == 4a21725268e160061103dadb063d0f382235d7e6 No changes between 4a21725268e160061103dadb063d0f382235d7e6 and refs/remotes/git-svn-devel Resetting to the latest refs/remotes/git-svn-devel As Dan pointed out earlier, I do not want to make my "master" commit history the one from SVN. Want I want to achieve is to have my past commit history be the one from GitHub, and then after that, I don't mind the double commit messages like in https://github.com/rmflight/categoryCompare/commit/762bf7046931096b730e21d8a9c4d0d02c734602 and https://github.com/rmflight/categoryCompare/commit/e132385d0ada77bb9a43e1f7e0027f6b6d59af19 3) With my fresh clone, if I follow the original instructions, I still end with the problem I described in my first email. $ git clone https://github.com/leekgroup/derfinderHelper.git Cloning into 'derfinderHelper'... remote: Counting objects: 387, done. remote: Total 387 (delta 0), reused 0 (delta 0), pack-reused 387 Receiving objects: 100% (387/387), 81.50 KiB | 0 bytes/s, done. Resolving deltas: 100% (214/214), done. Checking connectivity... done. cd derfinderHelper $ bash ../update_remotes.sh Commit to git as normal, when you want to push your commits to svn 1. `git checkout devel` to switch to the devel branch. (use release-X.X for release branches) 2. `git svn rebase` to get the latest SVN changes. 3. `git merge master --no-edit` to merge your changes from the master branch or skip this step and work directly on the current branch. 4. `git svn rebase && git svn dcommit --add-author-from` to sync and commit your changes to svn. $ git status On branch master Your branch is up-to-date with 'origin/master'. nothing to commit, working directory clean $ git checkout devel Switched to branch 'devel' Your branch is up-to-date with 'bioc/master'. $ git svn rebase Migrating from a git-svn v1 layout... Data from a previous version of git-svn exists, but .git/svn (required for this version (2.4.3) of git-svn) does not exist. Done migrating from a git-svn v1 layout Rebuilding .git/svn/refs/remotes/git-svn-devel/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358 ... r94975 = 89b8467a9e02d9f1d8ad2396c8d64cd44babd726 r95029 = 2372c1563d70030f278f2bf265d83e3013e67611 r95439 = d781eefa74f756c74561adf95bb638aa90935cc6 r95443 = 80527e2b9c1442e4d60127fd6d3f8a84cdb4a5db r95451 = cf659b64cca6bac275f7c15f93c9ab1407800aa7 r95474 = 4f5d77e2ea1427d0dbb4a4ffad163f7ad58facc4 r95475 = 31f6cf4046778942c9357a6378928652559217ff r96122 = e02c586ea34f902b4c068bcbe1d2d10d0830a00b r96159 = ed98baccbec23e0f70d8aba6a1eb11941c844081 r96165 = f56cb64e2fbd0cb7e4580047c1f27eb8400db67e r96168 = d8b8901ccfa13d30b8e9ecc5b195e7f6842a2194 r96450 = c5f4ad07ff97d733f36a1f2a6556fdbab7c46459 r96458 = 2f027fc7ee011b579bc51cc6bb062987fafb16cd r96463 = 97f90df0ec9cf1a6131bfd4479c6cca0981fa72c r96466 = a193e8c3ca4650a87b0f61416f0cd32169c193df r96488 = e3bb06e026e8890e9161d6504e208273998d74c5 r97003 = f2be8f26f80b369f14df9cd4db37b573db71a8e3 r97073 = 2698148110d3b45ef335e3ce1ce555af7459bbaa r100624 = 4cc67a757cd51ce529575197ab7dddcf7dfde286 r102591 = 9b856813fa041972a398ddc22362bf3c52789d5b r102594 = 441927a8a2d41ea0c7f0db7f05e1c2600a45fe0d r104736 = 601760f4c3fffbd897fa4f8fa3a631dbf8d0dda8 r104883 = 1a2fcc1b1a63b3e7398e5d9001f6c358369d6161 r104889 = cb528993af8e7d9d4d41a17027dc64aec84e0255 r104895 = ace63767281447e9497876c700f3538f28d238d9 r104898 = 08ec97478d7836265db955f3032c28490b212488 r104900 = b452efe2f8923c5f2229feecc1b399d56364d52d r104916 = 3e54179b27b9641cff04f699fb5b915e45347b94 r104998 = 3e8de0408d30bea6b06163a63d179dec5456eaa8 Done rebuilding .git/svn/refs/remotes/git-svn-devel/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358 Current branch devel is up to date. $ git merge master --no-edit Merge made by the 'recursive' strategy. $ git status On branch devel Your branch is ahead of 'bioc/master' by 73 commits. (use "git push" to publish your local commits) nothing to commit, working directory clean $ git svn rebase && git svn dcommit --add-author-from First, rewinding head to replay your work on top of it... Applying: Initial commit Using index info to reconstruct a base tree... Falling back to patching base and 3-way merge... Auto-merging README.md CONFLICT (add/add): Merge conflict in README.md Failed to merge in the changes. Patch failed at 0001 Initial commit The copy of the patch that failed is found in: /Users/lcollado/Dropbox/JHSPH/Code/derfinderHelper/.git/rebase-apply/patch When you have resolved this problem, run "git rebase --continue". If you prefer to skip this patch, run "git rebase --skip" instead. To check out the original branch and stop rebasing, run "git rebase --abort". rebase refs/remotes/git-svn-devel: command returned error: 1 $ git status rebase in progress; onto 3e8de04 You are currently rebasing branch 'devel' on '3e8de04'. (fix conflicts and then run "git rebase --continue") (use "git rebase --skip" to skip this patch) (use "git rebase --abort" to check out the original branch) Changes to be committed: (use "git reset HEAD <file>..." to unstage) new file: LICENSE Unmerged paths: (use "git reset HEAD <file>..." to unstage) (use "git add <file>..." to mark resolution) both added: README.md $ git rebase --abort $ git status On branch devel Your branch is ahead of 'bioc/master' by 73 commits. (use "git push" to publish your local commits) nothing to commit, working directory clean $ git svn dcommit --add-author-from Committing to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/derfinderHelper ... No changes 750d5e459ae6f882922144a6ba4641cdc8ba84b3~1 == 750d5e459ae6f882922144a6ba4641cdc8ba84b3 No changes between 750d5e459ae6f882922144a6ba4641cdc8ba84b3 and refs/remotes/git-svn-devel Resetting to the latest refs/remotes/git-svn-devel $ git status On branch devel Your branch is up-to-date with 'bioc/master'. nothing to commit, working directory clean 4) In an attempt to try to achieve my goal, I go back to the state after the merge (that is, after one git svn rebase). That is: ## Remove local repository and do a fresh clone git clone https://github.com/leekgroup/derfinderHelper.git cd derfinderHelper bash /path/to/update_remotes.sh git checkout devel git svn rebase git merge master --no-edit I know the second git svn rebase creates the conflicts, but I thought from http://stackoverflow.com/questions/2959443/why-is-the-meaning-of-ours-and-theirs-reversed-with-git-svn that I could get git svn to recursively choose my git history over my svn history. However, it doesn't work as shown below. From http://git-scm.com/docs/git-svn, under the "rebase" command, it says "This accepts all options that git svn fetch and git rebase accept." Below I try a couple of different syntaxes which I thought would work given http://git-scm.com/docs/git-rebase $ git svn rebase -s strategy recursive -X theirs Unknown option: X $ git svn rebase -s strategy "recursive" -X "theirs" Unknown option: X $ git svn rebase -s strategy recursive -Xtheirs Unknown option: X Unknown option: t Unknown option: e $ git svn rebase -s strategy recursive --strategy-option theirs Unknown option: strategy-option $ git svn rebase -s strategy "recursive -X theirs" First, rewinding head to replay your work on top of it... /usr/local/Cellar/git/2.4.3/libexec/git-core/git-rebase--merge: line 70: git-merge-strategy: command not found Unknown exit code (127) from command: git-merge-strategy ed5ceda167117937ea498d8713361c34e2fb84e3^ -- HEAD ed5ceda167117937ea498d8713361c34e2fb84e3 rebase --strategy=strategy refs/remotes/git-svn-devel: command returned error: 1 $ git rebase --abort $ git svn rebase -s theirs First, rewinding head to replay your work on top of it... /usr/local/Cellar/git/2.4.3/libexec/git-core/git-rebase--merge: line 70: git-merge-theirs: command not found Unknown exit code (127) from command: git-merge-theirs ed5ceda167117937ea498d8713361c34e2fb84e3^ -- HEAD ed5ceda167117937ea498d8713361c34e2fb84e3 rebase --strategy=theirs refs/remotes/git-svn-devel: command returned error: 1 $ git rebase --abort I know https://github.com/leekgroup/derfinderHelper/commit/ed5ceda167117937ea498d8713361c34e2fb84e3 is the first commit in my git history and https://github.com/Bioconductor-mirror/derfinderHelper/commit/3e8de0408d30bea6b06163a63d179dec5456eaa8is the last commit in the svn history. What frustrates me the most at this point is that the opposite strategy ("ours") works: ## Remove local repository and do a fresh clone git clone https://github.com/leekgroup/derfinderHelper.git cd derfinderHelper bash /path/to/update_remotes.sh git checkout devel git svn rebase git merge master --no-edit $ git svn rebase -s ours First, rewinding head to replay your work on top of it... Already applied: 0001 Initial commit Already applied: 0002 Delete LICENSE Already applied: 0003 Imported derfinder::fstats.apply(). Having the function in a separate package should speed up the permutation cycles when using BiocParallel::SnowParam() Already applied: 0004 minor formatting changes Already applied: 0005 Fix links ## more output Already applied: 0066 Change to leekgroup in vignettes Already applied: 0067 Make startup messages very rare Already applied: 0068 Fix to make messages very rare All done. Inspecting with "git log", I only see commits from the svn history. The opposite of what I wanted, and hence why I want to use "theirs". Given the syntax that works with "ours", I would expect $ git svn rebase -s theirs to work. Hm... That lead me to http://stackoverflow.com/questions/173919/is-there-a-theirs-version-of-git-merge-s-ours but it didn't apply to this problem because that's for merging, not rebasing. During all of this, I noticed that I could manually resolve the conflicts using "theirs" via the SourceTree app. Sadly, I don't know how to get the command SourceTree runs behind the scene but it lead me to believe that I could manually choose for all the conflicting files to use "theirs", then add them, then continue rebasing, etc. That's how I found http://stackoverflow.com/questions/24743769/git-resolve-conflict-using-ours-theirs-for-all-files and... ## Remove local repository and do a fresh clone git clone https://github.com/leekgroup/derfinderHelper.git cd derfinderHelper bash /path/to/update_remotes.sh git checkout devel git svn rebase git merge master --no-edit git svn dcommit --add-author-from git svn rebase ## For each conflict loop, do grep -lr '<<<<<<<' . | xargs git checkout --theirs git add * ## If at some point you added files starting with . ## you will have to add them manually git rebase --continue ## Once that's done, do git svn dcommit --add-author-from ## Then pull from the Bioc mirror git pull In my case, that did: $ git svn dcommit --add-author-from Committing to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/derfinderHelper ... A LICENSE M README.md Committed r105182 A LICENSE M README.md r105182 = 07e2529c91e3bd6f12fc798ac39e4120a4f8154b (refs/remotes/git-svn-devel) D LICENSE ## more output Committed r105249 M R/zzz.R r105249 = d35a0af365c1b7417564b598611371acd3dd7469 (refs/remotes/git-svn-devel) No changes between 9fa56b177a184b18f75c8636a758ce18770831df and refs/remotes/git-svn-devel Resetting to the latest refs/remotes/git-svn-devel $ git status On branch devel Your branch is ahead of 'bioc/master' by 68 commits. (use "git push" to publish your local commits) nothing to commit, working directory clean $ git pull >From https://github.com/Bioconductor-mirror/derfinderHelper 3e8de04..d35a0af master -> bioc/master Already up-to-date. And now https://github.com/Bioconductor-mirror/derfinderHelper looks like I wanted it to look. It has a single SVN commit per git commit I originally did. Plus the original commits made directly to SVN by the git-svn bridge and others at Bioconductor. Yay!!! 5) Everything should be in sync.... well, kind of. So I went back to my master branch, did a new commit to test things. Then... git checkout devel git svn rebase git merge master ## I had some conflicts to resolve here git svn rebase Let me back to that issue with the first commit. Oh no!! However, Dan's earlier solution did work. That is, after making a new commit on the master branch git checkout devel git svn rebase git merge master git svn dcommit --add-author-from Or it did work partially since https://github.com/Bioconductor-mirror/derfinderHelper/commit/402100dc8d78ccbb99a4d65dc6f748fb7474a69d does not include the message from https://github.com/leekgroup/derfinderHelper/commit/4b874a895701fe81c108cb4c98d07d0177ebcacd At this point, I think the best for me would be to make my "master" branch have the same history as "devel" (aka master from https://github.com/Bioconductor-mirror/derfinderHelper) (my git history is there, just under the svn style of commits and with a different username) and continue from there like https://github.com/rmflight/categoryCompare is doing. Before doing so, I'll save my current "master" into another branch and push it to GitHub, just as a backup. Otherwise, for every new commit, I'll have to re-write the full SVN commit history and that will take too long. Ugh... that was huge. In summary, if this is ok, I plan for each of my other pkgs to: ## Make a copy of the "master" branch ## Push local branches to Github ## Remove local repository and do a fresh clone git clone https://github.com/myUsername/MyPackage.git cd MyPackage bash /path/to/update_remotes.sh git checkout devel git svn rebase git merge master --no-edit git svn dcommit --add-author-from git svn rebase ## For each conflict loop, do grep -lr '<<<<<<<' . | xargs git checkout --theirs git add * git rebase --continue ## Once that's done, do git svn dcommit --add-author-from ## Then pull from the Bioc mirror git pull ## Delete the master branch ## Make a new master branch which is a copy from the devel branch ## Continue as https://github.com/rmflight/categoryCompare is doing Cheers, Leo On Fri, Jun 19, 2015 at 2:27 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > > > ----- Original Message ----- >> From: "Guangchuang Yu" <g...@connect.hku.hk> >> To: bioc-devel@r-project.org >> Sent: Wednesday, June 17, 2015 5:04:04 AM >> Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors >> >> Dear Dan, >> >> I update my package >> GOSemSim(https://github.com/GuangchuangYu/GOSemSim), >> with the following steps: >> >> 1. delete the git-svn-bridge >> 1. bash /path/to/update_remotes.sh >> 2. git checkout devel >> 3. git checkout master >> 4. git merge devel >> >> All was fine without any error. >> > > I asked Jim about this and he said this last step may have made git svn fail > to find the svn information. You can do this command here: > > git reset --hard a3ff1e7a3efd09b0c > > That's the commit before the merge. You should then be able to run "git svn > dcommit". > > > Dan > > >> But when I follow the instruction to test a commit to svn. >> >> 1. Each time you want to push git commits to svn: >> 1. git checkout devel to switch to the devel branch. (use >> release-X.X >> for release branches) >> 2. git svn rebase to get the latest SVN changes. >> 3. git merge master --no-edit to merge your changes from the >> master >> branch or skip this step and work directly on the current >> branch. >> 4. git svn rebase && git svn dcommit --add-author-from to sync >> and >> commit your changes to svn. You may be prompted here for your >> SVN username >> and password. >> >> >> ➜ GOSemSim git:(master) git checkout devel >> Switched to branch 'devel' >> Your branch is up-to-date with 'bioc/master'. >> ➜ GOSemSim git:(devel) git svn rebase >> Migrating from a git-svn v1 layout... >> Data from a previous version of git-svn exists, but >> .git/svn >> (required for this version (2.4.1) of git-svn) does not exist. >> Done migrating from a git-svn v1 layout >> Rebuilding >> .git/svn/refs/remotes/git-svn-devel/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358 >> ... >> r35719 = 714adc6875914b83b673bcf93f6eac976676388d >> r36178 = 199736e1f199d80a16121c0dca7e4aac015140bc >> ... >> ... >> r104302 = b7770b576acd1439d7e01a5115866fe6bb84d2d7 >> r104400 = a3ff1e7a3efd09b0c0a760f2d4053331ee8039d2 >> Done rebuilding >> .git/svn/refs/remotes/git-svn-devel/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358 >> Current branch devel is up to date. >> >> GOSemSim git:(devel) git merge master --no-edit >> Updating a3ff1e7..5b9b679 >> Fast-forward >> ➜ GOSemSim git:(devel) git svn rebase && git svn dcommit >> --add-author-from >> Unable to determine upstream SVN information from working tree >> history >> >> >> It throw the above error. Any idea? >> >> Bests, >> Guangchuang >> -- >> --~--~---------~--~----~------------~-------~--~----~ >> Guangchuang Yu, PhD Candidate >> State Key Laboratory of Emerging Infectious Diseases >> School of Public Health >> The University of Hong Kong >> Hong Kong SAR, China >> www: http://ygc.name >> -~----------~----~----~----~------~----~------~--~--- >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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
