Hi Steffen, The usual
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 --log` to merge your changes from the master branch or skip this step and work directly on the current branch. 4. `git svn dcommit --add-author-from` to sync and commit your changes to svn. worked out for me. Your latest commit #4b68af1d156b73 and #a03fba48f82b7 (updated NEWS file) have now been comitted to hedgehog. I am not sure what is going on for you, but when I desperate with git/git-svn, right before the nervous breakdown, I go for the 'have you tried to turn it on and off again' solution, which generally works: 1) make sure you have comitted/pushed to Github and have a backup of any files/dir you gitignore 2) rm -rf mzR 3) git clone g...@github.com:sneumann/mzR.git 4) use update_remotes.sh Let me know if there's anything I can help with. Best wishes, Laurent On 2 January 2017 22:12, Steffen Neumann wrote: > Hi all,and a happy new year! > > I am experiencing a lot of frustration getting changes from github > pushed to BioC svn, and that includes some fixes for build issues > in packages depending on xcms. I have tried several options: > > 1) git svn checkout, git remote add, git merge and git svn dcommit. > 2) git clone github repo, update_remotes.shand git svn rebase > > both of which seem to fail due to the same reason, > which seems to be somewhere around > > https://github.com/sneumann/xcms/commit/f9be4f4f23c49f56074670658bc9665e093c8f83 > Author: Steffen Neumann <sneum...@ipb-halle.de> > Date:Fri Apr 1 14:09:29 2016 +0200 > Add automatic repair for "m/z sort assumption violated !" error in findPeaks > (centWave) > > I fail to fix these issues, and I am pretty frustrated > since I fell into the git-svn tarpit not for the first time, > it seems to be not fool-proof :-( > > Below are the details, hoping for help. > > Yours, > Steffen > > 1) git svn checkout, git remote add, git merge and git svn dcommit. > > So, I have a fresh > > sneumann@acryl /vol/R/BioC/devel/xcms3 $ git svn checkout > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms > > Then I add the github remote: > > sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git remote add origin > g...@github.com:sneumann/xcms.git > sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git fetch --tags > remote: Counting objects: 1475, done. > [...] >>From github.com:sneumann/xcms > * [new branch]devel-> origin/devel > * [new branch]master-> origin/master > * [new branch]xcms3-> origin/xcms3 > > The devel branch is what I use to be in sync with BioC-SVN: > > sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git checkout devel > Branch devel set up to track remote branch devel from origin. > Switched to a new branch 'devel' > > sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git merge origin/xcms3 > Updating a4421c3..a112206 > Fast-forward > DESCRIPTION|6 +- > NAMESPACE|48 ++- > R/AllGenerics.R|38 +- > [...] > vignettes/new_functionality.org|88 ++++- > 41 files changed, 4890 insertions(+), 2250 deletions(-) > > sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git svn dcommit > Committing to > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms ... > D R/00Generics.R > > ERROR from SVN: > Filesystem has no item: > '/bioconductor/!svn/txr/125556-1/trunk/madman/Rpacks/xcms/R/00Generics.R' > path not found > W: a1122065a96cf6e69088417d82fe987cda188cd5 and refs/remotes/git-svn differ, > using rebase: > :100644 100644 d36b142908ab4507e95d495d3ec450008a210e8f > a3f97d8f779d878b86a73d534415e679415e90f3 M DESCRIPTION > :100755 100755 a58677bbe186fea1447948c7286bc47d04735efc > fe69bdd2e969a906fac87d4bddd64bd90258f0cd M NAMESPACE > :040000 040000 2f5317b4c96f1d267b43ef8deba1532df6cb56db > c760aa2196632e99c0e0e59ed9700b27cb001fa3 M R > :040000 040000 45a9a220d96c3cdabe03cd8792dfc9628f058dab > e89e65a3eb7db9d6590c12b8fb94306811557789 M inst > :040000 040000 8284909b39e4d90eb957aadc26f92a8df9907cb2 > 125b7635684f73f65185aea52a7564c11bf187c5 M man > :040000 040000 da9a1c166e3df0c13cd3ea61e44356039b649cd2 > dbee4fedf371d6570b91cc7f50fe930294eac1f2 M vignettes > First, rewinding head to replay your work on top of it... > Applying: Add automatic repair for "m/z sort assumption violated !" error in > findPeaks (centWave) > Using index info to reconstruct a base tree... > A R/xcmsRaw.R > .git/rebase-apply/patch:37: trailing whitespace. > scan <- getScan(object, scan=i) > .git/rebase-apply/patch:82: trailing whitespace. > xr@env$mz[1:length(o)] <- scan[o, "mz"] > .git/rebase-apply/patch:83: trailing whitespace. > xr@env$intensity[1:length(o)] <- scan[o, "intensity"] > .git/rebase-apply/patch:88: trailing whitespace. > > .git/rebase-apply/patch:90: new blank line at EOF. > + > warning: 5 lines add whitespace errors. > Falling back to patching base and 3-way merge... > Auto-merging inst/unitTests/runit.findPeaksCentWave.R > CONFLICT (add/add): Merge conflict in inst/unitTests/runit.findPeaksCentWave.R > CONFLICT (modify/delete): R/xcmsRaw.R deleted in > 4c6815a9b4f985658f19824dde21748e49b5dad0 and modified in Add automatic repair > for "m/z sort assumption violated !" error in findPeaks (centWave). Version > Add automatic repair for "m/z sort assumption violated !" error in findPeaks > (centWave) of R/xcmsRaw.R left in tree. > error: Failed to merge in the changes. > Patch failed at 0001 Add automatic repair for "m/z sort assumption violated > !" error in findPeaks (centWave) > The copy of the patch that failed is found in: .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: command returned error: 128 > > > > ----------------------------------------------------------------------------- > > 2) git clone github repo, update_remotes.shand git svn rebase > > > sneumann@acryl /vol/R/BioC/devel/xcms3 $ git clone > g...@github.com:sneumann/xcms.git > Cloning into 'xcms'... > remote: Counting objects: 6343, done. > remote: Compressing objects: 100% (188/188), done. > remote: Total 6343 (delta 124), reused 0 (delta 0), pack-reused 6155 > Receiving objects: 100% (6343/6343), 3.74 MiB | 1.39 MiB/s, done. > Resolving deltas: 100% (4806/4806), done. > Checking connectivity... done. > > sneumann@acryl /vol/R/BioC/devel/xcms3 $ cd xcms > sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ ../update_remotes.sh > Enter passphrase for key '/home/sneumann/.ssh/id_rsa': > devel already exists, create a custom branch to track bioc/master with > `git branch --track NEW_NAME bioc/master` > 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 --log` to merge your changes from the master branch > or skip this step and work directly on the current branch. > 4. `git svn dcommit --add-author-from` to sync and commit > your changes to svn. > > sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git branch --track > biocmaster bioc/master > Branch biocmaster set up to track remote branch master from bioc. > > sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (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 (2.7.4) 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 > ... > r11695 = 612044c47521e079cf31425550729010d9654abc > [...] > r125419 = 4c6815a9b4f985658f19824dde21748e49b5dad0 > Done rebuilding > .git/svn/refs/remotes/git-svn-devel/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358 > > First, rewinding head to replay your work on top of it... > Applying: Add automatic repair for "m/z sort assumption violated !" error in > findPeaks (centWave) > Using index info to reconstruct a base tree... > A R/xcmsRaw.R > .git/rebase-apply/patch:37: trailing whitespace. > scan <- getScan(object, scan=i) > .git/rebase-apply/patch:82: trailing whitespace. > xr@env$mz[1:length(o)] <- scan[o, "mz"] > .git/rebase-apply/patch:83: trailing whitespace. > xr@env$intensity[1:length(o)] <- scan[o, "intensity"] > .git/rebase-apply/patch:88: trailing whitespace. > > .git/rebase-apply/patch:90: new blank line at EOF. > + > warning: 5 lines add whitespace errors. > Falling back to patching base and 3-way merge... > Auto-merging inst/unitTests/runit.findPeaksCentWave.R > CONFLICT (add/add): Merge conflict in inst/unitTests/runit.findPeaksCentWave.R > CONFLICT (modify/delete): R/xcmsRaw.R deleted in > 4c6815a9b4f985658f19824dde21748e49b5dad0 and modified in Add automatic repair > for "m/z sort assumption violated !" error in findPeaks (centWave). Version > Add automatic repair for "m/z sort assumption violated !" error in findPeaks > (centWave) of R/xcmsRaw.R left in tree. > error: Failed to merge in the changes. > Patch failed at 0001 Add automatic repair for "m/z sort assumption violated > !" error in findPeaks (centWave) > The copy of the patch that failed is found in: .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: 128 -- Laurent Gatto | @lgatt0 http://cpu.sysbiol.cam.ac.uk/ http://lgatto.github.io/ _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel