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.sh and 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.sh and 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 -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
