Dear Dan, Thanks for your information. I have successfully commit to Bioc svn via github yesterday, see https://github.com/Bioconductor-mirror/DOSE/commits/master.
Today I modify some code, and push it to github. But when I try to push it to Bioc svn, it throw error indicating that everything is conflict: ➜ DOSE git:(master) git checkout devel Previous HEAD position was c8a294e... implement dotplot for enrichResult Switched to branch 'devel' Your branch is ahead of 'bioc/master' by 70 commits. (use "git push" to publish your local commits) ➜ DOSE git:(devel) git svn rebase First, rewinding head to replay your work on top of it... Applying: Initial commit Applying: move to github Using index info to reconstruct a base tree... <stdin>:325: trailing whitespace. ##' cnetplot method generics <stdin>:326: trailing whitespace. ##' <stdin>:327: trailing whitespace. ##' <stdin>:328: trailing whitespace. ##' @docType methods <stdin>:329: trailing whitespace. ##' @name cnetplot warning: squelched 467 whitespace errors warning: 472 lines add whitespace errors. Falling back to patching base and 3-way merge... warning: Cannot merge binary files: data/Info_Contents_human_DO.rda (HEAD vs. move to github) warning: Cannot merge binary files: data/EG2DO.rda (HEAD vs. move to github) warning: Cannot merge binary files: data/DOSEEnv.rda (HEAD vs. move to github) warning: Cannot merge binary files: data/DO2EG.rda (HEAD vs. move to github) Auto-merging vignettes/DOSE.bib CONFLICT (add/add): Merge conflict in vignettes/DOSE.bib Auto-merging vignettes/DOSE.Rnw CONFLICT (add/add): Merge conflict in vignettes/DOSE.Rnw Auto-merging man/theme_dose.Rd CONFLICT (add/add): Merge conflict in man/theme_dose.Rd Auto-merging man/summary-methods.Rd CONFLICT (add/add): Merge conflict in man/summary-methods.Rd Auto-merging man/simplot.Rd CONFLICT (add/add): Merge conflict in man/simplot.Rd Auto-merging man/show-methods.Rd CONFLICT (add/add): Merge conflict in man/show-methods.Rd Auto-merging man/setting.graph.attributes.Rd CONFLICT (add/add): Merge conflict in man/setting.graph.attributes.Rd Auto-merging man/setReadable.Rd CONFLICT (add/add): Merge conflict in man/setReadable.Rd Auto-merging man/scaleNodeColor.Rd CONFLICT (add/add): Merge conflict in man/scaleNodeColor.Rd Auto-merging man/rebuildAnnoData.Rd CONFLICT (add/add): Merge conflict in man/rebuildAnnoData.Rd Auto-merging man/plot-methods.Rd CONFLICT (add/add): Merge conflict in man/plot-methods.Rd Auto-merging man/netplot.Rd CONFLICT (add/add): Merge conflict in man/netplot.Rd Auto-merging man/list2graph.Rd CONFLICT (add/add): Merge conflict in man/list2graph.Rd Auto-merging man/gseaplot.Rd CONFLICT (add/add): Merge conflict in man/gseaplot.Rd Auto-merging man/gseaResult-class.Rd CONFLICT (add/add): Merge conflict in man/gseaResult-class.Rd Auto-merging man/gsea.Rd CONFLICT (add/add): Merge conflict in man/gsea.Rd Auto-merging man/gseAnalyzer.Rd CONFLICT (add/add): Merge conflict in man/gseAnalyzer.Rd Auto-merging man/getGeneSet.Rd CONFLICT (add/add): Merge conflict in man/getGeneSet.Rd Auto-merging man/getALLEG.Rd CONFLICT (add/add): Merge conflict in man/getALLEG.Rd Auto-merging man/geneSim.Rd CONFLICT (add/add): Merge conflict in man/geneSim.Rd Auto-merging man/gene2DO.Rd CONFLICT (add/add): Merge conflict in man/gene2DO.Rd Auto-merging man/fortify.gseaResult.Rd CONFLICT (add/add): Merge conflict in man/fortify.gseaResult.Rd Auto-merging man/fortify.enrichResult.Rd CONFLICT (add/add): Merge conflict in man/fortify.enrichResult.Rd Auto-merging man/enrichResult-class.Rd CONFLICT (add/add): Merge conflict in man/enrichResult-class.Rd Auto-merging man/enrichDO.Rd CONFLICT (add/add): Merge conflict in man/enrichDO.Rd Auto-merging man/enrich.internal.Rd CONFLICT (add/add): Merge conflict in man/enrich.internal.Rd Auto-merging man/doSim.Rd CONFLICT (add/add): Merge conflict in man/doSim.Rd Auto-merging man/computeIC.Rd CONFLICT (add/add): Merge conflict in man/computeIC.Rd Auto-merging man/cnetplot.internal.Rd CONFLICT (add/add): Merge conflict in man/cnetplot.internal.Rd Auto-merging man/cnetplot-methods.Rd CONFLICT (add/add): Merge conflict in man/cnetplot-methods.Rd Auto-merging man/barplot.enrichResult.Rd CONFLICT (add/add): Merge conflict in man/barplot.enrichResult.Rd Auto-merging man/TERMID2EXTID.Rd CONFLICT (add/add): Merge conflict in man/TERMID2EXTID.Rd Auto-merging man/TERM2NAME.Rd CONFLICT (add/add): Merge conflict in man/TERM2NAME.Rd Auto-merging man/EXTID2TERMID.Rd CONFLICT (add/add): Merge conflict in man/EXTID2TERMID.Rd Auto-merging man/EXTID2NAME.Rd CONFLICT (add/add): Merge conflict in man/EXTID2NAME.Rd Auto-merging man/DataSet.Rd CONFLICT (add/add): Merge conflict in man/DataSet.Rd Auto-merging man/DOSE-package.Rd CONFLICT (add/add): Merge conflict in man/DOSE-package.Rd Auto-merging man/ALLEXTID.Rd CONFLICT (add/add): Merge conflict in man/ALLEXTID.Rd Auto-merging data/Info_Contents_human_DO.rda CONFLICT (add/add): Merge conflict in data/Info_Contents_human_DO.rda Auto-merging data/EG2DO.rda CONFLICT (add/add): Merge conflict in data/EG2DO.rda Auto-merging data/DOSEEnv.rda CONFLICT (add/add): Merge conflict in data/DOSEEnv.rda Auto-merging data/DO2EG.rda CONFLICT (add/add): Merge conflict in data/DO2EG.rda Auto-merging R/utilities.R CONFLICT (add/add): Merge conflict in R/utilities.R Auto-merging R/simplot.R CONFLICT (add/add): Merge conflict in R/simplot.R Auto-merging R/gsea.R CONFLICT (add/add): Merge conflict in R/gsea.R Auto-merging R/gseAnalyzer.R CONFLICT (add/add): Merge conflict in R/gseAnalyzer.R Auto-merging R/geneSim.R CONFLICT (add/add): Merge conflict in R/geneSim.R Auto-merging R/enrichDO.R CONFLICT (add/add): Merge conflict in R/enrichDO.R Auto-merging R/enrich.internal.R CONFLICT (add/add): Merge conflict in R/enrich.internal.R Auto-merging R/cnetplot.R CONFLICT (add/add): Merge conflict in R/cnetplot.R Auto-merging R/barplot.R CONFLICT (add/add): Merge conflict in R/barplot.R Auto-merging R/DOSE-package.R CONFLICT (add/add): Merge conflict in R/DOSE-package.R Auto-merging R/AllGenerics.R CONFLICT (add/add): Merge conflict in R/AllGenerics.R Auto-merging NEWS CONFLICT (add/add): Merge conflict in NEWS Auto-merging NAMESPACE CONFLICT (add/add): Merge conflict in NAMESPACE Auto-merging DESCRIPTION CONFLICT (add/add): Merge conflict in DESCRIPTION Failed to merge in the changes. Patch failed at 0002 move to github The copy of the patch that failed is found in: /Users/guangchuangyu/github/DOSE/.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 ➜ DOSE git:(577c5d0) ✗ Can you help solving this? Best Regards, Guangchuang On Sat, Jun 20, 2015 at 2:27 AM, 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 > > > -- --~--~---------~--~----~------------~-------~--~----~ 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