Hi Guangchuang, I don't see any new commits from you in the git side, at least not in master:
https://github.com/GuangchuangYu/GOSemSim/commits/master Could it be that you have not pushed your changes to master? I tried the following and it worked for me: git clone https://github.com/GuangchuangYu/GOSemSim cd GOSemSim bash ../mirror/update_remotes.sh git checkout devel git svn rebase Dan ----- Original Message ----- > From: "Guangchuang Yu" <g...@connect.hku.hk> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: bioc-devel@r-project.org > Sent: Monday, June 22, 2015 6:02:25 AM > Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors > > > > > 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 > > -~----------~----~----~----~------~----~------~--~--- > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
