Dear Dan, I am talking about the DOSE package, not GOSemSim.
FYI, I have figured out how to commit to Bioc svn via the following command: git checkout devel rm -rf .git/rebase-apply git reset --hard 418b1dd git svn rebase git merge master --no-edit git svn dcommit --add-author-from see https://github.com/Bioconductor-mirror/DOSE/commits/master. Thank you for your help and patience. Best Regards, Guangchuang On Tue, Jun 23, 2015 at 2:45 AM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > 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 > > > > -~----------~----~----~----~------~----~------~--~--- > > > -- --~--~---------~--~----~------------~-------~--~----~ 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
