My understanding is that this happens if you ever had non-linear commit history in your github repository (i.e. more than one branch changed and then were merged together), or if you used the old git/svn bridge. As far as I understand it, the only solution (in the near term) is to cherry pick the commits you want, a la
https://bioconductor.org/developers/how-to/git-mirrors/#dealing-with-prior-history--merge-conflicts And this has to be done every time you want to sync git to svn. Dan ----- Original Message ----- > From: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com> > To: "bioc-devel" <bioc-devel@r-project.org> > Sent: Wednesday, June 22, 2016 6:11:24 PM > Subject: [Bioc-devel] git svn dcommit > So I have made some updates to minfi and they are "safe" in Github. I now > want to commit them to Bioconductor. I get pretty strange results, > although I never really understand what is going on. > > 1. I clone a fresh copy of minfi from Github. > 2. I do > # bash update_remotes.sh > (using proper path of course) > 3. I do > # git checkout devel > # git svn rebase > # git merge master --log > without any hiccups, and all seems to work so far. > > Then I do > # git svn dcommit --add-author-from > > and hell starts (see output below). What is kind of weird is that now it > wants me to do 241 (!!!!!) rebase. And it starts to involve commits or > changes in files that haven't been touch for months. This is really pretty > weird, given that I have completed the previous steps fine. > > Any idea? Otherwise I hope I can get special help at Stanford in a few > days ... > > Best, > Kasper > > > > > > > $ git svn dcommit --add-author-from > Committing to > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/minfi ... > M DESCRIPTION > > ERROR from SVN: > Item is out of date: Item '/trunk/madman/Rpacks/minfi/DESCRIPTION' is out > of date > W: 85e070dd7d7825132ca3e6399f2e4dc19195b627 and refs/remotes/git-svn-devel > differ, using rebase: > :100644 100644 0025283098af2a8f4376b1300533a4c5aabaea7b > 8ac95ea78753b0a25d97c5debecbc6b2ead04ac0 M DESCRIPTION > :100644 100644 64a40f0b2655c7953ff154b42d6fa849e14462d3 > 92430c671d00d2131f5dc59cd3dbaa54679b585a M NAMESPACE > :040000 040000 732260942165586cd80d15ad9aa923e0969f604f > 5098b8e0b0cabed337857680555df1ea6dc853f8 M R > :040000 040000 655f45f8ddd850a62a643151b73711c12ca0c5bb > 9e9250da0089f89b9fb9ab986c617dbe66a3aab2 M inst > :040000 040000 3b781c09f0472bdff07ee734418b1bc263a31bd9 > 0f59f20b6cc89eaeeb94626a4445e3da26cef08f M man > :040000 040000 dd0723ff2712c28820000b81fafc1eb2de441e86 > 83da824cbedf66e528e93ba03abf4adb7e243669 M vignettes > First, rewinding head to replay your work on top of it... > Applying: updated citation information > Using index info to reconstruct a base tree... > .git/rebase-apply/patch:34: trailing whitespace. > beanplot, > .git/rebase-apply/patch:35: trailing whitespace. > RColorBrewer, > .git/rebase-apply/patch:36: trailing whitespace. > nor1mix, > .git/rebase-apply/patch:37: trailing whitespace. > siggenes, > .git/rebase-apply/patch:38: trailing whitespace. > limma, > warning: squelched 287 whitespace errors > warning: 292 lines add whitespace errors. > Falling back to patching base and 3-way merge... > Auto-merging vignettes/minfi.bib > CONFLICT (add/add): Merge conflict in vignettes/minfi.bib > Auto-merging man/utils.Rd > CONFLICT (add/add): Merge conflict in man/utils.Rd > Auto-merging man/read.450k.sheet.Rd > CONFLICT (add/add): Merge conflict in man/read.450k.sheet.Rd > Auto-merging man/read.450k.exp.Rd > CONFLICT (add/add): Merge conflict in man/read.450k.exp.Rd > Auto-merging man/read.450k.Rd > CONFLICT (add/add): Merge conflict in man/read.450k.Rd > Auto-merging man/preprocessQuantile.Rd > CONFLICT (add/add): Merge conflict in man/preprocessQuantile.Rd > Auto-merging man/mdsPlot.Rd > CONFLICT (add/add): Merge conflict in man/mdsPlot.Rd > Auto-merging man/getAnnotation.Rd > CONFLICT (add/add): Merge conflict in man/getAnnotation.Rd > Auto-merging man/estimateCellCounts.Rd > CONFLICT (add/add): Merge conflict in man/estimateCellCounts.Rd > Auto-merging man/densityBeanPlot.Rd > CONFLICT (add/add): Merge conflict in man/densityBeanPlot.Rd > Auto-merging man/cpgCollapse.Rd > CONFLICT (add/add): Merge conflict in man/cpgCollapse.Rd > Auto-merging man/bumphunter.Rd > CONFLICT (add/add): Merge conflict in man/bumphunter.Rd > Auto-merging man/blockFinder.Rd > CONFLICT (add/add): Merge conflict in man/blockFinder.Rd > Auto-merging man/RGChannelSet-class.Rd > CONFLICT (add/add): Merge conflict in man/RGChannelSet-class.Rd > Auto-merging man/GenomicRatioSet-class.Rd > CONFLICT (add/add): Merge conflict in man/GenomicRatioSet-class.Rd > Auto-merging man/GenomicMethylSet-class.Rd > CONFLICT (add/add): Merge conflict in man/GenomicMethylSet-class.Rd > Auto-merging inst/unitTests/test_preprocess.R > CONFLICT (add/add): Merge conflict in inst/unitTests/test_preprocess.R > Auto-merging inst/NEWS.Rd > CONFLICT (add/add): Merge conflict in inst/NEWS.Rd > Auto-merging R/utils.R > CONFLICT (add/add): Merge conflict in R/utils.R > Auto-merging R/rset.R > CONFLICT (add/add): Merge conflict in R/rset.R > Auto-merging R/rgset.R > CONFLICT (add/add): Merge conflict in R/rgset.R > Auto-merging R/read.manifest.R > CONFLICT (add/add): Merge conflict in R/read.manifest.R > Auto-merging R/read.450k.R > CONFLICT (add/add): Merge conflict in R/read.450k.R > Auto-merging R/preprocessSwan.R > CONFLICT (add/add): Merge conflict in R/preprocessSwan.R > Auto-merging R/preprocess.R > CONFLICT (add/add): Merge conflict in R/preprocess.R > Auto-merging R/plot.R > CONFLICT (add/add): Merge conflict in R/plot.R > Auto-merging R/mset.R > CONFLICT (add/add): Merge conflict in R/mset.R > Auto-merging R/manifest.R > CONFLICT (add/add): Merge conflict in R/manifest.R > Auto-merging R/grset.R > CONFLICT (add/add): Merge conflict in R/grset.R > Auto-merging R/gmset.R > CONFLICT (add/add): Merge conflict in R/gmset.R > Auto-merging R/getSex.R > CONFLICT (add/add): Merge conflict in R/getSex.R > Auto-merging R/estimateCellCounts.R > CONFLICT (add/add): Merge conflict in R/estimateCellCounts.R > Auto-merging R/bumphunter.R > CONFLICT (add/add): Merge conflict in R/bumphunter.R > Auto-merging R/blocks.R > CONFLICT (add/add): Merge conflict in R/blocks.R > Auto-merging R/anno.R > CONFLICT (add/add): Merge conflict in R/anno.R > Auto-merging NAMESPACE > CONFLICT (add/add): Merge conflict in NAMESPACE > Auto-merging DESCRIPTION > CONFLICT (add/add): Merge conflict in DESCRIPTION > error: Failed to merge in the changes. > Patch failed at 0001 updated citation information > 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 > > kaspers-air:~/Work/packages_github/minfi (devel *+|REBASE 1/241) $ > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
