Hi, are there any discussions to support github as first class citizen source repository for github ?
I remember that some projects have a setup where pull-requests to the main repository are accepted automatically if they can be merged cleanly. As improvement over the normal SVN workflow, the pull request could trigger a single package build, and be accepted only if that build passes without error. I also experience the pain Kasper described in packages I am involved in, and feel that this is an unnecessary burden. Yours, Steffen On Mi, 2016-06-22 at 22:46 -0400, Kasper Daniel Hansen wrote: > That's crazy. Not so much that I have to do it once, but that I > apparently > will have to do this going forward forever. I can vaguely understand > that > this is caused by the incompatibility between a linear only history > and a > branching history. > > It also doesn't seem to work; when I try to cherry pick commits I get > stuff > like > > $ git cherry-pick 94ef58b7ff5e24a9f36844f084ea3cebc89e846b > error: Commit 94ef58b7ff5e24a9f36844f084ea3cebc89e846b is a merge but > no -m > option was given. > fatal: cherry-pick failed > > One workable, but unsatisfactory, solution is to just checkout the > master > branch onto the devel branch and then commit. This will make svn > loose my > commit history, but at this points its not clear that it is worth the > time > to get my commit history into svn. > > Best, > Kasper > > On Wed, Jun 22, 2016 at 9:35 PM, Dan Tenenbaum <dtene...@fredhutch.or > g> > wrote: > > > > > 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-wit > > h-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 > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- 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
