[Bioc-devel] git svn dcommit

Steffen Neumann sneumann at ipb-halle.de
Thu Jun 23 09:31:45 CEST 2016 

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 <dtenenba at 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" <kasperdanielhansen at gmail.com>
> > > To: "bioc-devel" <bioc-devel at 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 at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioc-devel at 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

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