[Bioc-devel] git svn dcommit

[Kasper Daniel Hansen]

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.org>
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-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" <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
>

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