[Bioc-devel] git svn dcommit

[Dan Tenenbaum]

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 Item is out of date: Item '/trunk/madman/Rpacks/minfi/DESCRIPTION' is out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) $
> 
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> 
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