[Bioc-devel] Bioconductor Git/GitHub Mirrors

Yu, Guangchuang gcyu at connect.hku.hk
Mon Jun 22 15:02:25 CEST 2015 

Dear Dan,

Thanks for your information. I have successfully commit to Bioc svn via
github yesterday, see
https://github.com/Bioconductor-mirror/DOSE/commits/master.

Today I modify some code, and push it to github.

But when I try to push it to Bioc svn, it throw error indicating that
everything is conflict:

➜  DOSE git:(master) git checkout devel
Previous HEAD position was c8a294e... implement dotplot for enrichResult
Switched to branch 'devel'
Your branch is ahead of 'bioc/master' by 70 commits.
  (use "git push" to publish your local commits)
➜  DOSE git:(devel) git svn rebase
First, rewinding head to replay your work on top of it...
Applying: Initial commit
Applying: move to github
Using index info to reconstruct a base tree...
<stdin>:325: trailing whitespace.
##' cnetplot method generics
<stdin>:326: trailing whitespace.
##'
<stdin>:327: trailing whitespace.
##'
<stdin>:328: trailing whitespace.
##' @docType methods
<stdin>:329: trailing whitespace.
##' @name cnetplot
warning: squelched 467 whitespace errors
warning: 472 lines add whitespace errors.
Falling back to patching base and 3-way merge...
warning: Cannot merge binary files: data/Info_Contents_human_DO.rda (HEAD
vs. move to github)
warning: Cannot merge binary files: data/EG2DO.rda (HEAD vs. move to github)
warning: Cannot merge binary files: data/DOSEEnv.rda (HEAD vs. move to
github)
warning: Cannot merge binary files: data/DO2EG.rda (HEAD vs. move to github)
Auto-merging vignettes/DOSE.bib
CONFLICT (add/add): Merge conflict in vignettes/DOSE.bib
Auto-merging vignettes/DOSE.Rnw
CONFLICT (add/add): Merge conflict in vignettes/DOSE.Rnw
Auto-merging man/theme_dose.Rd
CONFLICT (add/add): Merge conflict in man/theme_dose.Rd
Auto-merging man/summary-methods.Rd
CONFLICT (add/add): Merge conflict in man/summary-methods.Rd
Auto-merging man/simplot.Rd
CONFLICT (add/add): Merge conflict in man/simplot.Rd
Auto-merging man/show-methods.Rd
CONFLICT (add/add): Merge conflict in man/show-methods.Rd
Auto-merging man/setting.graph.attributes.Rd
CONFLICT (add/add): Merge conflict in man/setting.graph.attributes.Rd
Auto-merging man/setReadable.Rd
CONFLICT (add/add): Merge conflict in man/setReadable.Rd
Auto-merging man/scaleNodeColor.Rd
CONFLICT (add/add): Merge conflict in man/scaleNodeColor.Rd
Auto-merging man/rebuildAnnoData.Rd
CONFLICT (add/add): Merge conflict in man/rebuildAnnoData.Rd
Auto-merging man/plot-methods.Rd
CONFLICT (add/add): Merge conflict in man/plot-methods.Rd
Auto-merging man/netplot.Rd
CONFLICT (add/add): Merge conflict in man/netplot.Rd
Auto-merging man/list2graph.Rd
CONFLICT (add/add): Merge conflict in man/list2graph.Rd
Auto-merging man/gseaplot.Rd
CONFLICT (add/add): Merge conflict in man/gseaplot.Rd
Auto-merging man/gseaResult-class.Rd
CONFLICT (add/add): Merge conflict in man/gseaResult-class.Rd
Auto-merging man/gsea.Rd
CONFLICT (add/add): Merge conflict in man/gsea.Rd
Auto-merging man/gseAnalyzer.Rd
CONFLICT (add/add): Merge conflict in man/gseAnalyzer.Rd
Auto-merging man/getGeneSet.Rd
CONFLICT (add/add): Merge conflict in man/getGeneSet.Rd
Auto-merging man/getALLEG.Rd
CONFLICT (add/add): Merge conflict in man/getALLEG.Rd
Auto-merging man/geneSim.Rd
CONFLICT (add/add): Merge conflict in man/geneSim.Rd
Auto-merging man/gene2DO.Rd
CONFLICT (add/add): Merge conflict in man/gene2DO.Rd
Auto-merging man/fortify.gseaResult.Rd
CONFLICT (add/add): Merge conflict in man/fortify.gseaResult.Rd
Auto-merging man/fortify.enrichResult.Rd
CONFLICT (add/add): Merge conflict in man/fortify.enrichResult.Rd
Auto-merging man/enrichResult-class.Rd
CONFLICT (add/add): Merge conflict in man/enrichResult-class.Rd
Auto-merging man/enrichDO.Rd
CONFLICT (add/add): Merge conflict in man/enrichDO.Rd
Auto-merging man/enrich.internal.Rd
CONFLICT (add/add): Merge conflict in man/enrich.internal.Rd
Auto-merging man/doSim.Rd
CONFLICT (add/add): Merge conflict in man/doSim.Rd
Auto-merging man/computeIC.Rd
CONFLICT (add/add): Merge conflict in man/computeIC.Rd
Auto-merging man/cnetplot.internal.Rd
CONFLICT (add/add): Merge conflict in man/cnetplot.internal.Rd
Auto-merging man/cnetplot-methods.Rd
CONFLICT (add/add): Merge conflict in man/cnetplot-methods.Rd
Auto-merging man/barplot.enrichResult.Rd
CONFLICT (add/add): Merge conflict in man/barplot.enrichResult.Rd
Auto-merging man/TERMID2EXTID.Rd
CONFLICT (add/add): Merge conflict in man/TERMID2EXTID.Rd
Auto-merging man/TERM2NAME.Rd
CONFLICT (add/add): Merge conflict in man/TERM2NAME.Rd
Auto-merging man/EXTID2TERMID.Rd
CONFLICT (add/add): Merge conflict in man/EXTID2TERMID.Rd
Auto-merging man/EXTID2NAME.Rd
CONFLICT (add/add): Merge conflict in man/EXTID2NAME.Rd
Auto-merging man/DataSet.Rd
CONFLICT (add/add): Merge conflict in man/DataSet.Rd
Auto-merging man/DOSE-package.Rd
CONFLICT (add/add): Merge conflict in man/DOSE-package.Rd
Auto-merging man/ALLEXTID.Rd
CONFLICT (add/add): Merge conflict in man/ALLEXTID.Rd
Auto-merging data/Info_Contents_human_DO.rda
CONFLICT (add/add): Merge conflict in data/Info_Contents_human_DO.rda
Auto-merging data/EG2DO.rda
CONFLICT (add/add): Merge conflict in data/EG2DO.rda
Auto-merging data/DOSEEnv.rda
CONFLICT (add/add): Merge conflict in data/DOSEEnv.rda
Auto-merging data/DO2EG.rda
CONFLICT (add/add): Merge conflict in data/DO2EG.rda
Auto-merging R/utilities.R
CONFLICT (add/add): Merge conflict in R/utilities.R
Auto-merging R/simplot.R
CONFLICT (add/add): Merge conflict in R/simplot.R
Auto-merging R/gsea.R
CONFLICT (add/add): Merge conflict in R/gsea.R
Auto-merging R/gseAnalyzer.R
CONFLICT (add/add): Merge conflict in R/gseAnalyzer.R
Auto-merging R/geneSim.R
CONFLICT (add/add): Merge conflict in R/geneSim.R
Auto-merging R/enrichDO.R
CONFLICT (add/add): Merge conflict in R/enrichDO.R
Auto-merging R/enrich.internal.R
CONFLICT (add/add): Merge conflict in R/enrich.internal.R
Auto-merging R/cnetplot.R
CONFLICT (add/add): Merge conflict in R/cnetplot.R
Auto-merging R/barplot.R
CONFLICT (add/add): Merge conflict in R/barplot.R
Auto-merging R/DOSE-package.R
CONFLICT (add/add): Merge conflict in R/DOSE-package.R
Auto-merging R/AllGenerics.R
CONFLICT (add/add): Merge conflict in R/AllGenerics.R
Auto-merging NEWS
CONFLICT (add/add): Merge conflict in NEWS
Auto-merging NAMESPACE
CONFLICT (add/add): Merge conflict in NAMESPACE
Auto-merging DESCRIPTION
CONFLICT (add/add): Merge conflict in DESCRIPTION
Failed to merge in the changes.
Patch failed at 0002 move to github
The copy of the patch that failed is found in:
   /Users/guangchuangyu/github/DOSE/.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: 1

➜  DOSE git:(577c5d0) ✗

Can you help solving this?

Best Regards,
Guangchuang

On Sat, Jun 20, 2015 at 2:27 AM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

>
>
> ----- Original Message -----
> > From: "Guangchuang Yu" <gcyu at connect.hku.hk>
> > To: bioc-devel at r-project.org
> > Sent: Wednesday, June 17, 2015 5:04:04 AM
> > Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors
> >
> > Dear Dan,
> >
> > I update my package
> > GOSemSim(https://github.com/GuangchuangYu/GOSemSim),
> > with the following steps:
> >
> > 1. delete the git-svn-bridge
> > 1. bash /path/to/update_remotes.sh
> > 2. git checkout devel
> > 3.   git checkout master
> > 4. git merge devel
> >
> > All was fine without any error.
> >
>
> I asked Jim about this and he said this last step may have made git svn
> fail to find the svn information. You can do this command here:
>
> git reset --hard a3ff1e7a3efd09b0c
>
> That's the commit before the merge. You should then be able to run "git
> svn dcommit".
>
>
> Dan
>
>
> > But when I follow the instruction to test a commit to svn.
> >
> >    1. Each time you want to push git commits to svn:
> >       1. git checkout devel to switch to the devel branch. (use
> >       release-X.X
> >       for release branches)
> >       2. git svn rebase to get the latest SVN changes.
> >       3. git merge master --no-edit to merge your changes from the
> >       master
> >       branch or skip this step and work directly on the current
> >       branch.
> >       4. git svn rebase && git svn dcommit --add-author-from to sync
> >       and
> >       commit your changes to svn. You may be prompted here for your
> > SVN username
> >       and password.
> >
> >
> > ➜  GOSemSim git:(master) git checkout devel
> > Switched to branch 'devel'
> > Your branch is up-to-date with 'bioc/master'.
> > ➜  GOSemSim git:(devel) git svn rebase
> > Migrating from a git-svn v1 layout...
> > Data from a previous version of git-svn exists, but
> >     .git/svn
> >     (required for this version (2.4.1) of git-svn) does not exist.
> > Done migrating from a git-svn v1 layout
> > Rebuilding
> >
> .git/svn/refs/remotes/git-svn-devel/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358
> > ...
> > r35719 = 714adc6875914b83b673bcf93f6eac976676388d
> > r36178 = 199736e1f199d80a16121c0dca7e4aac015140bc
> > ...
> > ...
> > r104302 = b7770b576acd1439d7e01a5115866fe6bb84d2d7
> > r104400 = a3ff1e7a3efd09b0c0a760f2d4053331ee8039d2
> > Done rebuilding
> >
> .git/svn/refs/remotes/git-svn-devel/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358
> > Current branch devel is up to date.
> >
> >   GOSemSim git:(devel) git merge master --no-edit
> > Updating a3ff1e7..5b9b679
> > Fast-forward
> > ➜  GOSemSim git:(devel) git svn rebase && git svn dcommit
> > --add-author-from
> > Unable to determine upstream SVN information from working tree
> > history
> >
> >
> > It throw the above error. Any idea?
> >
> > Bests,
> > Guangchuang
> > --
> > --~--~---------~--~----~------------~-------~--~----~
> > Guangchuang Yu, PhD Candidate
> > State Key Laboratory of Emerging Infectious Diseases
> > School of Public Health
> > The University of Hong Kong
> > Hong Kong SAR, China
> > www: http://ygc.name
> > -~----------~----~----~----~------~----~------~--~---
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>



-- 
--~--~---------~--~----~------------~-------~--~----~
Guangchuang Yu, PhD Candidate
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong
Hong Kong SAR, China
www: http://ygc.name
-~----------~----~----~----~------~----~------~--~---

	[[alternative HTML version deleted]]

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