[Bioc-devel] Bioconductor Git/GitHub Mirrors

Yu, Guangchuang gcyu at connect.hku.hk
Tue Jun 23 07:19:19 CEST 2015 

Dear Dan,

I am talking about the DOSE package, not GOSemSim.

FYI, I have figured out how to commit to Bioc svn via the following command:

git checkout devel
rm -rf .git/rebase-apply
git reset --hard 418b1dd
git svn rebase
git merge master --no-edit
git svn dcommit --add-author-from

see https://github.com/Bioconductor-mirror/DOSE/commits/master.

Thank you for your help and patience.

Best Regards,
Guangchuang



On Tue, Jun 23, 2015 at 2:45 AM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

> Hi Guangchuang,
>
> I don't see any new commits from you in the git side, at least not in
> master:
>
> https://github.com/GuangchuangYu/GOSemSim/commits/master
>
> Could it be that you have not pushed your changes to master?
>
> I tried the following and it worked for me:
>
> git clone https://github.com/GuangchuangYu/GOSemSim
> cd GOSemSim
> bash ../mirror/update_remotes.sh
> git checkout devel
> git svn rebase
>
> Dan
>
> ----- Original Message -----
> > From: "Guangchuang Yu" <gcyu at connect.hku.hk>
> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> > Cc: bioc-devel at r-project.org
> > Sent: Monday, June 22, 2015 6:02:25 AM
> > Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors
> >
> >
> >
> >
> > 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
> >
> > -~----------~----~----~----~------~----~------~--~---
> >
>



-- 
--~--~---------~--~----~------------~-------~--~----~
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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