[Bioc-devel] Bioconductor Git/GitHub Mirrors

Dan Tenenbaum dtenenba at fredhutch.org
Mon Jun 22 20:45:02 CEST 2015 

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
> 
> -~----------~----~----~----~------~----~------~--~---
>

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