Re: [Bioc-devel] git transition for projects with prior git history

[Turaga, Nitesh]

The SVN repo is the most current version of your package as far as Bioconductor 
goes. Unfortunately, you have totally unrelated histories by the looks of it. 

I would suggest moving forward with the new git repo, after the transition is 
done on August 16th. I would not “delete” the repository you have per say, and 
keep a backup. 

Best,

Nitesh


> On Aug 10, 2017, at 6:30 PM, Stephanie M. Gogarten 
>  wrote:
> 
> I tried following the instructions in scenario 9 after adding a remote:
> $ git remote add upstream https://git.bioconductor.org/packages/GENESIS.git
> $ git fetch --all
> Fetching origin
> Fetching upstream
> warning: no common commits
> 
> When I merge both upstream and origin, I see all my commits in duplicate: one 
> from my original repo, and one from Bioconductor.
> 
> My repo has a rather complicated history: original author forked from the 
> Bioc mirror, I forked from his repo, submitted a pull request, he pushed 
> those changes back to SVN. Later I took over maintenance, set the Bioc mirror 
> as a remote, and pushed my changes directly using git cherry-pick.
> 
> I'm guessing that the only reasonable path forward here is to just delete the 
> current repo and start over after the transition, but I'm wondering if anyone 
> else has seen the "no common commits" message, or has any other ideas.
> 
> thanks,
> Stephanie
> 
> On 7/27/17 1:52 PM, McDavid, Andrew wrote:
>> Is there a recommended recipe to utilize the 
>> git.bioconductor.org remote with an existing 
>> git repo that has non-zero history?  I tried adding the 
>> git.bioconductor.org as a remote, making a 
>> branch, and then checking out a branch on that remote, but it gave my 
>> computer sad.  Do I need to clone a new repo instead?
>> Example:
>> $ git remote -vv
>> bioc https://github.com/Bioconductor-mirror/MAST.git (fetch)
>> bioc https://github.com/Bioconductor-mirror/MAST.git (push)
>> biocgit 
>> g...@git.bioconductor.org:packages/MAST 
>> (fetch)
>> biocgit 
>> g...@git.bioconductor.org:packages/MAST 
>> (push)
>> origin g...@github.com:RGLab/MAST.git (fetch)
>> origin g...@github.com:RGLab/MAST.git (push
>> $ git fetch biocgit
>> $ git checkout -b bgMaster --track biocgit/master
>> ...
>> 
>> ...
>> $ git merge master bgMaster
>> fatal: refusing to merge unrelated histories
>>  [[alternative HTML version deleted]]
>> ___
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>> 
> 
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Re: [Bioc-devel] git transition for projects with prior git history

[Stephanie M. Gogarten]

I tried following the instructions in scenario 9 after adding a remote:
$ git remote add upstream https://git.bioconductor.org/packages/GENESIS.git
$ git fetch --all
Fetching origin
Fetching upstream
warning: no common commits

When I merge both upstream and origin, I see all my commits in 
duplicate: one from my original repo, and one from Bioconductor.


My repo has a rather complicated history: original author forked from 
the Bioc mirror, I forked from his repo, submitted a pull request, he 
pushed those changes back to SVN. Later I took over maintenance, set the 
Bioc mirror as a remote, and pushed my changes directly using git 
cherry-pick.


I'm guessing that the only reasonable path forward here is to just 
delete the current repo and start over after the transition, but I'm 
wondering if anyone else has seen the "no common commits" message, or 
has any other ideas.


thanks,
Stephanie

On 7/27/17 1:52 PM, McDavid, Andrew wrote:

Is there a recommended recipe to utilize the 
git.bioconductor.org remote with an existing git repo 
that has non-zero history?  I tried adding the 
git.bioconductor.org as a remote, making a branch, and 
then checking out a branch on that remote, but it gave my computer sad.  Do I need to clone 
a new repo instead?

Example:
$ git remote -vv
bioc https://github.com/Bioconductor-mirror/MAST.git (fetch)
bioc https://github.com/Bioconductor-mirror/MAST.git (push)
biocgit 
g...@git.bioconductor.org:packages/MAST 
(fetch)
biocgit 
g...@git.bioconductor.org:packages/MAST (push)
origin g...@github.com:RGLab/MAST.git (fetch)
origin g...@github.com:RGLab/MAST.git (push

$ git fetch biocgit
$ git checkout -b bgMaster --track biocgit/master
...

...
$ git merge master bgMaster
fatal: refusing to merge unrelated histories

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Vignette for xcms fails to build on tokay1

[Neumann, Steffen]

Hi BioC, 

since that build error we have updated xcms to 2.99.6,
and have started to convert the xcmsDirect vignette to Rmd.
Now, we have the same kind of build error on the xcmsMsn vignette,
http://bioconductor.org/checkResults/devel/bioc-LATEST/xcms/tokay1-buildsrc.html

I think that just converting the vignettes will fix the symptoms, 
but we should really fix the cause of the error, for that 
we need some more diagnostics, we weren't yet able to reproduce.

Any ideas ?

Yours,
Steffen


On Sun, 2017-07-30 at 19:42 +, Neumann, Steffen wrote:
> Hi, 
> 
> Hi,
> 
> any suggestions or better diagnostics that could help us 
> fixing this, in case it really is something in xcms ? 
> 
> There were a few earlier reports with similar messages, 
> 
> back in 2013, slightly hinting at virus scanners: 
> http://r.789695.n4.nabble.com/quot-Failed-to-locate-the-texi2pdf-outp
> ut-file-quot-td4664111.html
> 
> Back in 2015, but both referring to SPB:
> https://github.com/Bioconductor/packagebuilder/issues/2
> https://github.com/Bioconductor/packagebuilder/issues/26
> 
> And from 2016 without any resolution:
> https://github.com/r-hub/rhub/issues/58
> 
> Yours,
> Steffen
> 
> 
> 
> On Thu, 2017-07-27 at 10:23 +, Rainer Johannes wrote:
> > Dear all,
> > 
> > one of the xcms vignettes fails to build on tokay1 recently with
> > the
> > error message:
> > 
> > Warning: running command
> > '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --pdf
> > "xcmsDirect.tex" --max-iterations=20 -I "C:/Users/biocbuild/bbs-
> > 3.6-
> > bioc/R/share/texmf/tex/latex" -I "C:/Users/biocbuild/bbs-3.6-
> > bioc/R/share/texmf/bibtex/bst"' had status 1
> > Error in find_vignette_product(name, by = "texi2pdf", engine =
> > engine) :
> >   Failed to locate the 'texi2pdf' output file (by engine
> > 'utils::Sweave') for vignette with name 'xcmsDirect'. The following
> > files exist in directory '.': 'FlowChart.graffle', 'FlowChart.pdf',
> > 'benchmarking.Rmd-notrun', 'biomed-central.csl', 'example.tsv',
> > 'new_functionality.R', 'new_functionality.Rmd',
> > 'new_functionality.html', 'new_functionality.org',
> > 'references.bib',
> > 'xcms.bib', 'xcms.org', 'xcmsDirect-005.pdf',
> > 'xcmsDirect.Rnw', 'xcmsDirect.tex', 'xcmsInstall.Rnw',
> > 'xcmsMSn.Rnw',
> > 'xcmsPreprocess.Rnw-notrun'
> > Calls:  -> find_vignette_product
> > Execution halted
> > 
> > is this some problem with tokay1 or is it related to the vignette
> > (I
> > have no problems building this vignette in my Windows build
> > machine)?
> > 
> > thanks, jo
> > 
> > 
> > [[alternative HTML version deleted]]
> > 
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> -- 
> 
> IPB HalleAG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3   http://msbi.bic-gh.de
> 06120 Halle  Tel. +49 (0) 345 5582 - 1470
>   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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Re: [Bioc-devel] git transition for projects with prior git history

[Turaga, Nitesh]

Thanks Kevin. This is a good test to see that it works as expected. 

Please note that those changes will not carry forward. 

Nitesh


> On Aug 10, 2017, at 2:46 PM, Kevin RUE  wrote:
> 
> Thanks Nitesh,
> 
> I managed to push some changes to my other package "GOexpress" during the 
> beta a few days ago, so I'm looking forward to the transition next week. For 
> that package, I didn't hesitate much to clone into a new repository and start 
> fresh there.
> 
> I think I'll do the same for "TVTB", I can always keep the old one for 
> reference.
> 
> Thanks for the reply.
> Kevin
> 
> 
> On Thu, Aug 10, 2017 at 5:34 PM, Turaga, Nitesh 
>  wrote:
> Hi Kevin,
> 
> If your Github and SVN repos separated so much, then I’d just wait for the 
> transition and then go from there.
> 
> Once the git server is alive, you can make a new GitHub repo at that point.
> 
> Nitesh
> 
> 
> > On Aug 10, 2017, at 10:18 AM, Kevin RUE  wrote:
> >
> > Hi all,
> >
> > I think I'm facing a similar scenario ("prior history"), although I have 
> > messed up my original GitHub repo 
> > (https://github.com/kevinrue/TVTB/commits/master) beyond my ability to 
> > synchronise it back to a working state.
> >
> > Basically, a few months ago, a bad mix of `git svn rebase` and `git merge 
> > master` replayed a whole lot of commit, likely the entire local history of 
> > commits, a couple of times (my Github  master branch now shows 1,043 
> > commits, against 333 in the Bioconductor-mirror/TVTB:master. I can safely 
> > say that I haven't been _that_ productive.
> >
> > After a few attempts to reset/merge/rebase/cry, I gave up the idea of 
> > reconciliation between my GitHub and the Bioc SVN; I abandoned my own 
> > GitHub repo and interacted with the SVN directly.
> >
> > Now my GitHub repo is behind the current state of my package in 
> > git.bioconductor.org (version 1.1.10 vs. 1.3.1), with different commit 
> > histories, that I can't even start to unravel.
> >
> > At that point, I dream of a way to simply update my own GitHub master to 
> > the current state of the git.bioconductor.org:packages/TVTB master branch, 
> > and use that commit as the root of all future development (branches). Is 
> > that something realistic/worth the effort ?
> >
> > I do have a feeling that the cleanest option would be to abandon my GitHub 
> > repo, clone from git.bioconductor.org, and make a new GitHub repo from that 
> > point... but I thought I'd ask one last time before giving up on the 
> > original repo.
> >
> > Many thanks in advance.
> > Kevin
> >
> >
> >
> >
> > On Fri, Jul 28, 2017 at 7:09 PM, McDavid, Andrew 
> >  wrote:
> > Hi Nitesh,
> >
> > Schematically, my git repo started with commit D, while bioconductor's 
> > started with A.  It's possible this was because I did something wrong 
> > managing the bioconductor repo, but since I can't rewrite history, there's 
> > not anything I can do about that now.  Their "founding" commits are 
> > distinct.
> >
> >
> >  BioconductorA---B---C
> >/ /
> >  MasterD---E---F---G---I
> >
> > Since then, I have I have been cherry-picking changes from master onto 
> > bioconductor per my understanding of recommended practice.
> > If I try to merge bioconductor onto master, or vice versa, I get the 
> > unrelated histories warning.  Vlad's suggestion works, but results in 
> > replaying ~700 commits onto the bioconductor repo...not so nice maybe.
> >
> > The https://github.com/Bioconductor-mirror/MAST.git repo is to make SVN 
> > commits from the git tree.
> >
> >
> > > On Jul 28, 2017, at 11:33 AM, Turaga, Nitesh 
> > >  wrote:
> > >
> > > I would be careful before using the --allow-unrelated-histories flag. 
> > > Please investigate where there is a difference.
> > >
> > > Also, i don't understand why you are using the bioconductor-git-mirror? 
> > > Your non-zero commit history should be related to bioconductor git server.
> > >
> > > Best
> > >
> > > Nitesh
> > >
> > > Get Outlook for Android
> > >
> > >
> > >
> > > From: Vladimir Kiselev
> > > Sent: Thursday, July 27, 5:11 PM
> > > Subject: Re: [Bioc-devel] git transition for projects with prior git 
> > > history
> > > To: McDavid, Andrew, bioc-devel@r-project.org
> > >
> > >
> > > Hi Andrew, I solved it by just adding '--allow-unrelated-histories' to 
> > > force the merge: 
> > > https://stackoverflow.com/questions/37937984/git-refusing-to-merge-unrelated-histories
> > >  Cheers, Vlad On Thu, Jul 27, 2017 at 9:53 PM McDavid, Andrew < 
> > > andrew_mcda...@urmc.rochester.edu> wrote: > Is there a recommended recipe 
> > > to utilize the git.bioconductor.org< > http://git.bioconductor.org> 
> > > remote with an existing git repo that has > non-zero history? I tried 
> > > adding the git.bioconductor.org< > http://git.bioconductor.org> as a 
> > > 

Re: [Bioc-devel] git transition for projects with prior git history

[Kevin RUE]

Thanks Nitesh,

I managed to push some changes to my other package "GOexpress" during the
beta a few days ago, so I'm looking forward to the transition next week.
For that package, I didn't hesitate much to clone into a new repository and
start fresh there.

I think I'll do the same for "TVTB", I can always keep the old one for
reference.

Thanks for the reply.
Kevin


On Thu, Aug 10, 2017 at 5:34 PM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi Kevin,
>
> If your Github and SVN repos separated so much, then I’d just wait for the
> transition and then go from there.
>
> Once the git server is alive, you can make a new GitHub repo at that point.
>
> Nitesh
>
>
> > On Aug 10, 2017, at 10:18 AM, Kevin RUE  wrote:
> >
> > Hi all,
> >
> > I think I'm facing a similar scenario ("prior history"), although I have
> messed up my original GitHub repo (https://github.com/kevinrue/
> TVTB/commits/master) beyond my ability to synchronise it back to a
> working state.
> >
> > Basically, a few months ago, a bad mix of `git svn rebase` and `git
> merge master` replayed a whole lot of commit, likely the entire local
> history of commits, a couple of times (my Github  master branch now shows
> 1,043 commits, against 333 in the Bioconductor-mirror/TVTB:master. I can
> safely say that I haven't been _that_ productive.
> >
> > After a few attempts to reset/merge/rebase/cry, I gave up the idea of
> reconciliation between my GitHub and the Bioc SVN; I abandoned my own
> GitHub repo and interacted with the SVN directly.
> >
> > Now my GitHub repo is behind the current state of my package in
> git.bioconductor.org (version 1.1.10 vs. 1.3.1), with different commit
> histories, that I can't even start to unravel.
> >
> > At that point, I dream of a way to simply update my own GitHub master to
> the current state of the git.bioconductor.org:packages/TVTB master
> branch, and use that commit as the root of all future development
> (branches). Is that something realistic/worth the effort ?
> >
> > I do have a feeling that the cleanest option would be to abandon my
> GitHub repo, clone from git.bioconductor.org, and make a new GitHub repo
> from that point... but I thought I'd ask one last time before giving up on
> the original repo.
> >
> > Many thanks in advance.
> > Kevin
> >
> >
> >
> >
> > On Fri, Jul 28, 2017 at 7:09 PM, McDavid, Andrew  rochester.edu> wrote:
> > Hi Nitesh,
> >
> > Schematically, my git repo started with commit D, while bioconductor's
> started with A.  It's possible this was because I did something wrong
> managing the bioconductor repo, but since I can't rewrite history, there's
> not anything I can do about that now.  Their "founding" commits are
> distinct.
> >
> >
> >  BioconductorA---B---C
> >/ /
> >  MasterD---E---F---G---I
> >
> > Since then, I have I have been cherry-picking changes from master onto
> bioconductor per my understanding of recommended practice.
> > If I try to merge bioconductor onto master, or vice versa, I get the
> unrelated histories warning.  Vlad's suggestion works, but results in
> replaying ~700 commits onto the bioconductor repo...not so nice maybe.
> >
> > The https://github.com/Bioconductor-mirror/MAST.git repo is to make SVN
> commits from the git tree.
> >
> >
> > > On Jul 28, 2017, at 11:33 AM, Turaga, Nitesh
>  wrote:
> > >
> > > I would be careful before using the --allow-unrelated-histories flag.
> Please investigate where there is a difference.
> > >
> > > Also, i don't understand why you are using the
> bioconductor-git-mirror? Your non-zero commit history should be related to
> bioconductor git server.
> > >
> > > Best
> > >
> > > Nitesh
> > >
> > > Get Outlook for Android
> > >
> > >
> > >
> > > From: Vladimir Kiselev
> > > Sent: Thursday, July 27, 5:11 PM
> > > Subject: Re: [Bioc-devel] git transition for projects with prior git
> history
> > > To: McDavid, Andrew, bioc-devel@r-project.org
> > >
> > >
> > > Hi Andrew, I solved it by just adding '--allow-unrelated-histories' to
> force the merge: https://stackoverflow.com/questions/37937984/git-
> refusing-to-merge-unrelated-histories Cheers, Vlad On Thu, Jul 27, 2017
> at 9:53 PM McDavid, Andrew < andrew_mcda...@urmc.rochester.edu> wrote: >
> Is there a recommended recipe to utilize the git.bioconductor.org< >
> http://git.bioconductor.org> remote with an existing git repo that has >
> non-zero history? I tried adding the git.bioconductor.org< >
> http://git.bioconductor.org> as a remote, making a branch, and then >
> checking out a branch on that remote, but it gave my computer sad. Do I >
> need to clone a new repo instead? > > Example: > $ git remote -vv > bioc
> https://github.com/Bioconductor-mirror/MAST.git (fetch) > bioc
> https://github.com/Bioconductor-mirror/MAST.git (push) > biocgit
> g...@git.bioconductor.org:packages/MAST > (fetch) > biocgit
> 

Re: [Bioc-devel] unable to push local changes to bioconductor svn repository

[Turaga, Nitesh]

In the meantime,

You can choose to simply checkout the SVN repo, and commit directly to it.

Nitesh


> On Aug 10, 2017, at 12:46 PM, Turaga, Nitesh  
> wrote:
> 
> Hi Gosia,
> 
> The cytofWorkflow was added to the wrong svn location, and then moved.
> 
> I really don't know whether Bioconductor-mirror mirrors workflow packages; I 
> think not, so the basic step of cloning from the mirror is not appropriate.
> 
> Roughly, I think the strategy would be to configure, on your own repository, 
> git-svn to reference the correct url in svn (...workflows/cytofWorkflow), as 
> well as any git remotes you wish to push to. I am not able to provide the 
> details on how this would be done (at the moment). 
> 
> Since we will transition to git.bioconductor.org next week, It will be 
> happening on the 16th of august. Maybe a better strategy is to simply wait 
> for the transition, then tackle the problem of syncing different git 
> repositories? (Especially workflows).
> 
> 
> Best,
> 
> Nitesh
> 
> 
>> On Aug 10, 2017, at 6:47 AM, Malgorzata Nowicka  wrote:
>> 
>> Hi Nitesh, 
>> 
>> If I skip the "update_remore.sh" step, I do not get the devel branch 
>> created. 
>> 
>> One thing I have noticed is that in the git log there is 
>> Rpacks/cytofWorkflow in the git-svn-id. Should'n it be 
>> workflows/cytofWorkflow as well? Maybe this causes the problems?
>> 
>> Best,
>> 
>> Gosia
>> 
>> 
>> 
>> $ git clone https://github.com/gosianow/cytofWorkflow.git
>> $ cd cytofWorkflow
>> $ git log
>> commit 24f8f340d0c27d7475f4c10a08f641d23799acae
>> Author: gosianow 
>> Date:   Wed Aug 9 15:13:53 2017 +0200
>> 
>>Fix: use summarize_all instead of summarize_each
>> 
>> commit ac7399e64e2bc55497fd432e7731b231173eceba
>> Author: mtmor...@fhcrc.org 
>> 
>> Date:   Fri Jun 9 09:31:13 2017 +
>> 
>>Adding cytofWorkflow, IsoformSwitchAnalyzeR
>> 
>> 
>>git-svn-id: 
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cytofWorkflow@130219
>>  bc3139a8-67e5-0310-9ffc-ced21a209358
>> 
>> $ git remote add bioc 
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/
>> $ git remote -v
>> bioc 
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/
>>  (fetch)
>> bioc 
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/
>>  (push)
>> origin   https://github.com/gosianow/cytofWorkflow.git (fetch)
>> origin   https://github.com/gosianow/cytofWorkflow.git (push)
>> 
>> $ git branch -a
>> * master
>>  remotes/origin/HEAD -> origin/master
>>  remotes/origin/master
>> 
>> 
>> 
>>> On 9 Aug 2017, at 16:37, Turaga, Nitesh  
>>> wrote:
>>> 
>>> Hi Gosia,
>>> 
>>> I think you should repeat the steps, but completely skip the 
>>> “update_remote.sh” bit. 
>>> 
>>> It’s setting your URL to the wrong location, I’ll show it below: 
>>> 
>>> $ git svn --username=m.nowicka dcommit --add-author-from
>>> Committing to 
>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cytofWorkflow 
>>> ...
>>> M   vignettes/cytofWorkflow.Rmd
>>> 
>>> The location here, when you commit is supposed to be  
>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow,
>>>  but instead you are commiting to the ‘Rpacks’ software package repo. This 
>>> is a problem with update_remotes.sh. 
>>> 
>>> The new steps you should follow are:
>>> 
>>> $ git clone https://github.com/gosianow/cytofWorkflow.git
>>> 
>>> $ cd cytofWorkflow
>>> 
>>> $ git log
>>> 
>>> $ git remote add bioc 
>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/
>>> 
>>> $ git remote -v
>>> 
>>> bioc
>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/
>>>  (fetch)
>>> bioc
>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/
>>>  (push)
>>> origin  https://github.com/gosianow/cytofWorkflow.git (fetch)
>>> origin  https://github.com/gosianow/cytofWorkflow.git (push)
>>> 
>>> $ git branch -a
>>> 
>>> devel
>>> * master
>>> remotes/git-svn-devel
>>> remotes/origin/HEAD -> origin/master
>>> remotes/origin/master
>>> 
>>> $ git checkout devel
>>> 
>>> /t/cytofWorkflow ❯❯❯ 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 (2.11.0 (Apple Git-81)) 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
>>>  ...
>>> r130219 = ac7399e64e2bc55497fd432e7731b231173eceba
>>> Done rebuilding 
>>> 

Re: [Bioc-devel] unable to push local changes to bioconductor svn repository

[Turaga, Nitesh]

Hi Gosia,

The cytofWorkflow was added to the wrong svn location, and then moved.

I really don't know whether Bioconductor-mirror mirrors workflow packages; I 
think not, so the basic step of cloning from the mirror is not appropriate.

Roughly, I think the strategy would be to configure, on your own repository, 
git-svn to reference the correct url in svn (...workflows/cytofWorkflow), as 
well as any git remotes you wish to push to. I am not able to provide the 
details on how this would be done (at the moment). 

Since we will transition to git.bioconductor.org next week, It will be 
happening on the 16th of august. Maybe a better strategy is to simply wait for 
the transition, then tackle the problem of syncing different git repositories? 
(Especially workflows).


Best,

Nitesh


> On Aug 10, 2017, at 6:47 AM, Malgorzata Nowicka  wrote:
> 
> Hi Nitesh, 
> 
> If I skip the "update_remore.sh" step, I do not get the devel branch created. 
> 
> One thing I have noticed is that in the git log there is Rpacks/cytofWorkflow 
> in the git-svn-id. Should'n it be workflows/cytofWorkflow as well? Maybe this 
> causes the problems?
> 
> Best,
> 
> Gosia
> 
> 
> 
> $ git clone https://github.com/gosianow/cytofWorkflow.git
> $ cd cytofWorkflow
> $ git log
> commit 24f8f340d0c27d7475f4c10a08f641d23799acae
> Author: gosianow 
> Date:   Wed Aug 9 15:13:53 2017 +0200
> 
> Fix: use summarize_all instead of summarize_each
> 
> commit ac7399e64e2bc55497fd432e7731b231173eceba
> Author: mtmor...@fhcrc.org 
> 
> Date:   Fri Jun 9 09:31:13 2017 +
> 
> Adding cytofWorkflow, IsoformSwitchAnalyzeR
> 
> 
> git-svn-id: 
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cytofWorkflow@130219
>  bc3139a8-67e5-0310-9ffc-ced21a209358
> 
> $ git remote add bioc 
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/
> $ git remote -v
> bioc  
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/ 
> (fetch)
> bioc  
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/ 
> (push)
> originhttps://github.com/gosianow/cytofWorkflow.git (fetch)
> originhttps://github.com/gosianow/cytofWorkflow.git (push)
> 
> $ git branch -a
> * master
>   remotes/origin/HEAD -> origin/master
>   remotes/origin/master
> 
> 
> 
>> On 9 Aug 2017, at 16:37, Turaga, Nitesh  
>> wrote:
>> 
>> Hi Gosia,
>> 
>> I think you should repeat the steps, but completely skip the 
>> “update_remote.sh” bit. 
>> 
>> It’s setting your URL to the wrong location, I’ll show it below: 
>> 
>> $ git svn --username=m.nowicka dcommit --add-author-from
>> Committing to 
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cytofWorkflow ...
>>  M   vignettes/cytofWorkflow.Rmd
>> 
>> The location here, when you commit is supposed to be  
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow,
>>  but instead you are commiting to the ‘Rpacks’ software package repo. This 
>> is a problem with update_remotes.sh. 
>> 
>> The new steps you should follow are:
>> 
>> $ git clone https://github.com/gosianow/cytofWorkflow.git
>> 
>> $ cd cytofWorkflow
>> 
>> $ git log
>> 
>> $ git remote add bioc 
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/
>> 
>> $ git remote -v
>> 
>> bioc 
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/
>>  (fetch)
>> bioc 
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/
>>  (push)
>> origin   https://github.com/gosianow/cytofWorkflow.git (fetch)
>> origin   https://github.com/gosianow/cytofWorkflow.git (push)
>> 
>> $ git branch -a
>> 
>> devel
>> * master
>> remotes/git-svn-devel
>> remotes/origin/HEAD -> origin/master
>> remotes/origin/master
>> 
>> $ git checkout devel
>> 
>> /t/cytofWorkflow ❯❯❯ 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 (2.11.0 (Apple Git-81)) 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
>>  ...
>> r130219 = ac7399e64e2bc55497fd432e7731b231173eceba
>> Done rebuilding 
>> .git/svn/refs/remotes/git-svn-devel/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358
>> W: Ignoring error from SVN, path probably does not exist: (160013): 
>> Filesystem has no item: 
>> '/bioconductor/!svn/rvr/130320/trunk/madman/Rpacks/cytofWorkflow' path not 
>> found
>> W: Do not be alarmed at the above message git-svn is just searching 
>> aggressively for old history.
>> This may take a 

Re: [Bioc-devel] git transition for projects with prior git history

[Turaga, Nitesh]

Hi Andrew,

How important are these “founding” commits? The new git server will also start 
from “A”, as they go off the SVN repo state. 

The recommended practice will change once we move to the git server. I would 
not merge the branches, if they have unrelated histories. If it is possible to 
just go from the new git repo produced after the transition, that would be the 
ideal solution.

Should be easy to port specific commits, on top of the git repo, after August 
16th.

Best,

Nitesh


> On Jul 28, 2017, at 2:09 PM, McDavid, Andrew 
>  wrote:
> 
> Hi Nitesh,
> 
> Schematically, my git repo started with commit D, while bioconductor's 
> started with A.  It's possible this was because I did something wrong 
> managing the bioconductor repo, but since I can't rewrite history, there's 
> not anything I can do about that now.  Their "founding" commits are distinct.
> 
> 
> BioconductorA---B---C
>   / /
> MasterD---E---F---G---I
> 
> Since then, I have I have been cherry-picking changes from master onto 
> bioconductor per my understanding of recommended practice.  
> If I try to merge bioconductor onto master, or vice versa, I get the 
> unrelated histories warning.  Vlad's suggestion works, but results in 
> replaying ~700 commits onto the bioconductor repo...not so nice maybe.
> 
> The https://github.com/Bioconductor-mirror/MAST.git repo is to make SVN 
> commits from the git tree.
> 
> 
>> On Jul 28, 2017, at 11:33 AM, Turaga, Nitesh  
>> wrote:
>> 
>> I would be careful before using the --allow-unrelated-histories flag. Please 
>> investigate where there is a difference.
>> 
>> Also, i don't understand why you are using the bioconductor-git-mirror? Your 
>> non-zero commit history should be related to bioconductor git server. 
>> 
>> Best
>> 
>> Nitesh
>> 
>> Get Outlook for Android
>> 
>> 
>> 
>> From: Vladimir Kiselev
>> Sent: Thursday, July 27, 5:11 PM
>> Subject: Re: [Bioc-devel] git transition for projects with prior git history
>> To: McDavid, Andrew, bioc-devel@r-project.org
>> 
>> 
>> Hi Andrew, I solved it by just adding '--allow-unrelated-histories' to force 
>> the merge: 
>> https://stackoverflow.com/questions/37937984/git-refusing-to-merge-unrelated-histories
>>  Cheers, Vlad On Thu, Jul 27, 2017 at 9:53 PM McDavid, Andrew < 
>> andrew_mcda...@urmc.rochester.edu> wrote: > Is there a recommended recipe to 
>> utilize the git.bioconductor.org< > http://git.bioconductor.org> remote with 
>> an existing git repo that has > non-zero history? I tried adding the 
>> git.bioconductor.org< > http://git.bioconductor.org> as a remote, making a 
>> branch, and then > checking out a branch on that remote, but it gave my 
>> computer sad. Do I > need to clone a new repo instead? > > Example: > $ git 
>> remote -vv > bioc https://github.com/Bioconductor-mirror/MAST.git (fetch) > 
>> bioc https://github.com/Bioconductor-mirror/MAST.git (push) > biocgit 
>> g...@git.bioconductor.org:packages/MAST > (fetch) > biocgit 
>> g...@git.bioconductor.org:packages/MAST > (push) > origin 
>> g...@github.com:RGLab/MAST.git (fetch) > origin 
>> g...@github.com:RGLab/MAST.git (push > > $ git fetch biocgit > $ git 
>> checkout -b bgMaster --track biocgit/master > ... > > ... > $ git merge 
>> master bgMaster > fatal: refusing to merge unrelated histories > > 
>> [[alternative HTML version deleted]] > > 
>> ___ > Bioc-devel@r-project.org 
>> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- 
>> http://genat.uk [[alternative HTML version deleted]] 
>> ___ Bioc-devel@r-project.org 
>> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel 
>> 
>> 
>> This email message may contain legally privileged and/or confidential 
>> information. If you are not the intended recipient(s), or the employee or 
>> agent responsible for the delivery of this message to the intended 
>> recipient(s), you are hereby notified that any disclosure, copying, 
>> distribution, or use of this email message is prohibited. If you have 
>> received this message in error, please notify the sender immediately by 
>> e-mail and delete this email message from your computer. Thank you.
> 



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] git transition for projects with prior git history

[Turaga, Nitesh]

Hi Kevin,

If your Github and SVN repos separated so much, then I’d just wait for the 
transition and then go from there. 

Once the git server is alive, you can make a new GitHub repo at that point.

Nitesh


> On Aug 10, 2017, at 10:18 AM, Kevin RUE  wrote:
> 
> Hi all,
> 
> I think I'm facing a similar scenario ("prior history"), although I have 
> messed up my original GitHub repo 
> (https://github.com/kevinrue/TVTB/commits/master) beyond my ability to 
> synchronise it back to a working state.
> 
> Basically, a few months ago, a bad mix of `git svn rebase` and `git merge 
> master` replayed a whole lot of commit, likely the entire local history of 
> commits, a couple of times (my Github  master branch now shows 1,043 commits, 
> against 333 in the Bioconductor-mirror/TVTB:master. I can safely say that I 
> haven't been _that_ productive.
> 
> After a few attempts to reset/merge/rebase/cry, I gave up the idea of 
> reconciliation between my GitHub and the Bioc SVN; I abandoned my own GitHub 
> repo and interacted with the SVN directly.
> 
> Now my GitHub repo is behind the current state of my package in 
> git.bioconductor.org (version 1.1.10 vs. 1.3.1), with different commit 
> histories, that I can't even start to unravel.
> 
> At that point, I dream of a way to simply update my own GitHub master to the 
> current state of the git.bioconductor.org:packages/TVTB master branch, and 
> use that commit as the root of all future development (branches). Is that 
> something realistic/worth the effort ?
> 
> I do have a feeling that the cleanest option would be to abandon my GitHub 
> repo, clone from git.bioconductor.org, and make a new GitHub repo from that 
> point... but I thought I'd ask one last time before giving up on the original 
> repo.
> 
> Many thanks in advance.
> Kevin
> 
> 
> 
> 
> On Fri, Jul 28, 2017 at 7:09 PM, McDavid, Andrew 
>  wrote:
> Hi Nitesh,
> 
> Schematically, my git repo started with commit D, while bioconductor's 
> started with A.  It's possible this was because I did something wrong 
> managing the bioconductor repo, but since I can't rewrite history, there's 
> not anything I can do about that now.  Their "founding" commits are distinct.
> 
> 
>  BioconductorA---B---C
>/ /
>  MasterD---E---F---G---I
> 
> Since then, I have I have been cherry-picking changes from master onto 
> bioconductor per my understanding of recommended practice.
> If I try to merge bioconductor onto master, or vice versa, I get the 
> unrelated histories warning.  Vlad's suggestion works, but results in 
> replaying ~700 commits onto the bioconductor repo...not so nice maybe.
> 
> The https://github.com/Bioconductor-mirror/MAST.git repo is to make SVN 
> commits from the git tree.
> 
> 
> > On Jul 28, 2017, at 11:33 AM, Turaga, Nitesh 
> >  wrote:
> >
> > I would be careful before using the --allow-unrelated-histories flag. 
> > Please investigate where there is a difference.
> >
> > Also, i don't understand why you are using the bioconductor-git-mirror? 
> > Your non-zero commit history should be related to bioconductor git server.
> >
> > Best
> >
> > Nitesh
> >
> > Get Outlook for Android
> >
> >
> >
> > From: Vladimir Kiselev
> > Sent: Thursday, July 27, 5:11 PM
> > Subject: Re: [Bioc-devel] git transition for projects with prior git history
> > To: McDavid, Andrew, bioc-devel@r-project.org
> >
> >
> > Hi Andrew, I solved it by just adding '--allow-unrelated-histories' to 
> > force the merge: 
> > https://stackoverflow.com/questions/37937984/git-refusing-to-merge-unrelated-histories
> >  Cheers, Vlad On Thu, Jul 27, 2017 at 9:53 PM McDavid, Andrew < 
> > andrew_mcda...@urmc.rochester.edu> wrote: > Is there a recommended recipe 
> > to utilize the git.bioconductor.org< > http://git.bioconductor.org> remote 
> > with an existing git repo that has > non-zero history? I tried adding the 
> > git.bioconductor.org< > http://git.bioconductor.org> as a remote, making a 
> > branch, and then > checking out a branch on that remote, but it gave my 
> > computer sad. Do I > need to clone a new repo instead? > > Example: > $ git 
> > remote -vv > bioc https://github.com/Bioconductor-mirror/MAST.git (fetch) > 
> > bioc https://github.com/Bioconductor-mirror/MAST.git (push) > biocgit 
> > g...@git.bioconductor.org:packages/MAST > (fetch) > biocgit 
> > g...@git.bioconductor.org:packages/MAST > (push) > origin 
> > g...@github.com:RGLab/MAST.git (fetch) > origin git
>  @github.com:RGLab/MAST.git (push > > $ git fetch biocgit > $ git checkout -b 
> bgMaster --track biocgit/master > ... > > ... > $ git merge master bgMaster > 
> fatal: refusing to merge unrelated histories > > [[alternative HTML version 
> deleted]] > > ___ > 
> Bioc-devel@r-project.org mailing list > 
> 

Re: [Bioc-devel] git transition for projects with prior git history

[Kevin RUE]

Hi all,

I think I'm facing a similar scenario ("prior history"), although I have
messed up my original GitHub repo (https://github.com/kevinrue/
TVTB/commits/master) beyond my ability to synchronise it back to a working
state.

Basically, a few months ago, a bad mix of `git svn rebase` and `git merge
master` replayed a whole lot of commit, likely the entire local history of
commits, a couple of times (my Github  master branch now shows 1,043
commits, against 333 in the Bioconductor-mirror/TVTB:master. I can safely
say that I haven't been _that_ productive.

After a few attempts to reset/merge/rebase/cry, I gave up the idea of
reconciliation between my GitHub and the Bioc SVN; I abandoned my own
GitHub repo and interacted with the SVN directly.

Now my GitHub repo is behind the current state of my package in
git.bioconductor.org (version 1.1.10 vs. 1.3.1), with different commit
histories, that I can't even start to unravel.

At that point, I dream of a way to simply update my own GitHub master to
the current state of the git.bioconductor.org:packages/TVTB master branch,
and use that commit as the root of all future development (branches). Is
that something realistic/worth the effort ?

I do have a feeling that the cleanest option would be to abandon my GitHub
repo, clone from git.bioconductor.org, and make a new GitHub repo from that
point... but I thought I'd ask one last time before giving up on the
original repo.

Many thanks in advance.
Kevin




On Fri, Jul 28, 2017 at 7:09 PM, McDavid, Andrew <
andrew_mcda...@urmc.rochester.edu> wrote:

> Hi Nitesh,
>
> Schematically, my git repo started with commit D, while bioconductor's
> started with A.  It's possible this was because I did something wrong
> managing the bioconductor repo, but since I can't rewrite history, there's
> not anything I can do about that now.  Their "founding" commits are
> distinct.
>
>
>  BioconductorA---B---C
>/ /
>  MasterD---E---F---G---I
>
> Since then, I have I have been cherry-picking changes from master onto
> bioconductor per my understanding of recommended practice.
> If I try to merge bioconductor onto master, or vice versa, I get the
> unrelated histories warning.  Vlad's suggestion works, but results in
> replaying ~700 commits onto the bioconductor repo...not so nice maybe.
>
> The https://github.com/Bioconductor-mirror/MAST.git repo is to make SVN
> commits from the git tree.
>
>
> > On Jul 28, 2017, at 11:33 AM, Turaga, Nitesh
>  wrote:
> >
> > I would be careful before using the --allow-unrelated-histories flag.
> Please investigate where there is a difference.
> >
> > Also, i don't understand why you are using the bioconductor-git-mirror?
> Your non-zero commit history should be related to bioconductor git server.
> >
> > Best
> >
> > Nitesh
> >
> > Get Outlook for Android
> >
> >
> >
> > From: Vladimir Kiselev
> > Sent: Thursday, July 27, 5:11 PM
> > Subject: Re: [Bioc-devel] git transition for projects with prior git
> history
> > To: McDavid, Andrew, bioc-devel@r-project.org
> >
> >
> > Hi Andrew, I solved it by just adding '--allow-unrelated-histories' to
> force the merge: https://stackoverflow.com/questions/37937984/git-
> refusing-to-merge-unrelated-histories Cheers, Vlad On Thu, Jul 27, 2017
> at 9:53 PM McDavid, Andrew < andrew_mcda...@urmc.rochester.edu> wrote: >
> Is there a recommended recipe to utilize the git.bioconductor.org< >
> http://git.bioconductor.org> remote with an existing git repo that has >
> non-zero history? I tried adding the git.bioconductor.org< >
> http://git.bioconductor.org> as a remote, making a branch, and then >
> checking out a branch on that remote, but it gave my computer sad. Do I >
> need to clone a new repo instead? > > Example: > $ git remote -vv > bioc
> https://github.com/Bioconductor-mirror/MAST.git (fetch) > bioc
> https://github.com/Bioconductor-mirror/MAST.git (push) > biocgit
> g...@git.bioconductor.org:packages/MAST > (fetch) > biocgit
> g...@git.bioconductor.org:packages/MAST > (push) > origin 
> g...@github.com:RGLab/MAST.git
> (fetch) > origin git
>  @github.com:RGLab/MAST.git (push > > $ git fetch biocgit > $ git
> checkout -b bgMaster --track biocgit/master > ... > > ... > $ git merge
> master bgMaster > fatal: refusing to merge unrelated histories > >
> [[alternative HTML version deleted]] > > 
> ___
> > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/
> listinfo/bioc-devel > -- http://genat.uk [[alternative HTML version
> deleted]] ___
> Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/
> listinfo/bioc-devel
> >
> >
> > This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> 

Re: [Bioc-devel] unable to push local changes to bioconductor svn repository

[Malgorzata Nowicka]

Hi Nitesh, 

If I skip the "update_remore.sh" step, I do not get the devel branch created. 

One thing I have noticed is that in the git log there is Rpacks/cytofWorkflow 
in the git-svn-id. Should'n it be workflows/cytofWorkflow as well? Maybe this 
causes the problems?

Best,

Gosia



$ git clone https://github.com/gosianow/cytofWorkflow.git
$ cd cytofWorkflow
$ git log
commit 24f8f340d0c27d7475f4c10a08f641d23799acae
Author: gosianow 
Date:   Wed Aug 9 15:13:53 2017 +0200

Fix: use summarize_all instead of summarize_each

commit ac7399e64e2bc55497fd432e7731b231173eceba
Author: mtmor...@fhcrc.org 

Date:   Fri Jun 9 09:31:13 2017 +

Adding cytofWorkflow, IsoformSwitchAnalyzeR


git-svn-id: 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cytofWorkflow@130219
 bc3139a8-67e5-0310-9ffc-ced21a209358

$ git remote add bioc 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/ 

$ git remote -v
bioc
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/ 
(fetch)
bioc
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/ 
(push)
origin  https://github.com/gosianow/cytofWorkflow.git (fetch)
origin  https://github.com/gosianow/cytofWorkflow.git (push)

$ git branch -a
* master
  remotes/origin/HEAD -> origin/master
  remotes/origin/master



> On 9 Aug 2017, at 16:37, Turaga, Nitesh  wrote:
> 
> Hi Gosia,
> 
> I think you should repeat the steps, but completely skip the 
> “update_remote.sh” bit. 
> 
> It’s setting your URL to the wrong location, I’ll show it below: 
> 
> $ git svn --username=m.nowicka dcommit --add-author-from
> Committing to 
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cytofWorkflow ...
>   M   vignettes/cytofWorkflow.Rmd
> 
> The location here, when you commit is supposed to be  
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow, 
> but instead you are commiting to the ‘Rpacks’ software package repo. This is 
> a problem with update_remotes.sh. 
> 
> The new steps you should follow are:
> 
> $ git clone https://github.com/gosianow/cytofWorkflow.git
> 
> $ cd cytofWorkflow
> 
> $ git log
> 
> $ git remote add bioc 
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/
> 
> $ git remote -v
> 
> bioc  
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/ 
> (fetch)
> bioc  
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/ 
> (push)
> originhttps://github.com/gosianow/cytofWorkflow.git (fetch)
> originhttps://github.com/gosianow/cytofWorkflow.git (push)
> 
> $ git branch -a
> 
> devel
> * master
> remotes/git-svn-devel
> remotes/origin/HEAD -> origin/master
> remotes/origin/master
> 
> $ git checkout devel
> 
> /t/cytofWorkflow ❯❯❯ 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 (2.11.0 (Apple Git-81)) 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
>  ...
> r130219 = ac7399e64e2bc55497fd432e7731b231173eceba
> Done rebuilding 
> .git/svn/refs/remotes/git-svn-devel/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358
> W: Ignoring error from SVN, path probably does not exist: (160013): 
> Filesystem has no item: 
> '/bioconductor/!svn/rvr/130320/trunk/madman/Rpacks/cytofWorkflow' path not 
> found
> W: Do not be alarmed at the above message git-svn is just searching 
> aggressively for old history.
> This may take a while on large repositories
> Current branch devel is up to date.
> 
> 
> Please try the following steps. After that, make whatever changes you need 
> to, and try the 
> 
> • `git merge master —log` to merge your changes from the master branch or 
> skip this step and work directly on the current branch.
> 
> to sync and commit your changes to svn.
> 
> $ git svn dcommit --add-author-from 
> 
> 
> 
> Try that and let me know.
> 
> Best,
> 
> Nitesh
> 
> 
>> On Aug 9, 2017, at 9:44 AM, Malgorzata Nowicka  wrote:
>> 
>> Hello Nitesh, 
>> 
>> thank you for your response.
>> 
>> Following your steps, git snv rebase works, but I get an error at git svn 
>> --username=m.nowicka dcommit --add-author-from step:
>> 
>> $ git clone https://github.com/gosianow/cytofWorkflow.git
>> 
>> $ curl -O 
>> https://raw.githubusercontent.com/Bioconductor/mirror/master/update_remotes.sh
>> 
>> $ cd cytofWorkflow
>> 
>> $  bash ../update_remotes.sh
>> 
>> $ git remote