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 <gosia.nowi...@uzh.ch>
Date:   Wed Aug 9 15:13:53 2017 +0200

    Fix: use summarize_all instead of summarize_each

commit ac7399e64e2bc55497fd432e7731b231173eceba
Author: mtmor...@fhcrc.org 
<mtmor...@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Fri Jun 9 09:31:13 2017 +0000

    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/ 
<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 <nitesh.tur...@roswellpark.org> 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 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 <gosia.nowi...@uzh.ch> 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 remove bioc
>> 
>> $  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 checkout devel
>> Switched to branch '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 (1.9.1) 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
>>  ...
>> 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.
>> 
>> 
>> $ git merge master --log
>> Updating ac7399e..24f8f34
>> Fast-forward
>> vignettes/cytofWorkflow.Rmd | 10 +++++-----
>> 1 file changed, 5 insertions(+), 5 deletions(-)
>> 
>> $ git svn --username=m.nowicka dcommit --add-author-from
>> Committing to 
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cytofWorkflow ...
>>      M       vignettes/cytofWorkflow.Rmd
>> 
>> ERROR from SVN:
>> URL access forbidden for unknown reason: Access to 
>> '/bioconductor/!svn/txr/131862-4/trunk/madman/Rpacks/cytofWorkflow/vignettes/cytofWorkflow.Rmd'
>>  forbidden: Additional errors:: PUT of 
>> '/bioconductor/!svn/txr/131862-4/trunk/madman/Rpacks/cytofWorkflow/vignettes/cytofWorkflow.Rmd':
>>  403 Forbidden
>> W: 24f8f340d0c27d7475f4c10a08f641d23799acae and refs/remotes/git-svn-devel 
>> differ, using rebase:
>> :040000 040000 9c7bec20b6bdfa48a192b3116e4dc5ac84f62e49 
>> 60724811228c0228ddd7d237321443220f5bb6cd M   vignettes
>> Current branch devel is up to date.
>> ERROR: Not all changes have been committed into SVN, however the committed
>> ones (if any) seem to be successfully integrated into the working tree.
>> Please see the above messages for details.
>> 
>> 
>> $ git config -l
>> filter.lfs.required=true
>> filter.lfs.clean=git-lfs clean -- %f
>> filter.lfs.smudge=git-lfs smudge -- %f
>> filter.lfs.process=git-lfs filter-process
>> user.name=Malgorzata Nowicka
>> user.email=gosia.nowi...@uzh.ch
>> push.default=matching
>> filter.lfs.clean=git-lfs clean %f
>> filter.lfs.smudge=git-lfs smudge %f
>> filter.lfs.required=true
>> core.editor=vim
>> core.repositoryformatversion=0
>> core.filemode=true
>> core.bare=false
>> core.logallrefupdates=true
>> remote.origin.url=https://github.com/gosianow/cytofWorkflow.git
>> remote.origin.fetch=+refs/heads/*:refs/remotes/origin/*
>> branch.master.remote=origin
>> branch.master.merge=refs/heads/master
>> svn-remote.devel.url=https://hedgehog.fhcrc.org/bioconductor//trunk/madman/Rpacks/cytofWorkflow
>> svn-remote.devel.fetch=:refs/remotes/git-svn-devel
>> remote.bioc.url=https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/
>> remote.bioc.fetch=+refs/heads/*:refs/remotes/bioc/*
>> 
>> 
>>> On 8 Aug 2017, at 16:42, Turaga, Nitesh <nitesh.tur...@roswellpark.org> 
>>> wrote:
>>> 
>>> Hi Gosia,
>>> 
>>> I tried to reproduce your error. But I’m not sure there have been any 
>>> changes on either your Github repo, or your SVN. Both repositories are at 
>>> the exact same location right now. 
>>> 
>>> Please try these commands on a “fresh” clone of your GitHub repo. 
>>> 
>>> $ git clone https://github.com/gosianow/cytofWorkflow.git
>>> 
>>> $ cd cytofWorkflow
>>> 
>>> $ git log
>>> 
>>> $ bash update_remotes.sh
>>> 
>>> $ git remote remove bioc
>>> 
>>> $ 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 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 
>>> 
>>> Best,
>>> 
>>> Nitesh
>>> 
>>>> On Jul 19, 2017, at 10:01 AM, Shepherd, Lori 
>>>> <lori.sheph...@roswellpark.org> wrote:
>>>> 
>>>> You are correct that it is because this is a workflow package and not a 
>>>> software package.  The workflow package location is
>>>> 
>>>> 
>>>> /trunk/madman/workflows/
>>>> 
>>>> 
>>>> It should be updated there.
>>>> 
>>>> 
>>>> 
>>>> Lori Shepherd
>>>> 
>>>> Bioconductor Core Team
>>>> 
>>>> Roswell Park Cancer Institute
>>>> 
>>>> Department of Biostatistics & Bioinformatics
>>>> 
>>>> Elm & Carlton Streets
>>>> 
>>>> Buffalo, New York 14263
>>>> 
>>>> ________________________________
>>>> From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of 
>>>> Malgorzata Nowicka <gosia.nowi...@uzh.ch>
>>>> Sent: Wednesday, July 19, 2017 9:46:33 AM
>>>> To: bioc-devel@r-project.org
>>>> Subject: [Bioc-devel] unable to push local changes to bioconductor svn 
>>>> repository
>>>> 
>>>> Hello,
>>>> 
>>>> I have followed Scenario number 2 for my svn mirror for the cytofWorkflow 
>>>> package (more precisely workflow) and I encounter the same problem as 
>>>> described below by Zongli.
>>>> 
>>>> Below are my exact steps. The same steps worked for my other package 
>>>> DRIMSeq.
>>>> 
>>>> Could it be because it is a workflow and not a regular package? If I do 
>>>> not change the update_remotes.sh file, there are even more errors because 
>>>> cytofWorkflow is not at 
>>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ 
>>>> <https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/>.
>>>> 
>>>> How should I fix it?
>>>> 
>>>> Thank you for your help,
>>>> 
>>>> Gosia
>>>> 
>>>> 
>>>> ### I have forked https://github.com/Bioconductor-mirror/cytofWorkflow 
>>>> <https://github.com/Bioconductor-mirror/cytofWorkflow> to my repo 
>>>> https://github.com/gosianow/cytofWorkflow.git 
>>>> <https://github.com/gosianow/cytofWorkflow.git>
>>>> ### I have added a commit to https://github.com/gosianow/cytofWorkflow.git 
>>>> <https://github.com/gosianow/cytofWorkflow.git>
>>>> ### Now, I would like to update the bioc svn
>>>> 
>>>> $ git clone https://github.com/gosianow/cytofWorkflow.git 
>>>> <https://github.com/gosianow/cytofWorkflow.git>
>>>> 
>>>> $ curl -O 
>>>> https://raw.githubusercontent.com/Bioconductor/mirror/master/update_remotes.sh
>>>>  
>>>> <https://raw.githubusercontent.com/Bioconductor/mirror/master/update_remotes.sh>
>>>> 
>>>> $ cd cytofWorkflow
>>>> 
>>>> ### Replace Rpacks with workflows in update_remotes.sh as cytofWorkflow is 
>>>> in 
>>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/
>>>>  
>>>> <https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/>
>>>> 
>>>> $ bash ../update_remotes.sh
>>>> 
>>>> $ git branch -a
>>>> 
>>>> $ git checkout 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 (2.11.0 (Apple Git-81)) of git-svn) does 
>>>> not exist.
>>>> Done migrating from a git-svn v1 layout
>>>> Unable to determine upstream SVN information from working tree history
>>>> 
>>>> 
>>>> 
>>>>> On 12 May 2017, at 15:52, Martin Morgan <martin.mor...@roswellpark.org> 
>>>>> wrote:
>>>>> 
>>>>> On 05/11/2017 10:02 AM, Xu, Zongli (NIH/NIEHS) [E] wrote:
>>>>>> Hi,
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> I got a new Linux computer, cloned my package from github, made some
>>>>>> changes. I am able to update the changes to github, but can not push
>>>>>> it to Bioconductor svn repository. Can someone help me to solve the
>>>>>> problem.
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> The following is what I did:
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> git svn clone https://github.com/xuz1/ENmix
>>>>> 
>>>>> The github repository is just a git repository, not SVN; you should 
>>>>> follow the directions at scenario 2 of
>>>>> 
>>>>> http://bioconductor.org/developers/how-to/git-mirrors/ 
>>>>> <http://bioconductor.org/developers/how-to/git-mirrors/>
>>>>> 
>>>>> checkout the git repository, add svn remotes, rebase with svn, make git 
>>>>> commits, then dcommit to svn.
>>>>> 
>>>>> Martin
>>>>> 
>>>>> 
>>>>>> 
>>>>>> cd ENmix
>>>>>> 
>>>>>> bash ../update_remotes.sh
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> #push to github
>>>>>> 
>>>>>> git checkout master
>>>>>> 
>>>>>> git add -A .
>>>>>> 
>>>>>> git commit -a -s -m "commit made by Xu"
>>>>>> 
>>>>>> git remote -v
>>>>>> 
>>>>>> git push origin master
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> #push to Bioconductor svn
>>>>>> 
>>>>>> git checkout devel
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> I am good up to here, but when I run the following command
>>>>>> 
>>>>>> git svn rebase --username  z.xu
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> It showed the following error message:
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> Data from a previous version of git-svn exists, but
>>>>>> 
>>>>>> .git/svn
>>>>>> 
>>>>>> (required for this version (1.7.1) of git-svn) does not exist.
>>>>>> 
>>>>>> Done migrating from a git-svn v1 layout
>>>>>> 
>>>>>> Unable to determine upstream SVN information from working tree
>>>>>> history
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> Can anyone guide me what should I do to solve this problem.
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> Zongli
>>>>>> 
>>>>>> [[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...{{dropped:2}}
>>>>> 
>>>>> _______________________________________________
>>>>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel 
>>>>> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>>>> 
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>>>> 
>>>> _______________________________________________
>>>> Bioc-devel@r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>> 
>>>> 
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>>>> 
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>>> 
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