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 
<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/ 
<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
>>>> 
>>> 
>>> 
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