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

[Turaga, Nitesh]

Hi Gosia,

The workflow package transition will take place a few weeks after the Software 
and the Data package transition. Till that point, I suggest you use SVN 
directly to commit to the server.

Sorry for the confusion.

Best,

Nitesh

> On Aug 11, 2017, at 7:10 AM, Malgorzata Nowicka  wrote:
> 
> Hi, 
> 
> All is clear now. I will wait for the transition then.
> 
> Thank you for all the help.
> 
> Gosia
> 
> 
>> On 10 Aug 2017, at 18:52, Turaga, Nitesh  
>> wrote:
>> 
>> 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)
> 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

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

[Malgorzata Nowicka]

Hi, 

All is clear now. I will wait for the transition then.

Thank you for all the help.

Gosia


> On 10 Aug 2017, at 18:52, Turaga, Nitesh  
> wrote:
> 
> 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/.

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 
>>> .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: 
>>> 

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 while on large repositories
>> Current branch devel is up to date.
>> 
>> 
>> Please try the following steps. After that, make whatever 

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

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

[Turaga, Nitesh]

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  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)
> originhttps://github.com/gosianow/cytofWorkflow.git (fetch)
> originhttps://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 fo

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

[Malgorzata Nowicka]

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:
:04 04 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  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)
> 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
>  re

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

[Turaga, Nitesh]

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  
> 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  on behalf of Malgorzata 
> Nowicka 
> 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/ 
> .
> 
> How should I fix it?
> 
> Thank you for your help,
> 
> Gosia
> 
> 
> ### I have forked https://github.com/Bioconductor-mirror/cytofWorkflow 
>  to my repo 
> https://github.com/gosianow/cytofWorkflow.git 
> 
> ### I have added a commit to https://github.com/gosianow/cytofWorkflow.git 
> 
> ### Now, I would like to update the bioc svn
> 
> $ git clone https://github.com/gosianow/cytofWorkflow.git 
> 
> 
> $ curl -O 
> 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/ 
> 
> 
> $ 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 

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

[Shepherd, Lori]

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  on behalf of Malgorzata 
Nowicka 
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/ 
.

How should I fix it?

Thank you for your help,

Gosia


### I have forked https://github.com/Bioconductor-mirror/cytofWorkflow 
 to my repo 
https://github.com/gosianow/cytofWorkflow.git 

### I have added a commit to https://github.com/gosianow/cytofWorkflow.git 

### Now, I would like to update the bioc svn

$ git clone https://github.com/gosianow/cytofWorkflow.git 


$ curl -O 
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/ 


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

[Martin Morgan]

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/

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

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