[Bioc-devel] unable to push local changes to bioconductor svn repository
Turaga, Nitesh
Nitesh.Turaga at RoswellPark.org
Wed Aug 9 16:37:49 CEST 2017
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.nowicka at 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.nowicka at 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.Turaga at 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.Shepherd at 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-bounces at r-project.org> on behalf of Malgorzata Nowicka <gosia.nowicka at uzh.ch>
>>> Sent: Wednesday, July 19, 2017 9:46:33 AM
>>> To: bioc-devel at 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.morgan at 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 at 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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>>>
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