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 >>>> >>> >>> >>> 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> >> >> [[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. >> [[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. 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