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