Hi all, I maintain maftools bioconductor package. I recently fixed several bugs which had resulted in build fail on devel branch of Bioconductor. However, I am unable to push them to upstream master. I have gone through help pages on Bioconductor page as well several other solutions online but I am not able to fix it. Please accept my apologies in advance if this has been already discussed before. Below are my git commands and error: $ git branch devel $ git checkout devel Switched to branch 'devel' $ git fetch upstream $ git merge upstream/master Auto-merging DESCRIPTION CONFLICT (content): Merge conflict in DESCRIPTION Automatic merge failed; fix conflicts and then commit the result. $ vi DESCRIPTION Fixed merge conflict $ git add . $ git commit -m "bug fixes" $ git status On branch devel nothing to commit, working tree clean $ git push upstream master To git.bioconductor.org:packages/maftools.git ! [rejected] master -> master (non-fast-forward) error: failed to push some refs to 'git at git.bioconductor.org:packages/maftools.git' hint: Updates were rejected because a pushed branch tip is behind its remote hint: counterpart. Check out this branch and integrate the remote changes hint: (e.g. 'git pull ...') before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details. Could you please suggest me on how to proceed. -Anand.
[Bioc-devel] Pushing to upstream master
8 messages · Turaga, Nitesh, Anand MT
Hi, Have your tried the command mentioned in the error message git pull This is important. Once that is done, ?IF? you have merge conflicts, please do http://bioconductor.org/developers/how-to/git/resolve-conflicts/ Best, Nitesh
On Dec 17, 2018, at 10:22 AM, Anand MT <anand_mt at hotmail.com> wrote: Hi all, I maintain maftools bioconductor package. I recently fixed several bugs which had resulted in build fail on devel branch of Bioconductor. However, I am unable to push them to upstream master. I have gone through help pages on Bioconductor page as well several other solutions online but I am not able to fix it. Please accept my apologies in advance if this has been already discussed before. Below are my git commands and error: $ git branch devel $ git checkout devel Switched to branch 'devel' $ git fetch upstream $ git merge upstream/master Auto-merging DESCRIPTION CONFLICT (content): Merge conflict in DESCRIPTION Automatic merge failed; fix conflicts and then commit the result. $ vi DESCRIPTION Fixed merge conflict $ git add . $ git commit -m "bug fixes" $ git status On branch devel nothing to commit, working tree clean $ git push upstream master To git.bioconductor.org:packages/maftools.git ! [rejected] master -> master (non-fast-forward) error: failed to push some refs to 'git at git.bioconductor.org:packages/maftools.git' hint: Updates were rejected because a pushed branch tip is behind its remote hint: counterpart. Check out this branch and integrate the remote changes hint: (e.g. 'git pull ...') before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details. Could you please suggest me on how to proceed. -Anand.
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I need more information to help you. Please check http://bioconductor.org/developers/how-to/git/faq/, #14 especially. And any others you may need.
On Dec 17, 2018, at 12:46 PM, Anand MT <anand_mt at hotmail.com> wrote: Hi Nitesh, Yes, I have pulled from upstream but still the same issue. $ git pull upstream master From git.bioconductor.org:packages/maftools * branch master -> FETCH_HEAD Already up to date. $ git status On branch devel nothing to commit, working tree clean $ git push upstream master To git.bioconductor.org:packages/maftools.git ! [rejected] master -> master (non-fast-forward) error: failed to push some refs to 'git at git.bioconductor.org:packages/maftools.git' hint: Updates were rejected because a pushed branch tip is behind its remote hint: counterpart. Check out this branch and integrate the remote changes hint: (e.g. 'git pull ...') before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details.
On 17 Dec 2018, at 5:43 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote: Hi, Have your tried the command mentioned in the error message git pull This is important. Once that is done, ?IF? you have merge conflicts, please do http://bioconductor.org/developers/how-to/git/resolve-conflicts/ Best, Nitesh
On Dec 17, 2018, at 10:22 AM, Anand MT <anand_mt at hotmail.com> wrote: Hi all, I maintain maftools bioconductor package. I recently fixed several bugs which had resulted in build fail on devel branch of Bioconductor. However, I am unable to push them to upstream master. I have gone through help pages on Bioconductor page as well several other solutions online but I am not able to fix it. Please accept my apologies in advance if this has been already discussed before. Below are my git commands and error: $ git branch devel $ git checkout devel Switched to branch 'devel' $ git fetch upstream $ git merge upstream/master Auto-merging DESCRIPTION CONFLICT (content): Merge conflict in DESCRIPTION Automatic merge failed; fix conflicts and then commit the result. $ vi DESCRIPTION Fixed merge conflict $ git add . $ git commit -m "bug fixes" $ git status On branch devel nothing to commit, working tree clean $ git push upstream master To git.bioconductor.org:packages/maftools.git ! [rejected] master -> master (non-fast-forward) error: failed to push some refs to 'git at git.bioconductor.org:packages/maftools.git' hint: Updates were rejected because a pushed branch tip is behind its remote hint: counterpart. Check out this branch and integrate the remote changes hint: (e.g. 'git pull ...') before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details. Could you please suggest me on how to proceed. -Anand.
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Hi Nitesh, I have checked my remotes, they are fine. $ git remote -v origin https://github.com/PoisonAlien/maftools.git (fetch) origin https://github.com/PoisonAlien/maftools.git (push) upstream git at git.bioconductor.org:packages/maftools.git (fetch) upstream git at git.bioconductor.org:packages/maftools.git (push) I had no issues earlier pushing to master/release branch (in earlier releases). I also did a fresh pull on a new branch, I still have the same issue. $ git branch devel $ git checkout devel Switched to branch 'devel' $ git pull upstream master
Hi Anand, The issue is the way you have updated your version numbers. Note that the last commit on upstream/master was the release version bump where your package has a version ?1.9.0?. Please update the version to ?1.9.1? and try pushing after the merge. I?ve outlined the steps you should take to push successfully below. Post release, you are first supposed to sync before making changes. This is the protocol. 1. Sync your master with upstream/master. 2. Test your push. 3. Add new changes, 4. Update the version as a new commit. 5. Push to GitHub and git.bioconductor. Please try this and let me know if you are able to push. Best, Nitesh
On Dec 18, 2018, at 10:18 AM, Anand MT <anand_mt at hotmail.com> wrote: git at git.bioconductor.org:packages/maftools.git
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7 days later
Hi Anand, I?m not sure if the configuration on your machine is compromised in some way, but most likely everything is fine. I tested the exact same commands as you have and it seems to have worked. Steps: 10871 git clone https://github.com/PoisonAlien/maftools.git 10872 cd maftools 10873 git remote add upstream git at git.bioconductor.org:packages/maftools 10874 git fetch ?all 10875 git merge upstream/master <This is where I have a merge conflict> 10879 emacs DESCRIPTION <remove the bad version number marked as HEAD> 10881 git commit [master 579af19] Merge remote-tracking branch 'upstream/master' 10883 git log ?oneline <Show a smooth commit history> 10884 git status git push upstream master Counting objects: 54, done. Delta compression using up to 4 threads. Compressing objects: 100% (31/31), done. Writing objects: 100% (54/54), 9.84 KiB | 9.84 MiB/s, done. Total 54 (delta 38), reused 37 (delta 22) To git.bioconductor.org:packages/maftools 8a302b3..579af19 master -> master You should have your git.bioconductor.org:packages/maftools repo synced with your GitHub now. Please check. Best, Nitesh
On Dec 18, 2018, at 11:12 AM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote: Hi Anand, The issue is the way you have updated your version numbers. Note that the last commit on upstream/master was the release version bump where your package has a version ?1.9.0?. Please update the version to ?1.9.1? and try pushing after the merge. I?ve outlined the steps you should take to push successfully below. Post release, you are first supposed to sync before making changes. This is the protocol. 1. Sync your master with upstream/master. 2. Test your push. 3. Add new changes, 4. Update the version as a new commit. 5. Push to GitHub and git.bioconductor. Please try this and let me know if you are able to push. Best, Nitesh
On Dec 18, 2018, at 10:18 AM, Anand MT <anand_mt at hotmail.com> wrote: git at git.bioconductor.org:packages/maftools.git
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