Thank you Martin! I made the updates according to reviewers' comments from Bioinformatics, so I would say these are "new features".
So does this mean I'm all set and the updates will be available on Bioconducotr for the next release? Best, Ding 2018-03-28 11:45 GMT-04:00 Martin Morgan <martin.mor...@roswellpark.org>: > > > On 03/28/2018 11:19 AM, Hongxu Ding wrote: > >> Thank you very much Morgan! I followed your suggestions and solved the >> problem. >> >> I think the problem is the version is 1.1.0 on Bioconductor, and the >> version of my new update is 1.0.1. I bumped the version to 1.1.1 and used >> *_git push g...@git.bioconductor.org:packages/iterClust.git master_* for >> updating my package: >> >> *Counting objects: 47, done. >> Delta compression using up to 4 threads. >> Compressing objects: 100% (27/27), done. >> Writing objects: 100% (47/47), 10.24 KiB | 209.00 KiB/s, done. >> Total 47 (delta 30), reused 31 (delta 20) >> To git.bioconductor.org:packages/iterClust.git >> d0a36e4..429821b master -> master* >> >> Another question, what should I do to the release branch of my GitHub >> repository? Specifically, should I also push my updates to Bioconductor, >> and if so what version, e.g. 1.1.1 should I use? >> > > If your changes were 'bug fixes', then they would normally also be added > to the release branch. If they were 'new features' then they would only be > added to the master branch. > > The version scheme is outlined at > > http://bioconductor.org/developers/how-to/version-numbering/ > > for version number x.y.z, the rule is to increment z to z + 1. In release > your package has version 1.0.0, so the release version will be 1.0.1, > 1.0.2, ... > > There will be another release soon > > http://bioconductor.org/developers/release-schedule/ > > resulting in RELEASE_3_7 and version 1.2.0, and in master 1.3.0. We do the > version bumps associated with the release. > > Martin > > >> Thank you very much! >> Ding >> >> 2018-03-28 4:05 GMT-04:00 Martin Morgan <martin.mor...@roswellpark.org >> <mailto:martin.mor...@roswellpark.org>>: >> >> >> >> On 03/27/2018 11:14 AM, Hongxu Ding wrote: >> >> Dear Nitesh, >> >> I think I have similar problem... >> >> I tried to push some updates to Bioconductor using *git push >> upstream >> master *and having the following problem*:* >> >> >> >> >> >> >> >> >> *To git.bioconductor.org:packages/iterClust.git ! [rejected] >> master >> -> master (non-fast-forward)error: failed to push some refs to >> 'g...@git.bioconductor.org:packages/iterClust.git'hint: Updates >> were >> rejected because the tip of your current branch is behindhint: >> its remote >> counterpart. Integrate the remote changes (e.g.hint: 'git pull >> ...') before >> pushing again.hint: See the 'Note about fast-forwards' in 'git >> push --help' >> for details.* >> >> >> This just looks like there is a change in the repository at >> git.bioconductor.org <http://git.bioconductor.org> that is not >> >> present in your local repository. Did you try to >> >> git pull >> >> as suggested? Probably the issue is that the package has had its >> version 'bumped' for the last release >> >> iterClust master$ git log --oneline -n 3 >> d0a36e4 bump x.y.z versions to odd y after creation of RELEASE_3_6 >> branch >> d1b1afa bump x.y.z versions to even y prior to creation of >> RELEASE_3_6 branch >> 03daa79 20171005 >> >> >> and you have not incorporated the version bump in your own >> repository. (consider also more informative commit messages). >> >> Martin >> >> >> My *git remote -v* output: >> >> >> >> >> *origin g...@github.com:hd2326/iterClust.git (fetch)origin >> g...@github.com:hd2326/iterClust.git (push)upstream >> g...@git.bioconductor.org:packages/iterClust.git (fetch)upstream >> g...@git.bioconductor.org:packages/iterClust.git (push)* >> >> and my *git log --oneline** output*: >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> *da9b838 (HEAD -> master, origin/master) Merge pull request #2 >> from >> hd2326/releasef0b0cab 1.0.2431f1a6 1.0.25b8334b 1.0.22adc1d6 >> 1.0.2f9f9057 >> Merge pull request #1 from hd2326/mastera36f952 2017120103daa79 >> 20171005df8e1d9 201709255a6f49c 20170925a396510 20170925a1e3a9b >> 2017092553257c1 20170925bba0041 20170925d60f929 201709257639318 >> 2017092523ed47b 20170908fe94a79 2017090854c939e 2017090881890f3 >> 20170908feefc44 201709083905d52 2017090863a7b21 20170908e4bbdc5 >> 20170908fcdc396 20170908406d29b vignettescbf66ea doca24d4d9 >> updated >> Detailed section2933f89 Initial commit* >> >> >> Would you please help me on the problem? >> >> Thank you very much! >> >> Ding >> >> >> >> >> 2018-03-26 10:40 GMT-04:00 Turaga, Nitesh >> <nitesh.tur...@roswellpark.org >> <mailto:nitesh.tur...@roswellpark.org>>: >> >> Hi Yuande, >> >> This is being blocked because you have completely unrelated >> histories from >> what you have on your Github to the Bioc-git repo. We >> deliberately don’t >> allow force pushing. >> >> Are you sure you want to merge the unrelated histories? This >> is important >> to consider, particularly because we’ve had this problem of >> packages having >> duplicate commits.Please make sure your Github Repo does not >> have any >> duplicate commits. (“git log --oneline”) >> >> If you think the Github repo is at a state where it needs to >> synced to the >> Bioc-git repo, let me know and I’ll take a look at it and >> sync it for you. >> >> Send me the link to your Github repo or just send me the >> output to “git >> remove -v”. >> >> Best, >> >> Nitesh >> >> On Mar 25, 2018, at 11:55 AM, Yuande Tan >> <tanyua...@gmail.com <mailto:tanyua...@gmail.com>> wrote: >> >> Dear All, >> I tried to git push upstream master but I met problem: >> >> To git.bioconductor.org:packages/MBttest.git >> >> ! [rejected] master -> master (non-fast-forward) >> >> error: failed to push some refs to >> 'g...@git.bioconductor.org <mailto:git@git.bioconductor.o >> rg>: >> >> packages/MBttest.git' >> >> hint: Updates were rejected because the tip of your >> current branch is >> >> behind >> >> >> hint: its remote counterpart. Integrate the remote >> changes (e.g. >> >> hint: 'git pull ...') before pushing again. >> >> >> Actually fixed merge conflict by using git add . and git >> commit -m >> "Resolved merge conflict by incorporating both >> suggestions." >> >> and git add ../README.md and git commit -m "add >> README.md file." >> >> I used git pull --allow-unrelated-histories origin master >> >> and I got >> >> >> From https://github.com/Yuande/MBttest >> <https://github.com/Yuande/MBttest> >> >> * branch master -> FETCH_HEAD >> >> Already up to date. >> >> I still did *~/.ssh*$ git push upstream master and I got >> the same error >> (non-fast-forward). >> >> >> When I used *~/.ssh*$ git push -f upstream master, I got >> "error: hook >> declined to update refs/heads/master" >> >> >> >> So how do I address this "hook declined" error? >> >> >> Thanks >> >> >> Yuande Tan >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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> >> >> >> >> >> This email message may contain legally privileged and/or >> confidential >> information. 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