Thanks Lori, your email finally made me understand the relationship between my repo and Bioc repo. I have to admit that I was not familiar of remote vs. upstream.
Now, I have pushed everything to RELEASE_3_11. But the tests did not trigger. I will push to develop as well early next week. Best wishes. *Stefano * Stefano Mangiola | Postdoctoral fellow Papenfuss Laboratory The Walter Eliza Hall Institute of Medical Research +61 (0)466452544 Il giorno gio 4 giu 2020 alle ore 23:11 Shepherd, Lori < [email protected]> ha scritto: > > The master branch is the development branch (Bioc 3.12) . The version > of x.y.z The y is always odd in devel and even in release. This is the > very first section on the page you referenced. > http://bioconductor.org/developers/how-to/version-numbering/ > > We do not jump full y versions in the middle of a release. > > The current RELEASE_3_11 version is 1.0.0 = the appropriate version > bump on this branch is 1.0.1 > > The current master version is 1.1.0 = the appropriate version bump on > this branch is 1.1.1 > > > If you are unfamiliar with git and github branches I encourage you to read > more documentation about it. There are many helpful tutorials. > You can have as many branches on your local github repository as you like. > We recommend creating unique branches for bioconductor releases to mimic > our branch structure. In general, and to make it less confusing we would > highly recommend using the master branch as the development branch and link > that to the master (development version) of Bioconductor. This would be > consistent and then you can following the guides and tutorials listed on > the Bioconductor help pages > > http://bioconductor.org/developers/how-to/git/ > > > The release branch is designed to always be a stable branch and should > only be updated for bug corrections. > The master branch should be for development and new features. > > > > We will assume you ran the following to set up your remotes as > recommended: > git remote add upstream [email protected]:packages/tidybulk.git > > > if you do > git remote -v > > you should see something similar: > origin <link to your github> (fetch) > origin <link to your github> (push) > upstream [email protected]:packages/tidybulk.git (fetch) > upstream [email protected]:packages/tidybulk.git (push) > > > To create and work on a release branch: > > git fetch --all > # this gets all branches from all remotes > > > # The following would only need to be run once EVER! > git checkout -b RELEASE_3_11 upstream/RELEASE_3_11 > > # this says checkout a branch (-b) call it RELEASE_3_11 and have it > copied/link to the code at upstream/RELEASE_3_11 (the #bioconductor > upstream remote branch of RELEASE_3_11) > > After it is created, to switch to this branch on a daily basis you can > simply: > git checkout RELEASE_3_11 > > > > git pull upstream RELEASE_3_11 > # pulls changes from the upstream RELEASE_3_11 remote > > > # The following would only need to be run once EVER! It creates a branch > on your local github called RELEASE_3_11 > git push -u origin RELEASE_3_11 > > > > Make your code changes to fix bugs! Make sure to do a valid version bump > by bumping the z of version x.y.z > > git add <files> > git commit # give an informative commit message > > > git push upstream RELEASE_3_11 > # This should push to the Bioconductor git repository > > git push origin RELEASE_3_11 > # This should push to your github local git repository > > > git checkout master > # Switch back to your master branch for development and code changes > > > If you are ever confused on what branch you are on you can do > git branch > > > To work on the devel master branch the commands would be similar to above > but using master > > git pull upstream master # pulls from git bioconductor > git pull origin master # pull from your individual github > > # make changes, commit changes > > git push upstream master # pushes to git Bioconductor > git push origin master # push to your github > > > Hopefully that helped clarified and will get you started. > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* stefano <[email protected]> > *Sent:* Thursday, June 4, 2020 12:56 AM > *To:* Shepherd, Lori <[email protected]> > *Cc:* [email protected] <[email protected]> > *Subject:* Re: Bioconductor package tidybulk > > Thanks Lori, > > I have to questions > > 1) > I got versioning error > > > ``` > > rstudio-1 267 % git push upstream master > Counting objects: 372, done. > Delta compression using up to 32 threads. > Compressing objects: 100% (276/276), done. > Writing objects: 100% (290/290), 1.13 MiB | 0 bytes/s, done. > Total 290 (delta 208), reused 21 (delta 13) > remote: Resolving deltas: 100% (208/208), completed with 41 local objects. > *remote: Error: Illegal version bump from '1.1.0' to '1.2.1'. Check * > remote: http://bioconductor.org/developers/how-to/version-numbering/ > <http://secure-web.cisco.com/1Juo69PrrnIOXU2DlRv55eEvQE69YG8gNnojLbxZZWpn2-BCpwQ95EvShTW84fzr36gEkai208agWd63Ju9NfDXE-J9WHITwNW8oj6a0nxd1bS_UtLog1j_kotLO3TRPxw6votAQ8BdaCk4PzIaCZRX2wTPTRQsHNIV1_U4F47Y3w5QyE-kq7njCZrhtOzxb6HxIn6mtY-Xgj7a3Wkas_WsiIDmeKI8MdDFgePj_CwYe7BMLtq680xbPHpzYD-KvS32jkv_R8yL5Bqf2xd1lUZxeJU7rCj4PTKVa0Q9JgSdl3ax7Ozze9-LxNvuOsmqKWWGorQqVctJQPHiJjwDlmPjmeCsjgtgODdtBWqLJ73s4/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fversion-numbering%2F> > remote: for details > To [email protected]:packages/tidybulk.git > > ``` > > Even reading the guide > http://bioconductor.org/developers/how-to/version-numbering/ > <http://secure-web.cisco.com/1Juo69PrrnIOXU2DlRv55eEvQE69YG8gNnojLbxZZWpn2-BCpwQ95EvShTW84fzr36gEkai208agWd63Ju9NfDXE-J9WHITwNW8oj6a0nxd1bS_UtLog1j_kotLO3TRPxw6votAQ8BdaCk4PzIaCZRX2wTPTRQsHNIV1_U4F47Y3w5QyE-kq7njCZrhtOzxb6HxIn6mtY-Xgj7a3Wkas_WsiIDmeKI8MdDFgePj_CwYe7BMLtq680xbPHpzYD-KvS32jkv_R8yL5Bqf2xd1lUZxeJU7rCj4PTKVa0Q9JgSdl3ax7Ozze9-LxNvuOsmqKWWGorQqVctJQPHiJjwDlmPjmeCsjgtgODdtBWqLJ73s4/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fversion-numbering%2F> > I don't understand what applies to my case > > > > 2) I still don't know what is the best way to manage github development > with Bioconductor development. > > > I have my Master branch and I am pushing it to Bioconductor. Can I have a > RELEASE branch pushed to Bioconductor rather than my master branch? > > > guide: "Repeat for the release branch, replacing master with the name of > the release branch, e.g., RELEASE_3_6." > > > Thanks. > > Best wishes. > > *Stefano * > > > > Stefano Mangiola | Postdoctoral fellow > > Papenfuss Laboratory > > The Walter Eliza Hall Institute of Medical Research > > +61 (0)466452544 > > > Il giorno mer 3 giu 2020 alle ore 23:36 Shepherd, Lori < > [email protected]> ha scritto: > > It will not be tested before integration. We assume that all maintainers > and R CMD build and R CMD check before submitting changes to Bioconductor. > > You will need to have activated your git credentials account > > https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/ > <https://secure-web.cisco.com/1Aev5P9rDulkX5gOO8VsMROu0hqZcaU8fT3GP3AsyJYVM9ZzDQvHlsVkbzeE5uPiKDW76VZwZ3dFyNb8zGzGedrlNvKLuUclm-kcov6rBNxdEZC-UhloV7M-ybiYfSTo_9W9bVXIABeFOmC9RDlfjHPMBzpGAXgiSnFf5l9K5oZD2ttL2bFFzyPVpHc98pUcmuZnen8jgx7jpHxlJFEawIVU-cudLdHJRrrNkdaugeByvKC8QmZVUl5yXhLW4u6W1lt8pI3lSWOkBrmRgF7WmwU8fYTV4Bt9KeQha0JL0Ib9xgNh7Z8_Fp1tahQkwEDcvWHuhHTGYdGdQEeOAX9EAsg/https%3A%2F%2Fgit.bioconductor.org%2FBiocCredentials%2Flogin%2F%3Fnext%3D%2FBiocCredentials%2F> > > And follow the instructions for pushing to git.bioconductor.org > <http://secure-web.cisco.com/1tu10p-DtLwvt_Da5m6yfRWyEgCLKIttPMfLoP3QlI066eirYetcxcfKZxywtszpwBOI-HXVBFYGxT5HvijqFtWL7O7_Zjr-XYb9wiSmV8IzxJM4zQlSf_TZutg6lzUjtNw6qzutYzLhPuDrtXAWn5l9LzB3a6zQM4fOq2p5zz9-uY9qHeNvD9xBNMcBK8hjshH4JG3jV5BsTwRLsA0-lpp0CThGV35Cx7-aa55-G0DmN5onTbNlXqsO86CxJG0SEZ2-L9xGF-VVBgNI6g9ian3TxNbcjVdafZO9bacD0DGVsh_is1U_C_rrJLcCwum_BVFADYTVu1TSeEpqlnhx5mw/http%3A%2F%2Fgit.bioconductor.org> > . > We provide many help instruction files for different scenarios > > http://bioconductor.org/developers/how-to/git/ > <http://secure-web.cisco.com/1H0LIZjlbeI4hZ6lwLBpmwzeK1pJm_lvmM4EwXQRDqho3xCDLinHlAxc07U3mNV7suKrnr_1AfmGquSG6e-yn_XbbpGOECsw7mPV-meDnIfDmwkfm2CwS_i3IZIAkA6cxyGKdej44dWdQjbkKWg2JGtWv8loY6wj63Lbijzig-aulyMswz9PUgRYM0tM8U9UHwyValzmseILpTPkTCSTyJu7PBZGdFFxaicBJgFmBtZoyFQCFf7oXPizmmSyKvEh0MwgXgvznurtQXe5rMBDkwqySlrRTkXrbjuoxB9WPl-u8pWRhEjCve7ik5tNFoQacKKwNcxMCZ2aw7ySrEdkLFSZu41YG_a4r9FRfsL-DcJY/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2F> > > > You will most notably be interested in > Syncing to Bioconductor > http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ > <http://secure-web.cisco.com/1KZeBzEmS1uWIu3n6-dmHGrHtnY7o7_9uZjIzXpYceEvUgdbfHYiEnDuPGG29xPpe3Cq38dl6VxMCZHvMy2vz4QI7KqYKeBJIjAPcCXoW48yqNwZNwtT46CGd18cIxep7bqfEYsXVJYa_v21zdF6vq_AoEMdFolfkBi1RzkvRBSBu1mtnaSNxb2p266dTQXvReetXZ888aOqIlJLHV7aOr21aPL-JbZkdc0pH5Pobr_whr4fdIqjMBSSHjJtLgIpkhBojlnXd2s8htweMWUdyIJvxAa6oLGHSeq5I8pFJ9VaYQfiwsMKmg9Og6zgNbnV6Qi3HaigpOvMDngGfpjcU6Tdv2Z_2RWPnbC0kU3GaXqM/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F> > > and pushing fixes to release and devel > http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ > <http://secure-web.cisco.com/11yyfZ49Z7npZG1IQtNUChMTmptQod64On2gbAqHzqYn1F1s9qvsOhhqenc0W0Yz_LFDKi7C2l4qBlnP8kH5NQxApFKOpNh4MXd_V6F4f9cFuXZnY7RY_H4l_Ui8Dkcs3hxkE8VlyCpQls-YMNdbres6dkRdxTAlFP2nnPOZR-C5AOEwXXFl8TIQsMCouGEI9NyhwARVEBhxbDS2zb0IbAQUV2JOoX8XQLURMsmSHh3bOqFPstQWvtl51bPts8OqEBi1Q1-vx1abhxEtXWhb_ZEQMGjq8aK62LeukCl_bnHMdd3OOVJjuv0ygZyn4wUK_Pwx5aGl7iMBLEt_FuEnhZazI5Tlf9slOoZNiVaGHuck/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fbug-fix-in-release-and-devel%2F> > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* stefano <[email protected]> > *Sent:* Wednesday, June 3, 2020 4:29 AM > *To:* Shepherd, Lori <[email protected]>; > [email protected] <[email protected]> > *Subject:* Re: Bioconductor package tidybulk > > Hello Again, > > I would be happy to submit the github master with the patch tonight if you > could please confirm the commit command. Will it be tested before > integration I assume. > > Thanks a lot! > > Best wishes. > > *Stefano * > > > > Stefano Mangiola | Postdoctoral fellow > > Papenfuss Laboratory > > The Walter Eliza Hall Institute of Medical Research > > +61 (0)466452544 > > > Il giorno mer 3 giu 2020 alle ore 12:26 stefano <[email protected]> > ha scritto: > > Thanks Lori, (it seems outlook lost my sent email) > > > > sorry I missed this. It's so strange, few days ago I checked at > > > https://www.bioconductor.org/packages/devel/bioc/html/tidybulk.html > <https://secure-web.cisco.com/1ymalO2Wo2gRPT4USwKYJChnovSH3sx87LQTVbhEAL5rIc3rN6fxBVq0xvtPe8K_Q-R_eFRNkhIlQj7WO0ojRaWF_pEyWlhdIOd2PMRLmE2OPNqgY5f94zo8UYWUGdcvlZcVx8reWZ3HqP5ZigV5z6s1O1vpAhOg7Ilz6E1U3-x5Ew-CEeVKmnYZe96PicWrzG2pfFGcttYa35E5pwKrrGI-dm5Sy6FKZhrPJtO-Qm65EpKlgjJg-S1H0Dng6El9eZl79ifySj3rIrEtYwcVvsRCgOGmn5RqrxF4_1vKVJl7MF59rIRIHqt-OR9BXO6Ol7hNnQze5_Kl_SbkOEyd9h_FG7hn_MIzYBsitEyDD5-8/https%3A%2F%2Fwww.bioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2Ftidybulk.html> > > > and the build was OK for devel and stable versions. > > > I have done the fix > > > commit d1fe5beb290765181e0ce377b890f453c62ea9da > > > Should I (?) > > > - integrate the commit to the tidybulk version present in Bioconductor, > and push > > - or push the update github repo > > > Could you point me to the resource tat states how to push to Bioconductor, > so I'm sure I am doing the right thing. > > > Thanks alot. > > > Best wishes. > > *Stefano * > > > > Stefano Mangiola | Postdoctoral fellow > > Papenfuss Laboratory > > The Walter Eliza Hall Institute of Medical Research > > +61 (0)466452544 > > > Il giorno mer 3 giu 2020 alle ore 07:10 Shepherd, Lori < > [email protected]> ha scritto: > > Hello Package Maintainer, > > The Bioconductor Team would like to notify you that your package is > currently > failing on release and devel versions of Bioconductor and has been for an > extended period of time. This is very problematic. Please fix your > package to > R CMD build and R CMD check cleanly immediately to avoid deprecation of > your > package. If you are having trouble or have any further questions please > reach > out to the developers mailing list at [email protected] > > > We appreciate your immediate attention to this matter. > > Cheers > > http://bioconductor.org/checkResults/devel/bioc-LATEST/tidybulk > <http://secure-web.cisco.com/1V0Xuq_KL0x1Cl4QqzHrj1dnBRaQhCCuV-22PXesIk07DaPPjoJ3QsrSPROh_5cXbYpawIN5i2Nq1BZR_hLHXPuM6pjQ-3eMVQGnIfUDaGyUaM2r0OKlVcRHQal8uBYNnIvQH6S2oehrbakBF8VT50ga-chmesQYDXRVuPo_IWNS6IIR3LBhvBnY1hv5_raI9CsjS9fUpU-G09_CAyRyUA17JrLjrtMAT4Bxi5T0NN53kKg2ZP4Unsqwtr5Oix4WaXxRCKrMa0s77HeePZYvUAYnkfUYZCiYXuVsqmRytlG92KumBHz-0P1es_zBp5JVmqn-Y3mjMBOwl7Vy8Lx1o8anxo8xN9qChrHFrl14SjZQ/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Ftidybulk> > http://bioconductor.org/checkResults/release/bioc-LATEST/tidybulk > <http://secure-web.cisco.com/1gjLzb1cWpFF_sHsM57h5yIYvuiIuFDLZmakncmleiFa_KJWoTiDpmLs9wxxenQRe9bjnc5MCunwT6ishis6WIailFEBNiwNXyJWEXo9_I4MXs7HnnVHP8L-aUJI9D52getJRFvo3Y1oau4z0D0sMu_33XBgwAkFIcpDb8aleVdkalFB6T0bdquwBcfn_pO0zBXW8UgXsoFB3_RvbY4sgsDnymfSGqVXlwELCaQ9euMvV9waafBekDjsrAOD5H7L_t2wd91GpDyI8LNZhIFPO1vmUtCO5BkFrYxJvEEoLmqNSftO5yyQ2UqMuB8OQeacnKOLGwd0V-6_USxeGmvqSxVi2BDpIV7ukHTLkFTScrn4/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2Ftidybulk> > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > This email message may contain legally privileged and/or confidential > information. 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