Hello Lori and All, I confirm that the bioconductor page for a package (e.g., https://www.bioconductor.org/packages/release/bioc/html/tidybulk.html ) has a bug in practice. Namely that even though the icon build is green
https://wehieduau-my.sharepoint.com/:i:/g/personal/mangiola_s_wehi_edu_au/EbdbpGqJ8zZKhYjE3mJq8CsB6viFK6Ci6AoAQRzcD8hDbQ?e=lub86A the actual build (e.g., http://bioconductor.org/checkResults/release/bioc-LATEST/tidybulk/) can be failing. If this is wanted, or tolerated, it is very confusing for developers (and users) because communicate false confidence and leads to unwanted neglection (as happened to me) . Best wishes. *Stefano * Stefano Mangiola | Postdoctoral fellow Papenfuss Laboratory The Walter Eliza Hall Institute of Medical Research +61 (0)466452544 Il giorno sab 6 giu 2020 alle ore 11:08 stefano <mangiolastef...@gmail.com> ha scritto: > 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 < > lori.sheph...@roswellpark.org> 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 g...@git.bioconductor.org: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 g...@git.bioconductor.org:packages/tidybulk.git (fetch) >> upstream g...@git.bioconductor.org: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 <mangiolastef...@gmail.com> >> *Sent:* Thursday, June 4, 2020 12:56 AM >> *To:* Shepherd, Lori <lori.sheph...@roswellpark.org> >> *Cc:* bioc-devel@r-project.org <bioc-devel@r-project.org> >> *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 g...@git.bioconductor.org: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 < >> lori.sheph...@roswellpark.org> 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 <mangiolastef...@gmail.com> >> *Sent:* Wednesday, June 3, 2020 4:29 AM >> *To:* Shepherd, Lori <lori.sheph...@roswellpark.org>; >> bioc-devel@r-project.org <bioc-devel@r-project.org> >> *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 < >> mangiolastef...@gmail.com> 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 < >> lori.sheph...@roswellpark.org> 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 bioc-devel@r-project.org >> >> >> 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. 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. >> >> >> 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. >> >> >> 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
