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/ remote: for details To g...@git.bioconductor.org:packages/tidybulk.git ``` Even reading the guide http://bioconductor.org/developers/how-to/version-numbering/ 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/ > > And follow the instructions for pushing to git.bioconductor.org. > We provide many help instruction files for different scenarios > > http://bioconductor.org/developers/how-to/git/ > > > You will most notably be interested in > Syncing to Bioconductor > http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ > > and pushing fixes to release and devel > http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ > > > > 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. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
