Thank you for the quick reply, Robert, this indeed answered my question. Kind regards,
Jeroen ________________________________ From: Robert M. Flight <rfligh...@gmail.com> Sent: Thursday, December 23, 2021 12:58 PM To: Jeroen Gilis <jeroen.gi...@ugent.be> Cc: bioc-devel <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] EXTERNAL: R: release of new version of package Jeroen, Yes, you will have to move up that version number. However, the way to do that is to git pull upstream master This will bring in the changes that have been made to version numbers by the Bioconductor team. If you don't do the pull first, you will likely get error messages and conflicts when you make your changes. After the pull and merge, THEN start making your changes you want to make, and push those to both GitHub and Bioconductor. Hope that helps. Robert On Thu, Dec 23, 2021, 5:29 AM Jeroen Gilis <jeroen.gi...@ugent.be<mailto:jeroen.gi...@ugent.be>> wrote: Hi everyone, I have a related question that could be relevant to the original poster. Concrete example; the Bioconductor satuRn package http://bioconductor.org/packages/release/bioc/html/satuRn.html<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FsatuRn.html&data=04%7C01%7Cjeroen.gilis%40ugent.be%7Cf7a035a7ca3a4680bd6d08d9c60b8245%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637758575012377269%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=%2BRqbjtjQHFj%2BUzfw8nu3iYNe7baUcMVZF0NAACjb64Q%3D&reserved=0> that I am maintaining. It was first released in RELEASE_3_13, so that was version 1.1.0 both on my Git and Bioconductor. For RELEASE_3_14, I did not actively follow up the package, resulting in a current package version of 1.1.0 on git, 1.2.0 on bioc 3.14 and 1.3.0 on bioc devel. I now want to update the package. Does this mean I have to jump from version 1.1.0 on my git to 1.3.1 in my git (and bioc devel) to propagate these changes to bioc devel? Kind regards, Jeroen Gilis ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on behalf of Marcel Ramos <marcel.ramospe...@roswellpark.org<mailto:marcel.ramospe...@roswellpark.org>> Sent: Monday, December 20, 2021 8:02 PM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> Subject: Re: [Bioc-devel] EXTERNAL: R: release of new version of package Hi Emanuela, You should not be pushing new features to the RELEASE_3_14 branch. This is meant to be stable throughout the course of the release cycle. Make sure you are pushing your new commits to the devel branch of Bioconductor with: git push upstream master Based on your git history, it looks like you were able to make changes. Do not forget to bump the Z version of your package, e.g., 1.5.1 in devel so that the new version of the package propagates. This can take between 24 - 48 hours. Best regards, Marcel On 12/20/21 1:43 PM, Emanuela Iovino wrote: > Dear Nitesh > thank you for your answer. > I followed Bioconductor instruction but when I pushed on > > upstream/RELEASE_3_14 I received always Everything up-to-date. > > Before to follow Bioconductor instruction I already had pushed all my > modification on my Github repository and I don't know if it got me a problem > in next steps. > > I checked the last commit > onhttps://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FuncoverappLib%2F&data=04%7C01%7Cjeroen.gilis%40ugent.be%7C271fc28226574a4ba0d708d9c3eb6540%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637756238053093335%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=pWDS9dMrj03KscaX%2FXvEmzt9IfZFjcS0bsTTlYDhgYs%3D&reserved=0<http://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FuncoverappLib%2F&data=04%7C01%7Cjeroen.gilis%40ugent.be%7C271fc28226574a4ba0d708d9c3eb6540%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637756238053093335%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=pWDS9dMrj03KscaX%2FXvEmzt9IfZFjcS0bsTTlYDhgYs%3D&reserved=0> > and it doesn't match with my last modification. > > Have I to repeat all steps? > > Thanks > > Emanuela > > > > ________________________________ > Da: Nitesh Turaga<nturaga.b...@gmail.com<mailto:nturaga.b...@gmail.com>> > Inviato: luned� 20 dicembre 2021 15:36 > A: Emanuela Iovino<emanuela.iov...@unibo.it<mailto:emanuela.iov...@unibo.it>> > Cc:bioc-devel@r-project.org<mailto:cc%3abioc-de...@r-project.org> > <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> > Oggetto: Re: [Bioc-devel] release of new version of package > > Hi, > > You�ll want these two tutorials since I�m guessing you have a Github Repo and > along with the git.bioconductor repo. > > So you�ll first have to sync (1), then push your updates to both Github and > Bioc server(2) > > (1)https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F&data=04%7C01%7Cjeroen.gilis%40ugent.be%7C271fc28226574a4ba0d708d9c3eb6540%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637756238053093335%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rvYzIfbIe%2FBe9SZ7ZN1s6%2BRBK7yYU90bWX1ONiZE4K0%3D&reserved=0<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F&data=04%7C01%7Cjeroen.gilis%40ugent.be%7Cf7a035a7ca3a4680bd6d08d9c60b8245%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637758575012377269%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=4KrNhfLma5s8JpKS2aDysXe6JG2pNXmhn4kbjpS4IXw%3D&reserved=0> > > (2)https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fpush-to-github-bioc%2F&data=04%7C01%7Cjeroen.gilis%40ugent.be%7C271fc28226574a4ba0d708d9c3eb6540%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637756238053093335%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=6b1EA%2Bo0eUCUGzkLlMgfuhlm3q3vrN4qmSbmqCyNxHg%3D&reserved=0<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fpush-to-github-bioc%2F&data=04%7C01%7Cjeroen.gilis%40ugent.be%7Cf7a035a7ca3a4680bd6d08d9c60b8245%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637758575012377269%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=SWK9lxJwrk0ZlCrpq5JT6jxAKJ58fnp57Gxk21Lel3M%3D&reserved=0> > > Best > > Nitesh Turaga > Scientist II, Department of Data Science, > Bioconductor Core Team Member > Dana Farber Cancer Institute > >> On Dec 20, 2021, at 9:32 AM, Emanuela >> Iovino<emanuela.iov...@unibo.it<mailto:emanuela.iov...@unibo.it>> wrote: >> >> Hello everyone >> I'm the developer and the maintainer of Bioconductor package uncoverappLib . >> I recently added some features to package and I would like to know how >> update to Biocondunctor . Do I follow new package workflow ? >> (https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fnew-package-workflow%2F&data=04%7C01%7Cjeroen.gilis%40ugent.be%7C271fc28226574a4ba0d708d9c3eb6540%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637756238053093335%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=j2z7cyT6guPZBiTRFFsUO7I6S0T2JMNLSsP69EYsrIw%3D&reserved=0<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fnew-package-workflow%2F&data=04%7C01%7Cjeroen.gilis%40ugent.be%7Cf7a035a7ca3a4680bd6d08d9c60b8245%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637758575012377269%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=GjEPA9otJrNCDaQdWlXmBeJj%2FTs2JXAZrw2VH66W6do%3D&reserved=0>). >> Many thanks in advance >> >> Emanuela Iovino >> PhD Student in Data Science and Computation >> Division of Medical Genetics >> Dept. Medical and Surgical Sciences - DIMEC >> University of Bologna >> Pol.S.Orsola-Malpighi, via Massarenti 9, >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list >> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=04%7C01%7Cjeroen.gilis%40ugent.be%7C271fc28226574a4ba0d708d9c3eb6540%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637756238053093335%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=NGTowiVRTd2As0%2BR1cdNrGiIP3KVg40NJY%2BTXX29Rhs%3D&reserved=0<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=04%7C01%7Cjeroen.gilis%40ugent.be%7Cf7a035a7ca3a4680bd6d08d9c60b8245%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637758575012377269%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9%2FeewpFA7rfC6DfgosZDUwiM3%2FGGOugzCAPnhtnF03s%3D&reserved=0> > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=04%7C01%7Cjeroen.gilis%40ugent.be%7C271fc28226574a4ba0d708d9c3eb6540%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637756238053093335%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=NGTowiVRTd2As0%2BR1cdNrGiIP3KVg40NJY%2BTXX29Rhs%3D&reserved=0<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=04%7C01%7Cjeroen.gilis%40ugent.be%7Cf7a035a7ca3a4680bd6d08d9c60b8245%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637758575012377269%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9%2FeewpFA7rfC6DfgosZDUwiM3%2FGGOugzCAPnhtnF03s%3D&reserved=0> --- Marcel Ramos Bioconductor Core Team Roswell Park Comprehensive Cancer Center Dept. of Biostatistics & Bioinformatics Elm St. & Carlton St. Buffalo, New York 14263 This email message may contain legally privileged and/or...{{dropped:4}} _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=04%7C01%7Cjeroen.gilis%40ugent.be%7C271fc28226574a4ba0d708d9c3eb6540%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637756238053093335%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=NGTowiVRTd2As0%2BR1cdNrGiIP3KVg40NJY%2BTXX29Rhs%3D&reserved=0<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=04%7C01%7Cjeroen.gilis%40ugent.be%7Cf7a035a7ca3a4680bd6d08d9c60b8245%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637758575012377269%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9%2FeewpFA7rfC6DfgosZDUwiM3%2FGGOugzCAPnhtnF03s%3D&reserved=0> [[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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=04%7C01%7Cjeroen.gilis%40ugent.be%7Cf7a035a7ca3a4680bd6d08d9c60b8245%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637758575012377269%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9%2FeewpFA7rfC6DfgosZDUwiM3%2FGGOugzCAPnhtnF03s%3D&reserved=0> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
