Hi, all. I've noticed that my package has returned an error in the Bioc build (https://bioconductor.org/packages/devel/bioc/html/BioNERO.html). As it was accepted last month and this will be my first change to the package after acceptance, I would like to check some things: 1. Can I change the code and push now that Bioc is frozen or do I have to wait a few days for the next release? 2. Is the procedure to push changes the same as I've done during the review process (git push upstream master, then git push origin master)? Thank you. ========================= Fabr?cio de Almeida Silva Undergraduate degree in Biological Sciences (UENF) MSc. candidate in Plant Biotechnology (PGBV/UENF - RJ/Brazil) Laborat?rio de Qu?mica e Fun??o de Prote?nas e Pept?deos (LQFPP/CBB/UENF - RJ/Brazil) Lattes CNPq: http://lattes.cnpq.br/3119358824056108 Personal website: https://almeidasilvaf.github.io/home/
[Bioc-devel] Fixing build error for the first time
3 messages · Shepherd, Lori, Fabricio de Almeida
The RELEASE_3_12 branch was frozen but the devel (master) branch is not. You may continue to push to upstream master to make relevant changes. Yes that procedure would stay the same to push to the devel branch of git.bioconductor and your individual github repo. In the future (after the next release) to make changes to a release branch you would push to the appropriate RELEASE_X_Y (the upcoming would be RELEASE_3_13) . We only recommend bug fixes or ERROR corrections on a RELEASE branch and keep new features on the devel branch. See this document that summarized http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ Please note: Unlike the submission process, daily builds are not built on push. The builders only pull changes and do build/check once per day. There is some information on timing found here but it can take up to 48 hours to reflect changes if the push is close after the start of the daily builds. http://bioconductor.org/developers/how-to/troubleshoot-build-report/ Cheers Bioconductor - Bug fixes<http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/> Fix bugs in devel and release. Goal: Maintainers will have to fix bugs from time to time, and make sure the patch is available both in the master branch and the current release branch. Steps: Sync existing repositories.. git fetch --all git checkout master git merge upstream/master git merge origin/master git checkout <RELEASE_X_Y> git merge upstream/<RELEASE_X_Y> git merge origin/<RELEASE_X_Y> bioconductor.org Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Fabricio de Almeida <fabricio_almeidasilva at hotmail.com>
Sent: Wednesday, May 5, 2021 2:45 PM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Fixing build error for the first time
Sent: Wednesday, May 5, 2021 2:45 PM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Fixing build error for the first time
Hi, all. I've noticed that my package has returned an error in the Bioc build (https://secure-web.cisco.com/18jmU5NJek2Kwlsf3noyPn3Biy3PtIe-5UugFna_3oaRCDvFUtOL4UYdPcKCfdx3_3hnNysozJjtoNLIUWqbieRIf0ol0AeNkKzeLXyzZG3cL3zIWRY9dNJK1Gi6nXBbNFWsNpctwU_bghtdk03e-AFKSTSAPlovRDhlixzrdJfr_JYRLbWZttdFoywVO1WyjaxxMZQKORdDGHdm659e9ITKbcZrIGlBFDJoKv2EFiumgwYtA8SpDwnNpiCtsm-e0diYSnFsOo40eNRzfEiHkK3a1-cft81alF6FMMYW1OPa2Z2CI_YDm1xdxl53rMXSB/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FBioNERO.html As it was accepted last month and this will be my first change to the package after acceptance, I would like to check some things: 1. Can I change the code and push now that Bioc is frozen or do I have to wait a few days for the next release? 2. Is the procedure to push changes the same as I've done during the review process (git push upstream master, then git push origin master)? Thank you. ========================= Fabr?o de Almeida Silva Undergraduate degree in Biological Sciences (UENF) MSc. candidate in Plant Biotechnology (PGBV/UENF - RJ/Brazil) Laborat? de Qu?ca e Fun? de Prote?s e Pept?os (LQFPP/CBB/UENF - RJ/Brazil) Lattes CNPq: http://secure-web.cisco.com/1YNdn2iO4zJxTId95mUCuHe8pSmkEnnOdB2D94KNISKyL1-Pa1VlrDZQvKAhQ74uwszY4aCd3A0xjssy6s91fpLHR1cvq_ercbYPwJTqrYlf6C4R7qRYLXjmuKB8l7cZNVEs8GAN1Ii0kzfaFbEtjuM0tG6VveRzDb9S25dgOwsgrBD2mr6LgTxBxBaDyhPcnvwihGQsfe6CDvPv44FbfqfMljeKnT7CxenBW23JAf0r7YiY9GxfZa8c4aCW9ChZrOI2TWrgVIxBbzDwY1_4SoRFO5tS2KB4o9_DhMG5RwD2ENtFKDJlSASbsKgouQZb1/http%3A%2F%2Flattes.cnpq.br%2F3119358824056108 Personal website: https://secure-web.cisco.com/1V7cGnCtCUDV5iTr6kQqe5ivyhKSRML2Uyk4vVfk_BlzOUdxQS7CWRJ3g4fJuVBIc_r4l4_5qXFp5GcjBGU9egHplwBaYP6pUb4-hYiZ04tKKds_9yxNdhNnZk6Ez5hX3HyhAIDupadJhPZt5f4bN0hxLqHMXNjrh84Z0Ki8hCo44NrDIQlV9OVgJ5fjCD8w4aMqI8lJJzvxdgB-7J2VnpDNDtH8ZZlSbCD0qp97qHoLs6zV5f3qJisZdpLkc3VJpkFwpEO97Ra9EaDmlX095fGnD-tYVvvfXQdhXo7bn_dPoYOYdxrcqY-xvVHNUSJva/https%3A%2F%2Falmeidasilvaf.github.io%2Fhome%2F [[alternative HTML version deleted]] 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.
Thank you very much, Lori. Now it is very clear. ========================= Fabr?cio de Almeida Silva Undergraduate degree in Biological Sciences (UENF) MSc. candidate in Plant Biotechnology (PGBV/UENF - RJ/Brazil) Laborat?rio de Qu?mica e Fun??o de Prote?nas e Pept?deos (LQFPP/CBB/UENF - RJ/Brazil) Lattes CNPq: http://lattes.cnpq.br/3119358824056108 Personal website: https://almeidasilvaf.github.io/home/
De: Kern, Lori <Lori.Shepherd at RoswellPark.org>
Enviado: quarta-feira, 5 de maio de 2021 13:59 Para: Fabricio de Almeida <fabricio_almeidasilva at hotmail.com>; bioc-devel at r-project.org <bioc-devel at r-project.org> Assunto: Re: Fixing build error for the first time The RELEASE_3_12 branch was frozen but the devel (master) branch is not. You may continue to push to upstream master to make relevant changes. Yes that procedure would stay the same to push to the devel branch of git.bioconductor and your individual github repo. In the future (after the next release) to make changes to a release branch you would push to the appropriate RELEASE_X_Y (the upcoming would be RELEASE_3_13) . We only recommend bug fixes or ERROR corrections on a RELEASE branch and keep new features on the devel branch. See this document that summarized http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ Please note: Unlike the submission process, daily builds are not built on push. The builders only pull changes and do build/check once per day. There is some information on timing found here but it can take up to 48 hours to reflect changes if the push is close after the start of the daily builds. http://bioconductor.org/developers/how-to/troubleshoot-build-report/ Cheers Bioconductor - Bug fixes<http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/> Fix bugs in devel and release. Goal: Maintainers will have to fix bugs from time to time, and make sure the patch is available both in the master branch and the current release branch. Steps: Sync existing repositories.. git fetch --all git checkout master git merge upstream/master git merge origin/master git checkout <RELEASE_X_Y> git merge upstream/<RELEASE_X_Y> git merge origin/<RELEASE_X_Y> bioconductor.org Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Fabricio de Almeida <fabricio_almeidasilva at hotmail.com> Sent: Wednesday, May 5, 2021 2:45 PM To: bioc-devel at r-project.org <bioc-devel at r-project.org> Subject: [Bioc-devel] Fixing build error for the first time Hi, all. I've noticed that my package has returned an error in the Bioc build (https://secure-web.cisco.com/18jmU5NJek2Kwlsf3noyPn3Biy3PtIe-5UugFna_3oaRCDvFUtOL4UYdPcKCfdx3_3hnNysozJjtoNLIUWqbieRIf0ol0AeNkKzeLXyzZG3cL3zIWRY9dNJK1Gi6nXBbNFWsNpctwU_bghtdk03e-AFKSTSAPlovRDhlixzrdJfr_JYRLbWZttdFoywVO1WyjaxxMZQKORdDGHdm659e9ITKbcZrIGlBFDJoKv2EFiumgwYtA8SpDwnNpiCtsm-e0diYSnFsOo40eNRzfEiHkK3a1-cft81alF6FMMYW1OPa2Z2CI_YDm1xdxl53rMXSB/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FBioNERO.html As it was accepted last month and this will be my first change to the package after acceptance, I would like to check some things: 1. Can I change the code and push now that Bioc is frozen or do I have to wait a few days for the next release? 2. Is the procedure to push changes the same as I've done during the review process (git push upstream master, then git push origin master)? Thank you. ========================= Fabr?o de Almeida Silva Undergraduate degree in Biological Sciences (UENF) MSc. candidate in Plant Biotechnology (PGBV/UENF - RJ/Brazil) Laborat? de Qu?ca e Fun? de Prote?s e Pept?os (LQFPP/CBB/UENF - RJ/Brazil) Lattes CNPq: http://secure-web.cisco.com/1YNdn2iO4zJxTId95mUCuHe8pSmkEnnOdB2D94KNISKyL1-Pa1VlrDZQvKAhQ74uwszY4aCd3A0xjssy6s91fpLHR1cvq_ercbYPwJTqrYlf6C4R7qRYLXjmuKB8l7cZNVEs8GAN1Ii0kzfaFbEtjuM0tG6VveRzDb9S25dgOwsgrBD2mr6LgTxBxBaDyhPcnvwihGQsfe6CDvPv44FbfqfMljeKnT7CxenBW23JAf0r7YiY9GxfZa8c4aCW9ChZrOI2TWrgVIxBbzDwY1_4SoRFO5tS2KB4o9_DhMG5RwD2ENtFKDJlSASbsKgouQZb1/http%3A%2F%2Flattes.cnpq.br%2F3119358824056108 Personal website: https://secure-web.cisco.com/1V7cGnCtCUDV5iTr6kQqe5ivyhKSRML2Uyk4vVfk_BlzOUdxQS7CWRJ3g4fJuVBIc_r4l4_5qXFp5GcjBGU9egHplwBaYP6pUb4-hYiZ04tKKds_9yxNdhNnZk6Ez5hX3HyhAIDupadJhPZt5f4bN0hxLqHMXNjrh84Z0Ki8hCo44NrDIQlV9OVgJ5fjCD8w4aMqI8lJJzvxdgB-7J2VnpDNDtH8ZZlSbCD0qp97qHoLs6zV5f3qJisZdpLkc3VJpkFwpEO97Ra9EaDmlX095fGnD-tYVvvfXQdhXo7bn_dPoYOYdxrcqY-xvVHNUSJva/https%3A%2F%2Falmeidasilvaf.github.io%2Fhome%2F [[alternative HTML version deleted]] 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.