Specifically, the instructions can be found here: http://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel
I always cherry-pick commit /hashes/ from the main branch into the RELEASE_3_XX branch. This method ensures good practice by requiring atomic commits (separate commits for codebase changes and version bumps). Best regards, Marcel On 10/3/22 1:43 PM, Kern, Lori wrote: > There are very detailed instructions at > > http://contributions.bioconductor.org/git-version-control.html > > It is hard to tell if this is the right procedure because it will depend on > how you cloned and what remotes you have set up. > > You should not cherry-pick all of master as there are likely version number > increases that should not be checked into a RELEASE_X_Y branch. It is better > to cherry-pick specific commits or as vince originally suggested checkout the > branch and manually make the changes > > Cheers, > > > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > ________________________________ > From: Bioc-devel<bioc-devel-boun...@r-project.org> on behalf of Wu, > Hao<hao...@emory.edu> > Sent: Friday, September 30, 2022 6:12 PM > To: Vincent Carey<st...@channing.harvard.edu> > Cc:bioc-devel@r-project.org <bioc-devel@r-project.org>; Harry > Feng<hxf...@case.edu> > Subject: Re: [Bioc-devel] [External] Re: error in bioconductor package DSS > > Okay, after some quick search, I did > > git checkout RELEASE_3_15 > git cherry-pick master > git push > > Is this what I should do? > > From: "Wu, Hao"<hao...@emory.edu> > Date: Friday, September 30, 2022 at 6:08 PM > To: Vincent Carey<st...@channing.harvard.edu> > Cc:"bioc-devel@r-project.org" <bioc-devel@r-project.org>, Harry > Feng<hxf...@case.edu> > Subject: Re: [External] Re: [Bioc-devel] error in bioconductor package DSS > > Vince, > > Thanks for the prompt reply. Can you provide more instruction on how I should > look at a particular branch and commit the changes to that? When I do git > clone, what branch did I get? > > Hao > > > From: Vincent Carey<st...@channing.harvard.edu> > Date: Friday, September 30, 2022 at 6:06 PM > To: "Wu, Hao"<hao...@emory.edu> > Cc:"bioc-devel@r-project.org" <bioc-devel@r-project.org>, Harry > Feng<hxf...@case.edu> > Subject: [External] Re: [Bioc-devel] error in bioconductor package DSS > > I don't think you are looking at the RELEASE_3_15 branch, but that is where > the error is occurring. > > On Fri, Sep 30, 2022 at 6:03 PM Wu, Hao > <hao...@emory.edu<mailto:hao...@emory.edu>> wrote: > Hello, > > I recently received an email regarding an error for > DSS:https://secure-web.cisco.com/1bXlscxhlzDngZQemtNqfj3Sne4WML7WdCfL74wHtks5FXijnKSYcEnTuJdU8RxiYuR1E9Zpm2ZyszqHesK0pzR84-h5UwcKUx-IiH3R_OsjDzpMRyAu38-Hh216FMGbd9oswxi35hFbRu_1wSP_P3xjjHjBL2ArMse38dTSfQl7Jb1q_XcpMmDjS0TIu754Z1RG0xB3FM0VECQlpnshcfrbBQleAiXubjJ9dUA5rCfRd5vXBrHKUfCOSzzLHrPGrm6OJoKfdYvBHdPjikBiO5O9wY5FHdmuNBC1OikNl5mLoetA8RqsDX2Bse5fpE36w/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.15%2Fbioc-LATEST%2FDSS%2Fpalomino3-buildsrc.html<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.15%2Fbioc-LATEST%2FDSS%2Fpalomino3-buildsrc.html&data=05%7C01%7Chao.wu%40emory.edu%7C02fb9e1ebad54540b2b208daa32ffe73%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638001723811885161%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=H3Em1Xm13tkGjw7b2%2FJP1OQtj4Gcv7OqIf8GwrCJgTM%3D&reserved=0>. > The error is about the parallel computing in Windows. However, I have > corrected this error a while ago, and it has passed the compilation before. > It�s not clear why the error appeared again, since in the source code on > bioconductor, the error shouldn�t be there. > > To be more specific, the message says that the error happened in line 338-340 > in the vignette (DSS.Rmd): > > Quitting from lines 338-340 (DSS.Rmd) > Error: processing vignette 'DSS.Rmd' failed with diagnostics: > Shrinkage estimator in parallel computing encountered errors. Please switch > to single core. > > However, if I do �git > clone...@git.bioconductor.org:packages/DSS<mailto:g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>:packages/DSS>� > to get the DSS source code, you can see lines 338-340 in DSS.Rmd are > commented out. It seems the system is still compiling the old version. I�m > very confused. 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