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 g...@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. Could someone help? Thank you very much. Hao Wu -- Professor Department of Biostatistics and Bioinformatics Rollins School of Public Health Emory University 1518 Clifton Rd., NE Atlanta, GA 30322 Phone: (404)727-8633 Fax: (404)727-1370 Web: http://secure-web.cisco.com/1kIqV2KeSlTIdc87EvxwyHQf6L69I3HKEzFKXTsY183pfFCuRWt7cib8433zjHMdveBuczoa72CWWEkn7rESTMpx4ivrnaHtnzNc67f5QeGqtj_100EdDsfHsk5smSFz-1isy_3BGXzZ_6USJFVy6vNCTjr8stcRH9NZDRta3onVI-6B3_MCcf8Am46FlTtii2Sh8u90lnOFTHsoV9RPnm6Piw0yaEThMtT-A0EzP7Ux7koOIVtiSLOqSekClEwSvycbSDLxV_yl6DO7LmmLRm1XFi0_YIQ5Wy19USpWLfHdu5sq5BE86pgFY_s4V3264/http%3A%2F%2Fhaowulab.org<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fhaowulab.org%2F&data=05%7C01%7Chao.wu%40emory.edu%7C02fb9e1ebad54540b2b208daa32ffe73%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638001723812041382%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LKekKN009MoPtjO2WM5iTsQtjqeXQrp1fUKvkBWkLPk%3D&reserved=0><http://secure-web.cisco.com/1rcBAzWPpuJf23wM4uZCSld9oOL4rVPMyPO1lEieDhhOtWvlvxdHEzy8MNgY90X3xQelCl6rYPRXI0GGaNceNGennDU8B6fYh5uWEt_wFVKhmkC2rZaWU_KZ02-E5opJ4Vc_hbab9ray8MxqUX2H_ndqfu0hwhYBC3jZioxo728gyt7u-Qs-YMNlDCeiuPepRbwA71IVYRCpQuk7B9MjjgXl10pmlir2Z5OE7DOSleOmFaCTwCsBiitNJJkLHOLiwO8NGLWPhgZGmGuN5ulcWf8EwCPRzY-pY5Bz3CGpdCj94xmxeO-P82qWz7OZ7xkRk/http%3A%2F%2Fhaowulab.org%2F<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fhaowulab.org%2F&data=05%7C01%7Chao.wu%40emory.edu%7C02fb9e1ebad54540b2b208daa32ffe73%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638001723812041382%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LKekKN009MoPtjO2WM5iTsQtjqeXQrp1fUKvkBWkLPk%3D&reserved=0>> Zoom: https://zoom.us/j/8294730806<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fzoom.us%2Fj%2F8294730806&data=05%7C01%7Chao.wu%40emory.edu%7C02fb9e1ebad54540b2b208daa32ffe73%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638001723812041382%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=yup2fQyHnnid5Cjlqs0nKy1og%2BiZe6DX5yL055mxktw%3D&reserved=0> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://secure-web.cisco.com/1Xv2wuLko0JAoL8CL3Gf79RlX65OV8-z1DtHkbSmsyzy_iV3jODXttWTiUmvHYGf1_msVyfa5nLenpJIMUn_22MFQn8TnXwamY3cxkLm0OhEUFGm9M-FD_g8OavwAnjVmIkdhjrPzWUtuyOiBF68a4m0kRJzNrehbEm0F0sc7YKjQLbf_9MaDFGnLWN2R-4KGBRxtYGrL2-mB9USLIckt908FKGjet5Ozn9Qv-fP73t_8Guwnx_umwIt_O3iabMP3nyj1QW5lZcJDG9I-CCk3vCYAeocHu63QRsvdYvahklRFddDUf1nc9Eqf_bKqdwYd/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=05%7C01%7Chao.wu%40emory.edu%7C02fb9e1ebad54540b2b208daa32ffe73%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638001723812041382%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=h5MpJsq8yGU7PXLL02jREqi4QSvcH0Mrwv8gf8P%2BN54%3D&reserved=0> The information in this e-mail is intended only for the person to whom it is addressed. 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