personally i do not use cherry-pick and perhaps others will comment on its role
i would git checkout RELEASE_3_15 make change to vignette git commit git push On Fri, Sep 30, 2022 at 6:12 PM Wu, Hao <hao...@emory.edu> wrote: > 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> wrote: > > Hello, > > I recently received an email regarding an error for DSS: > https://bioconductor.org/checkResults/3.15/bioc-LATEST/DSS/palomino3-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: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://haowulab.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://haowulab.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> > > > 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 mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-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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