[Bioc-devel] error in bioconductor package DSS

Mon Oct 3 21:58:37 CEST 2022

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-bounces using r-project.org>  on behalf of Wu, Hao<hao.wu using emory.edu>
> Sent: Friday, September 30, 2022 6:12 PM
> To: Vincent Carey<stvjc using channing.harvard.edu>
> Cc:bioc-devel using r-project.org  <bioc-devel using r-project.org>; Harry Feng<hxf155 using 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.wu using emory.edu>
> Date: Friday, September 30, 2022 at 6:08 PM
> To: Vincent Carey<stvjc using channing.harvard.edu>
> Cc:"bioc-devel using r-project.org"  <bioc-devel using r-project.org>, Harry Feng<hxf155 using 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<stvjc using channing.harvard.edu>
> Date: Friday, September 30, 2022 at 6:06 PM
> To: "Wu, Hao"<hao.wu using emory.edu>
> Cc:"bioc-devel using r-project.org"  <bioc-devel using r-project.org>, Harry Feng<hxf155 using 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.wu using emory.edu<mailto:hao.wu using 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 clonegit using git.bioconductor.org:packages/DSS<mailto:git using git.bioconductor.org<mailto:git using 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
>
>
> --
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