[Bioc-devel] [External] Re: error in bioconductor package DSS

Mon Oct 3 19:43:42 CEST 2022

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 clone git 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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Rollins School of Public Health
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