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

[Wu, Hao]

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://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 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


--
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 using r-project.org<mailto:Bioc-devel using 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. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners.org%2Fcomplianceline&data=05%7C01%7Chao.wu%40emory.edu%7C02fb9e1ebad54540b2b208daa32ffe73%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638001723812041382%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=yESMxeil%2BSFExx65fDRFlYYmGB2AnrnT8greVFsVA0M%3D&reserved=0> . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

	[[alternative HTML version deleted]]