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

[Vincent Carey]

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.wu using 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.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> 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: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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