Re: [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  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" 
> *Date: *Friday, September 30, 2022 at 6:08 PM
> *To: *Vincent Carey 
> *Cc: *"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 
> *Date: *Friday, September 30, 2022 at 6:06 PM
> *To: *"Wu, Hao" 
> *Cc: *"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  wrote:
>
> Hello,
>
> I recently received an email regarding an error for DSS:
> https://bioconductor.org/checkResults/3.15/bioc-LATEST/DSS/palomino3-buildsrc.html
> .
> 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 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
> 
>  
> >
> Zoom: https://zoom.us/j/8294730806
> 
>
>
>
>
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>
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> addressed. If you believe this e-mail

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

[Vincent Carey]

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  wrote:

> Hello,
>
> I recently received an email regarding an error for DSS:
> https://bioconductor.org/checkResults/3.15/bioc-LATEST/DSS/palomino3-buildsrc.html.
> 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 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
> Zoom: https://zoom.us/j/8294730806
>
>
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] error in bioconductor package DSS

[Wu, Hao]

Hello,

I recently received an email regarding an error for DSS: 
https://bioconductor.org/checkResults/3.15/bioc-LATEST/DSS/palomino3-buildsrc.html.
 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”
 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
Zoom: https://zoom.us/j/8294730806




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Re: [Bioc-devel] New maintainer for package - Updating a R package and pushing the commit

[Kern, Lori]

I will create your git credentials account and send you the temporary password 
in a private email.  Please do as Herve says by altering the DESCRIPTION and 
pushing to git.bioconductor.org.

You will be responsible for pushing the changes to git.bioconductor.org.  You 
can find many details at
https://contributions.bioconductor.org/git-version-control.html

Most immediately helpful will probably be the following for assistance setting 
up remotes:
https://contributions.bioconductor.org/git-version-control.html#new-package-workflow

Cheers,


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Hervé Pagès 
Sent: Thursday, September 29, 2022 5:58 PM
To: Tulip Nandu ; Kern, Lori 
; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] New maintainer for package - Updating a R package and 
pushing the commit

Hi Tulip,

On 29/09/2022 13:52, Tulip Nandu wrote:

> Hi Kern,
>
> Anusha no longer is associated with the lab. So I will need to have access to 
> the package. If you can create an account on GitCredentials that would be 
> great.

If that means Anusha is no longer going to maintain the package, then
their role in Authors@R would need to be switched from "cre" to "aut" or
"ctb" or whatever is appropriate.

As Lori said, the Maintainer and Author fields should get removed, and
your name and role moved to the Authors@R field.

Thanks,

H.

>
> I do have a github account.  tulipnandu is the username.
>
>
> https://secure-web.cisco.com/1sz7apuCmn4ohmCI87ibLXfXf2HV76G22UDgL3c3S3mC74LaBD59xyHINjjvQZLobFGBIwBE7uBbAQG37cd6fpIfYTT-kESDUcqUjRDfAHF4aUfYld15UCItSNFsgmKPXcaM9JTp9DMpiG1yWqineSY-XvOvciOmBslTzPrQTjSmnCjcV9Bjig7kPR2UV6bOQ-kee1qnpXXfQRK3WAmpK6A6mAuodm_ae5UfmtS7Obzwxs5SApgpFc0DjM8uCcxyJVpmOWhu7UiHYQdlS9h2j92Jx6qgxDDca79fUi7LcRE1zCLWjNjx7geIuxylxLuBK/https%3A%2F%2Fgithub.com%2Ftulipnandu
> [https://secure-web.cisco.com/1WFyb-uH1KKqS_8qxzHe822g-zoOK-K98o8CvfWtriy_VQsnIhXz5TmS-XLutbI4QuJJlr-jDUjeUwXnK_B05kL99Byvz6rZkxnMoOCNuc4beIgaVCv5o9pancBV5rRnZzP0EByH5mcEREDgmAsTRnHU7-cT7OVhSx-_GAPy6VsSjw7mI37X1_FHLlhC0j_3wJrruV-sbUAm00rPfcPt2UzLUjVUKaw-WnB7sS5X7B2D3TaS5K4tYfFi8QZ5khtk6JMvRZNoMMNGU8J5lV38h6T1HFnAA12zDhGTJ_UoiRSff1ndxBOKjZJVJzSb7oNYl/https%3A%2F%2Favatars.githubusercontent.com%2Fu%2F1099843%3Fv%3D4%3Fs%3D400
> tulipnandu - 
> Overview
> tulipnandu has 10 repositories available. Follow their code on GitHub.
> github.com
> Also I would need to push the changes in the src file to master on 
> bioconductor/git. If I can get some help with that, it would be great too.
>
> Regards,
>
> Tulip.
>
> 
> From: Kern, Lori 
> Sent: Thursday, September 29, 2022 6:52 AM
> To: Tulip Nandu ; bioc-devel@r-project.org 
> ; Anusha Nagari 
> Subject: Re: New maintainer for package - Updating a R package and pushing 
> the commit
>
>
> EXTERNAL MAIL
>
> This message was sent securely using 
> Zix�
>
> a few points:
>
> Normally only one person has maintainer access to a package this currently 
> was Anusha Nagari .  Should they also 
> retain maintainer access?
>
> Anusha was assigned because that is who is listed with Authors@R.  You 
> currently have a mixure of using Authors@R and Maintainer/Author field.  
> Please remove Author/Maintainer fields and only use Authors@R.
>
> In a normal procedure the currently listed maintainer would request the 
> switch or additional access.  Since I see you listed in the Maintainer field, 
> we can ignore this step for this situation. I will need to create an account 
> on our GitCredentials where you can manage your ssh keys for access.  We can 
> link a github account for access.  Do you have a personal github account you 
> would like