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

2022-10-03 Thread Kern, Lori 
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  on behalf of Wu, Hao 

Sent: Friday, September 30, 2022 6:12 PM
To: Vincent Carey 
Cc: bioc-devel@r-project.org ; Harry Feng 

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" 
Date: Friday, September 30, 2022 at 6:08 PM
To: Vincent Carey 
Cc: "bioc-devel@r-project.org" , Harry Feng 

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 

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 
mailto:hao...@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 
g...@git.bioconductor.org:packages/DSS<mailto:g...@git.bioconductor.org<mailto: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://secure-web.cisco.com/1kIqV2KeSlTIdc87EvxwyHQf6L69I3HKEzFKXTsY183pfFCuRWt7cib8433zjHMdveBuczoa72CWWEkn7rESTMpx4ivrnaHtnzNc67f5QeGqtj_100EdDsfHsk5smSFz-1isy_3BGXzZ_6USJFVy6vNCTjr8stcRH9NZDRta3onVI-6B3_MCcf8Am46FlTtii2Sh8u90lnOFTHsoV9RPnm6Piw0yaEThMtT-A0EzP7Ux7koOIVtiSLOqSekClEwSvycbSDLxV_yl6DO7LmmLRm1XFi0_YIQ5Wy19USpWLfHdu5sq5BE86pgFY_s4V3264/http%3A%2F%2Fhaowulab.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://secure-web.cisco.com/1rcBAzWPpuJf23wM4uZCSld9oOL4rVPMyPO1lEieDhhOtWvlvxdHEzy8MNg

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

2022-10-03 Thread 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" 
Date: Friday, September 30, 2022 at 6:08 PM
To: Vincent Carey 
Cc: "bioc-devel@r-project.org" , Harry Feng 

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 

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 
mailto:hao...@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.
 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: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]]

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

2022-10-03 Thread Wu, Hao 
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 

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 
mailto:hao...@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.
 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: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

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
 . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly

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

2022-09-30 Thread 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
> 
>
>
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail