[Bioc-devel] Error in SVMDO Package

Tue Aug 27 14:23:41 CEST 2024

Great ! 

I meant that my previous update from April was only appearing in code.bioconductor.org. 

Therefore, I was worried about my last push. 

Yet, I can see the updated version in code.bioconductor.org now. 

Kimden: "Lori Kern" <Lori.Shepherd using RoswellPark.org> 
Kime: "MUSTAFA ERHAN ÖZER" <erhanozer19 using marun.edu.tr> 
Kk: "Vincent Carey" <stvjc using channing.harvard.edu>, "bioc-devel" <bioc-devel using r-project.org>, "Bioc-devel" <bioc-devel-bounces using r-project.org> 
Gönderilenler: 27 Ağustos Salı 2024 14:21:30 
Konu: Re: Error in SVMDO Package 

Thank you. I do see the changes now pushed to git.bioconductor.org and the build report should reflect these changes within in the next 24 hours pending if you pushed in time for today or tomorrows builds. 

I'm not sure what you mean by SVMDO is not on code.bioconductor.org. I can find the package here: 
[ https://code.bioconductor.org/browse/SVMDO/ | https://code.bioconductor.org/browse/SVMDO/ ] 
and it does also reflect the recent changes pushed. 

Let us know if there are any further questions or concerns. 

Cheers, 

Lori Shepherd - Kern 

Bioconductor Core Team 

Roswell Park Comprehensive Cancer Center 

Department of Biostatistics & Bioinformatics 

Elm & Carlton Streets 

Buffalo, New York 14263 

From: MUSTAFA ERHAN ÖZER <erhanozer19 using marun.edu.tr> 
Sent: Tuesday, August 27, 2024 2:41 AM 
To: Kern, Lori <Lori.Shepherd using RoswellPark.org> 
Cc: Vincent Carey <stvjc using channing.harvard.edu>; bioc-devel <bioc-devel using r-project.org>; Bioc-devel <bioc-devel-bounces using r-project.org> 
Subject: Re: Error in SVMDO Package 
Good day, 

I tried to send the new updates of SVMDO package to and RELEASE_3_19 branches. 

I checked that SVMDO package name appears in the package list of git .bioconductor.org, but it is not in the table of code.bioconductor.org. 

Does that mean the updates were pushed without any problem? 
Is it going to appear in code.bioconductor.org later? 

Sincerely, 

Kimden: "Kern, Lori" <Lori.Shepherd using RoswellPark.org> 
Kime: "Vincent Carey" <stvjc using channing.harvard.edu>, "MUSTAFA ERHAN ÖZER" <erhanozer19 using marun.edu.tr> 
Kk: "bioc-devel" <bioc-devel using r-project.org>, "Bioc-devel" <bioc-devel-bounces using r-project.org> 
Gönderilenler: 26 Ağustos Pazartesi 2024 14:14:42 
Konu: Re: Error in SVMDO Package 

I do not see the changes pushed to git.bioconductor.org. Please check to make sure the remotes are set up correctly and there were no ERROR's when doing a git push. 

The release branch will NOT update automatically. You need to push the same changes to the RELEASE_ 3 _ 19 branch of git.bioconductor.org:packages/SVMDO 

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 MUSTAFA ERHAN ÖZER via Bioc-devel <bioc-devel using r-project.org> 
Sent: Monday, August 26, 2024 3:12 AM 
To: Vincent Carey <stvjc using channing.harvard.edu> 
Cc: bioc-devel <bioc-devel using r-project.org>; Bioc-devel <bioc-devel-bounces using r-project.org> 
Subject: Re: [Bioc-devel] Error in SVMDO Package 
Good day, 

I updated the devel branch of the SVMDO package, but I have not see it in code.bioconductor.org yet. 
I did the update approximately 2 hours ago. How long does it take to appear? 
Is it also going to automatically update release version of 3.19? 

Sincerely, 

Kimden: "Vincent Carey" <stvjc using channing.harvard.edu> 
Kime: "MUSTAFA ERHAN ÖZER" <erhanozer19 using marun.edu.tr> 
Kk: "Bioc-devel" <bioc-devel-bounces using r-project.org>, "bioc-devel" <bioc-devel using r-project.org> 
Gönderilenler: 26 Ağustos Pazartesi 2024 1:03:14 
Konu: Re: [Bioc-devel] Error in SVMDO Package 

On Sun, Aug 25, 2024 at 3:33 PM MUSTAFA ERHAN ÖZER via Bioc-devel < [ [ mailto:bioc-devel using r-project.org | 
mailto:bioc-devel using r-project.org ] | bioc-devel using r-project.org ] > wrote: 

Good day, 

The recent Multiple platform build/check report for BioC 3.19 of SVMDO package resulted in error for every platform. 

The error is " Error in `get_anno_data(ontology)`: ontology not supported yet... " 

The error essentially reports that "DO" is not a valid argument to enrichDO. SVMDO should use "HDO", I believe. 

Is this a package related issue that is going to be fixed by itself? 

Sincerely, 

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