[Bioc-devel] Error in SVMDO Package

[Kern, Lori]

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/
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 �ZER <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 �ZER" <erhanozer19 using marun.edu.tr>
Kk: "bioc-devel" <bioc-devel using r-project.org>, "Bioc-devel" <bioc-devel-bounces using r-project.org>
G�nderilenler: 26 A�ustos 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 �ZER 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 �ZER" <erhanozer19 using marun.edu.tr>
Kk: "Bioc-devel" <bioc-devel-bounces using r-project.org>, "bioc-devel" <bioc-devel using r-project.org>
G�nderilenler: 26 A�ustos Pazartesi 2024 1:03:14
Konu: Re: [Bioc-devel] Error in SVMDO Package



On Sun, Aug 25, 2024 at 3:33 PM MUSTAFA ERHAN �ZER via Bioc-devel < [ 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.

BQ_BEGIN


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

Sincerely,


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