[Bioc-devel] Error in SVMDO Package

[Mike Smith]

Dear Mustafa,

The contents of code.bioconductor.org updates every 15 minutes, and should
automatically reflect any changes in the central git repository.

It looks like your changes have been pushed to the devel and RELEASE_3_19
branches and can be seen here:

https://code.bioconductor.org/browse/SVMDO/commits/devel
https://code.bioconductor.org/browse/SVMDO/commits/RELEASE_3_19

Best,
Mike



On Tue, 27 Aug 2024 at 08:41, MUSTAFA ERHAN ÖZER via Bioc-devel <
bioc-devel using r-project.org> wrote:

> 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,
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> [ [ mailto:Bioc-devel using r-project.org | mailto:Bioc-devel using r-project.org ] |
> Bioc-devel using r-project.org ] mailing list
> [ [
> https://secure-web.cisco.com/1CAOziRIN8KtCy0GPCqlXsJRzah1K2gGcYuqfN3Qclu8hVOtNzTFxNGgsW5DRUzlm2APZJz-AXCOictagXJF1PPq4kJ1WJRDtFMk2YRBJHlgKPUgBCm2V2jKpZyEf1Wgc7lKW8XQ9RomQKQiPDvw4i1ULWCO3301ZXfL0jjVFJwwEZFPY7kCtrN2WGGyr8smhfBAdqd2sTkLos6u2Ea3Hq-YUGy62NYUvnIoNG2hfLS8M0b4KKBjDnUysG3-8Bw05ADUzABpGGiU8g1cZxRRrganrsmTP8VdT-CEqSfFZ0Zmx9C9nA0Hg1JY7jKP1JXL8/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> |
>
> https://secure-web.cisco.com/1CAOziRIN8KtCy0GPCqlXsJRzah1K2gGcYuqfN3Qclu8hVOtNzTFxNGgsW5DRUzlm2APZJz-AXCOictagXJF1PPq4kJ1WJRDtFMk2YRBJHlgKPUgBCm2V2jKpZyEf1Wgc7lKW8XQ9RomQKQiPDvw4i1ULWCO3301ZXfL0jjVFJwwEZFPY7kCtrN2WGGyr8smhfBAdqd2sTkLos6u2Ea3Hq-YUGy62NYUvnIoNG2hfLS8M0b4KKBjDnUysG3-8Bw05ADUzABpGGiU8g1cZxRRrganrsmTP8VdT-CEqSfFZ0Zmx9C9nA0Hg1JY7jKP1JXL8/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> ] | [
> https://secure-web.cisco.com/1CAOziRIN8KtCy0GPCqlXsJRzah1K2gGcYuqfN3Qclu8hVOtNzTFxNGgsW5DRUzlm2APZJz-AXCOictagXJF1PPq4kJ1WJRDtFMk2YRBJHlgKPUgBCm2V2jKpZyEf1Wgc7lKW8XQ9RomQKQiPDvw4i1ULWCO3301ZXfL0jjVFJwwEZFPY7kCtrN2WGGyr8smhfBAdqd2sTkLos6u2Ea3Hq-YUGy62NYUvnIoNG2hfLS8M0b4KKBjDnUysG3-8Bw05ADUzABpGGiU8g1cZxRRrganrsmTP8VdT-CEqSfFZ0Zmx9C9nA0Hg1JY7jKP1JXL8/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> |
>
> https://secure-web.cisco.com/1CAOziRIN8KtCy0GPCqlXsJRzah1K2gGcYuqfN3Qclu8hVOtNzTFxNGgsW5DRUzlm2APZJz-AXCOictagXJF1PPq4kJ1WJRDtFMk2YRBJHlgKPUgBCm2V2jKpZyEf1Wgc7lKW8XQ9RomQKQiPDvw4i1ULWCO3301ZXfL0jjVFJwwEZFPY7kCtrN2WGGyr8smhfBAdqd2sTkLos6u2Ea3Hq-YUGy62NYUvnIoNG2hfLS8M0b4KKBjDnUysG3-8Bw05ADUzABpGGiU8g1cZxRRrganrsmTP8VdT-CEqSfFZ0Zmx9C9nA0Hg1JY7jKP1JXL8/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> ] ]
>
>
>
>
> The information in this email is intended only for the...{{dropped:10}}