[Bioc-devel] Help updating data in ExperimentHub

[Vinh Tran]

Dear Lori,

Thanks for your quick reply! 

Yes, I was referring to the snapshot date of the PhyloProfileData data package. I have updated the raw data on the hosted server. In the inst/scripts/ directory of the data package I have two files make-data.R and make-metadata.R, which generate the .RData files and the metadata.csv, respectively. I will try updating the data version in the metadata file and submit again. Currently, neither the devel nor the release version reflexes the changes. 

I understand the importance of consistency and reproducibility. However, this data package is used solely as a demo data for the Bioconductor PhyloProfile package. In order to fully demonstrate the feature of the current version of PhyloProfile, we need to update the data, even in the release version.

Many thanks again for your support!

Best,
Vinh

--------------------------------
Dr. Vinh Tran

Applied Bioinformatics Group
Inst. of Cell Biology and Neuroscience
Goethe University
Max-von-Laue Str. 13
D-60438 Frankfurt am Main
Germany

Biologicum, Room 3.209
Phone +49 (0)69/798-42118

> On 20. Jun 2025, at 14:08, Kern, Lori <Lori.Shepherd using RoswellPark.org> wrote:
> 
> So a few follow up questions and comments
> 
> It seems like you a referencing an ExperimentHub data package with the snapshot date;  is that correct?
> 
> And if so, you mentioned you updated the raw data;  you have updated those files on the hosted server?  And did you request an update to the metadata in the experiment hub database.  The data files would need to be updated in order to have the correct download and access. 
> 
> The update will only be available using Bioconductor devel 3.22;  a snapshot of  4-12-2025 is for release not devel so you would have to use devel in order to see the change.   It is possible to update release but it is not recommended for consistency and to keep release as stable and reproducible for users as possible. 
> 
> If you need further assistance with updating the experiment hub data;   I suggest reaching out to hubs using bioconductor.org <mailto:hubs using bioconductor.org> 
> 
> 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 <mailto:bioc-devel-bounces using r-project.org>> on behalf of Vinh Tran <tran using bio.uni-frankfurt.de <mailto:tran using bio.uni-frankfurt.de>>
> Sent: Friday, June 20, 2025 7:54 AM
> To: bioc-devel using r-project.org <mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org <mailto:bioc-devel using r-project.org>>
> Subject: [Bioc-devel] Help updating data in ExperimentHub
>  
> Greetings,
> 
> I would like to update the data in our PhyloProfileData package. I have updated the raw data and also made changes to the make-data.R file which generates the .RData files for the package. However, after the latest build, the data remains unchanged, even after reinstalling R and all related packages. I also noticed that the snapshot date is still set to 12 April 2025, while the latest build was on 19 June 2025.
> 
> Could anyone please help me figure out what might be missing? Many thanks in advance!
> 
> Best regards,
> Vinh
> 
> 
> 
> --------------------------------
> Dr. Vinh Tran
> 
> Applied Bioinformatics Group
> Inst. of Cell Biology and Neuroscience
> Goethe University
> Max-von-Laue Str. 13
> D-60438 Frankfurt am Main
> Germany
> 
> Biologicum, Room 3.209
> Phone +49 (0)69/798-42118
> 
> 
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