[Bioc-devel] Reference ExperimentHub package in statistical package

[Kern, Lori]

In the review process, that is why we ask to submit related packages under the same issue.  They will be installed in the same location and available for testing before being added to the official Bioconductor repositories (once officially added available through BiocManager::install)

You can use the github link for testing on your machine, But put the data package as an appropriate Import/Suggests (or Depends) in the DESCRIPTION/NAMESPACE before submitting to Bioconductor issue review.

Cheers,


Lori Shepherd

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 Murphy, Alan E <a.murphy using imperial.ac.uk>
Sent: Tuesday, February 23, 2021 8:42 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Reference ExperimentHub package in statistical package

Hi,

I have submitted an ExperimentHub package ewceData to Bioconductor's Github for consideration here<https://secure-web.cisco.com/1UiX2YuztUVWUNVK0ym1BedqiDd81hYT0MWhD3sDFwbSDeWBfceE9dWu-etH6ZOMHPk1jW7Q17klFgksgEvGQSRHWRaYepITW-mlplfa3FItmoxXmOIThBy2_y_FCxbGrk6u5Mhl-Q_zA4rLPsZEVsSiEiLBF1s74fR_QcpClLEttSeOb9b5gH7j3PBDRQBey5i-g8Q0B5_eJV90rUOK3-93GA6D2X49oFEr_IK67L9-jWp2YjWHHmYyoA0gsD0H7NFmOrHGcOFn6MaKwNv2IMOgNJVdTFwqghfjSsjscdzftdaGiZpDgzeW6IRL4uDmc/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F1904>. I am next going to append a link to my statistical package repository once the status is updated to 'review in progress'. I am following the guide here:

https://secure-web.cisco.com/1Rto12LHxuVZvUgkhdKrWIgiMxvd6I2XOm9uhiO68XXYS8eRGc7o4InpcMM0B3oIGTHQx-zcyRfhxZhiDRjU-OW8mXl-QDHu0NHlkKXnPRjW1wI4Loeq6Hw5t8ysh4dWe9W6zNDnR7oWhlbIaEUT5DoeMfM04_s-hdiDgBfpV6hGEvNDJ66Zaflc1-ujRJdQ682wTnp16bm6uiGILMpQXriqc83KAiByrV2Cw9IO86lnlzKHrM5HUJ2tbMBTzWJLlswkFytJWh88C8b44R-m0OhEU7ONeJLaUeYJfeGobjJeEnakXKJusVr457r0MDlEl/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%23submitting-related-packages

In the meantime, I want to ensure that the statistical package doesn't fail any checks based on the use of the ExperimentHub package ewceData. However, I don't know how to reference ewceData for use in my statistical package? I need the data from ewceData for both the vignette but also in some functions. I am running the devel version of Bioconductor (BiocVersion 3.13) and as such thought ewceData would be available there but the following fails:

BiocManager::install("ewceData")

What is the best practice way to do this? I could install reference the Github repository for ewceData in my statistical package but I imagine this would cause many issues down the line?

Kind regards,
Alan.

Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

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