[Bioc-devel] bioconductor package testing

Brian Schilder br|@n_@ch||der @end|ng |rom @|umn|@brown@edu
Tue Dec 27 22:50:49 CET 2022

Hi Adam, and to any other Bioc developers who have encountered this scenario,

I would humbly offer my new R package rworkflows<https://github.com/neurogenomics/rworkflows/> for this purpose.
I started this project for exactly the situation you’re describing: wanting to test your package with a fresh install on multiple OS (Linux, Mac, Windows) before pushing the changes to Bioc. It sets up a GitHub Actions<https://github.com/features/actions> workflow that will do all Bioc (and/or CRAN) testing, render/launch documentation website via GitHub Pages, and build a containers hosted on Dockerhub. You can set this all up using a single R function- rworkflows::use_workflow()


Accompanying preprint should be up soon. An early release is currently on CRAN, but I’d recommend using the devel version on Github atm as it has more workflow customisation features. Please let me know if you have any questions in the meantime 😊

Brian Schilder
PhD Candidate
UK Dementia Research Institute at Imperial College London
Faculty of Medicine, Department of Brain Sciences, Neurogenomics Lab
Profile | bit.ly/imperial_profile<https://bit.ly/imperial_profile>
LinkedIn | linkedin.com/in/brian-schilder<https://www.linkedin.com/in/brian-schilder/>
Twitter | twitter.com/BMSchilder<http://www.twitter.com/BMSchilder>
Lab | neurogenomics.co.uk<http://neurogenomics.co.uk>
UK DRI | www.ukdri.ac.uk<http://www.ukdri.ac.uk/>

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Park, Adam Keebum <sein.park using psu.edu>
Date: Sunday, 25 December 2022 at 05:45
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] bioconductor package testing
Dear whom it may concern,

I hope I am contacting the right person for my inquiry.

(1) I wonder how I can test a package in advance of submitting to bioconductor,  especially with respect to dependencies. Dozens of R libraries should be installed with my package.

That is, I would like to simulate BiocManager::install("my package") and check if a fresh new user can run tutorials and vignettes code without any problem.

(2) Similarly, how could I simulate running Vignette codes in my local environment? As I understood so far, codes written in a Vignette(.Rmd) will be executable after being converted to a html document and being published in the bioconductor website.


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