[Bioc-devel] Automate package check workflow + Dockers for devel-vs-release

Shraddha Pai @hr@ddh@@p@| @end|ng |rom utoronto@c@
Tue Sep 21 23:33:54 CEST 2021

Hi everyone,

Answering my own question in case it's useful for anyone else (and someone
please correct if any errors here).

Looks like the current best practice is to use Github Actions for
automating package test with every git push.
I came across Leonardo Collado-Torres' helpful package "biocthis" which
sets up the basic BioC workflow in one command, along with a link to Jim
Hester's talk on Github Actions at Rstudio Conf 2020.

I'm now setting up my package so that a github push triggers a Github
Action to build and test the package on bioc-devel, followed by
building and pushing a Docker image with the package installed.

SO looking forward to not having to do this manually anymore!


On Mon, Sep 20, 2021 at 12:17 PM Shraddha Pai <shraddha.pai using utoronto.ca>

> Hello BioC community,
> Is there a recommended set of tools / workflow for automating build and
> check of a package update? I'm currently manually doing this. I've seen
> some discussion from 2015 around Travis CI (which I've yet to use) but not
> sure if that's current.
> If there's a workshop that covers this or notes from one, would
> appreciate knowing.
> Separately, I use two Docker builds - one release, one devel version of
> BioC - and manually launch each to run my tests. Is there an easier
> workflow for checking the package in both release and devel branches or
> setting up triggers for each?
> Thanks very much,
> Shraddha
> --
> *Shraddha Pai, PhD*
> Principal Investigator, OICR
> Assistant Professor, Department of Molecular Biophysics, University of
> Toronto
> shraddhapai.com; @spaiglass on Twitter
> https://pailab.oicr.on.ca
> *Ontario Institute for Cancer Research*
> MaRS Centre, 661 University Avenue, Suite 510, Toronto,
> Ontario, Canada M5G 0A3
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