search

uclahs-cds / package-CancerEvolutionVisualization

Publication Quality Phylogenetic Tree Plots
https://cran.r-project.org/web/packages/CancerEvolutionVisualization/
GNU General Public License v2.0
2 stars 0 forks source link

r-lib R CMD check workflow #41

Closed dan-knight closed 1 year ago

dan-knight commented 1 year ago

Replaces old Docker-based R CMD check CICD workflow with actions from r-lib.

dan-knight commented 1 year ago

what part, if any, of this workflow would we want to modularize?

The reusable, generic workflow would be largely the same. Maybe we'd add something to install the private BL packages if needed, but this would work as-is for most packages. We might just want to add an option for additional package installs on a repo-by-repo basis (Bioconductor, etc.).

stefaneng commented 1 year ago

This is my setup for private BL packages: https://github.com/uclahs-cds/project-ExOnc-IMPACT-CH/blob/4fb68c80e640b87da4f0fb7602962061e52812ff/.github/workflows/R-CMD-check.yaml

I use a PAT and install the packages before setup-dependencies. There is an issue (bug in pak or r-lib/actions) with ignoring dependencies. I could be using it wrong or there is an actual bug. You should be able to have dependencies listed in DESCRIPTION but have pak ignore them with:

BoutrosLab.utilities=?ignore
BoutrosLab.statistics.general=?ignore

This means that if using BL.utils or BL.statistics we can't add them to the DESCRIPTION file or else pak will try to install them from CRAN.

dan-knight commented 1 year ago

Merged this so that other PRs will use the new workflow. I moved @stefaneng's comment into this issue on the action repo itself. (This package doesn't use any private BL repos.)