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Fix and optimize CI #89

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Merged
cpanse merged 5 commits into from
Jun 12, 2025
Merged

Fix and optimize CI #89

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669f014
Fix CI
leoschwarz Jun 12, 2025
db917f2
use pak for ci
leoschwarz Jun 12, 2025
5fc601a
bump R to 4.5 for BioC 3.21
leoschwarz Jun 12, 2025
95fea34
Correctly name the package
leoschwarz Jun 12, 2025
190894b
optimize
leoschwarz Jun 12, 2025
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15 changes: 9 additions & 6 deletions .github/workflows/r.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,21 +25,24 @@ jobs:
runs-on: ubuntu-24.04
strategy:
matrix:
r-version: [4.3]
r-version: [4.5]
steps:
- uses: actions/checkout@v4
- name: Set up R ${{ matrix.r-version }}
uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.r-version }}
use-public-rspm: true
- name: Install Linux packages
run: sudo apt-get install -y mono-mcs mono-xbuild libcurl4-openssl-dev libicu-dev pandoc pandoc-citeproc texlive texlive-latex-extra texlive-fonts-extra
run: sudo apt-get install -y libcurl4-openssl-dev libicu-dev pandoc texlive texlive-latex-extra texlive-fonts-extra
shell: bash {0}
- name: Install dependencies
run: |
install.packages(c("remotes", "covr", "rcmdcheck", "rmarkdown", "protViz", "testthat", "knitr", "BiocManager"))
BiocManager::install(c("BiocStyle", "ExperimentHub", "tartar"))
remotes::install_deps(dependencies = TRUE)
install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))
cat("Repository being used:\n")
print(getOption("repos"))
pak::pkg_install(c("covr", "rcmdcheck", "rmarkdown", "protViz", "testthat", "knitr", "bioc::BiocStyle", "bioc::ExperimentHub", "bioc::tartare"))
pak::local_install_deps(dependencies = TRUE)
shell: Rscript {0}
- name: Check
run: rcmdcheck::rcmdcheck(build_args = "", args = "", error_on = "error", check_dir = "/tmp/rawrr.Rcheck")
Expand All @@ -51,4 +54,4 @@ jobs:
with:
name: rawrr.Rcheck
path: /tmp/rawrr.Rcheck
if-no-files-found: warn
if-no-files-found: warn