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Unlimited

Unlimited #283

Workflow file for this run

on:
push:
branches:
- devel
pull_request:
branches:
- devel
name: R-CMD-check
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.bioc-version }})
strategy:
fail-fast: false
matrix:
config:
- { os: windows-2022, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor', Ncpus: 4}
- { os: macOS-14, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor', Ncpus: 3}
- { os: macOS-12, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor', Ncpus: 3}
- { os: ubuntu-22.04, bioc-version: 'devel', bioc-mirror: 'https://ftp.gwdg.de/pub/misc/bioconductor', Ncpus: 4}
- { os: ubuntu-22.04, bioc-version: 'release', bioc-mirror: 'https://packagemanager.posit.co/bioconductor', Ncpus: 4}
steps:
## R CMD check complains about Windows line endings without this
- name: Configure git
run: |
git config --global core.autocrlf false
- name: Install system libraries
if: runner.os == 'Linux'
run: |
sudo apt-get update && sudo apt-get install libcurl4-openssl-dev
- uses: actions/checkout@v4
- name: Setup R and Bioconductor
uses: grimbough/bioc-actions/setup-bioc@v1
with:
bioc-version: ${{ matrix.config.bioc-version }}
bioc-mirror: ${{ matrix.config.bioc-mirror }}
- uses: r-lib/actions/setup-pandoc@v2
- name: temp rhdf5filters install
if: matrix.config.os == 'macOS-14'
run: |
sudo R -e 'source("https://mac.R-project.org/bin/install.R")' -e 'install.libs("openssl")'
- name: temp rhdf5filters install
if: matrix.config.os == 'macOS-14'
run: |
install.packages("remotes")
BiocManager::install("grimbough/rhdf5filters")
shell: Rscript {0}
- name: Install dependencies
uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: |
covr
rcmdcheck
- name: Bioc - Build, Install, Check
uses: grimbough/bioc-actions/build-install-check@v1
- name: Run BiocCheck
uses: grimbough/bioc-actions/run-BiocCheck@v1
with:
error-on: 'never'
arguments: '--no-check-bioc-help'
- name: Test coverage
if: runner.os == 'Windows'
run: |
covr::codecov()
shell: Rscript {0}