Empty #120
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on: | |
push: | |
pull_request: | |
branches: | |
- master | |
name: R-CMD-check | |
jobs: | |
R-CMD-check: | |
runs-on: ${{ matrix.config.os }} | |
container: ${{ matrix.config.image }} | |
name: ${{ matrix.config.os }} (${{ matrix.config.bioc }} - ${{ matrix.config.image }}) | |
strategy: | |
fail-fast: false | |
matrix: | |
config: | |
- { os: windows-latest, bioc: 'release'} | |
- { os: windows-latest, bioc: 'devel'} | |
- { os: macOS-latest, bioc: 'release'} | |
- { os: macOS-latest, bioc: 'devel'} | |
- { os: ubuntu-latest, bioc: 'release'} | |
- { os: ubuntu-latest, bioc: 'devel'} | |
env: | |
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
CRAN: ${{ matrix.config.cran }} | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
steps: | |
- name: Check out repo | |
uses: actions/checkout@v2 | |
- name: Set up R | |
uses: grimbough/bioc-actions/setup-bioc@v1 | |
if: matrix.config.image == null | |
with: | |
bioc-version: ${{ matrix.config.bioc }} | |
- name: Install magick dependencies | |
if: runner.os == 'macOS' | |
run: | | |
brew install imagemagick | |
brew install ffmpeg | |
- name: Install dependencies | |
uses: r-lib/actions/setup-r-dependencies@v1 | |
with: | |
extra-packages: rcmdcheck, optparse, magick, BiocManager, devtools | |
- name: Install BiocCheck | |
if: runner.os == 'Linux' | |
run: BiocManager::install("BiocCheck") | |
shell: Rscript {0} | |
- name: Set up pandoc | |
uses: r-lib/actions/setup-pandoc@v2 | |
if: matrix.config.image == null | |
- name: basilisk utils | |
if: matrix.config.os == 'windows-latest' && matrix.config.bioc == 'devel' | |
run: | | |
devtools::install_github("alanocallaghan/basilisk.utils") | |
shell: Rscript {0} | |
- name: Debug | |
if: matrix.config.os == 'windows-latest' && matrix.config.bioc == 'devel' | |
run: | | |
devtools::load_all() | |
m <- matrix(rnorm(2000), ncol=20) | |
out <- fitsne(m, random_state = 42L) | |
shell: Rscript {0} | |
- name: Check | |
uses: r-lib/actions/check-r-package@v2 | |
- name: BiocCheck | |
if: runner.os == 'Linux' | |
run: BiocCheck::BiocCheck(dir('check', 'tar.gz$', full.names = TRUE), `quit-with-status` = TRUE) | |
shell: Rscript {0} | |
- name: Show testthat output | |
if: always() | |
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
shell: bash | |
- name: Upload check results | |
if: failure() | |
uses: actions/upload-artifact@v1 | |
with: | |
name: ${{ runner.os }}-r${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-results | |
path: check | |
- name: Test coverage | |
if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'release' | |
run: | | |
install.packages("covr") | |
covr::codecov(token = "${{secrets.CODECOV_TOKEN}}") | |
shell: Rscript {0} | |