R-CMD-check-release #114
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on: | |
push: | |
branches: | |
- master | |
pull_request: | |
branches: | |
- master | |
schedule: | |
- cron: '0 8 * * 5' | |
name: R-CMD-check-release | |
jobs: | |
R-CMD-check-release: | |
if: "! contains(github.event.head_commit.message, '[ci skip]')" | |
runs-on: ${{ matrix.config.os }} | |
container: ${{ matrix.config.image }} | |
name: ${{ matrix.config.os }} (${{ matrix.config.r }} - ${{ matrix.config.bioc }} - ${{ matrix.config.image }}) | |
strategy: | |
fail-fast: false | |
matrix: | |
config: | |
- { os: windows-latest, r: '4.1 ', bioc: 'devel'} | |
- { os: macOS-latest, r: '4.1', bioc: 'devel'} | |
- { os: ubuntu-latest, r: '4.1', 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: r-lib/actions/setup-r@master | |
with: | |
r-version: ${{ matrix.config.r }} | |
- name: Set up pandoc | |
uses: r-lib/actions/setup-pandoc@master | |
- name: Install remotes | |
run: | | |
install.packages('remotes') | |
shell: Rscript {0} | |
- name: Set BiocManager version | |
run: | | |
install.packages('BiocManager') | |
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE) | |
shell: Rscript {0} | |
- name: Install matrixStats | |
run: | | |
install.packages("matrixStats") | |
remotes::install_github("const-ae/MatrixGenerics", ref = "master") | |
shell: Rscript {0} | |
- name: Install system dependencies | |
if: runner.os == 'Linux' | |
env: | |
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
run: | | |
Rscript -e "remotes::install_github('r-hub/sysreqs')" | |
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | |
sudo -s eval "$sysreqs" | |
sudo apt-get update && sudo apt-get -y install libcurl4-openssl-dev | |
- name: Install further dependencies | |
run: | | |
install.packages(c("sessioninfo", "rcmdcheck")) | |
BiocManager::install(c("BiocCheck", "BiocStyle")) | |
install.packages(c("Rcpp", "rmarkdown", "testthat", "knitr", "bench", "rmarkdown")) | |
shell: Rscript {0} | |
- name: Session info | |
run: | | |
options(width = 100) | |
pkgs <- installed.packages()[, "Package"] | |
sessioninfo::session_info(pkgs, include_base = TRUE) | |
shell: Rscript {0} | |
- name: Check | |
run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error", check_dir = "check") | |
shell: Rscript {0} | |
- name: BiocCheck | |
run: | | |
BiocCheck::BiocCheck(".") | |
shell: Rscript {0} | |
- name: Upload check results | |
if: failure() | |
uses: actions/upload-artifact@master | |
with: | |
name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
path: check | |
- 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@master | |
with: | |
name: ${{ runner.os }}-r${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-branch-release-results | |
path: check | |
- name: Test coverage | |
if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'devel' | |
run: | | |
install.packages("covr") | |
covr::codecov(type = "all", token = "${{secrets.CODECOV_TOKEN}}") | |
shell: Rscript {0} |