R-CMD-check #541
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name: R-CMD-check | |
on: | |
push: | |
pull_request: | |
branches: | |
- master | |
schedule: | |
- cron: '0 8 * * 5' | |
jobs: | |
R-CMD-check: | |
# define the operating systems and R versions we want to test on | |
strategy: | |
fail-fast: false | |
matrix: | |
config: | |
# - { os: macOS-latest, r: '4.1', bioc: '3.13'} | |
# - { os: windows-latest, r: '4.1', bioc: '3.13'} | |
# - { os: macOS-latest, r: 'devel', bioc: 'devel'} | |
- { os: macOS-latest, bioc: 'devel'} | |
# - { os: windows-latest, r: 'devel', bioc: 'devel'} | |
- { os: windows-latest, bioc: 'devel'} | |
# - { os: ubuntu-16.04, r: 'devel', bioc: 'devel', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"} | |
- { os: ubuntu-latest, image: 'bioconductor/bioconductor_docker:devel'} | |
# - { os: macOS-latest, r: 'devel', image: 'bioconductor/bioconductor_docker:devel'} | |
runs-on: ${{ matrix.config.os }} | |
container: ${{ matrix.config.image }} | |
name: ${{ matrix.config.os }} (BioC ${{ matrix.config.bioc }} - ${{ matrix.config.image }}) | |
env: | |
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
PKG_PATH: monaLisa | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
# CRAN: ${{ matrix.config.cran }} | |
# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
# steps to run in the defined environments | |
steps: | |
- name: Checkout repo | |
uses: actions/checkout@v2 | |
with: | |
path: ${{ env.PKG_PATH }} | |
- name: Set up pandoc | |
uses: r-lib/actions/setup-pandoc@v2 | |
if: matrix.config.image == null | |
- name: Set up R and install BiocManager | |
uses: grimbough/bioc-actions/setup-bioc@v1 | |
if: matrix.config.image == null | |
with: | |
bioc-version: ${{ matrix.config.bioc }} | |
- name: Install Homer | |
if: runner.os != 'Windows' && matrix.config.image == null | |
run: | | |
mkdir homer && pushd homer | |
wget http://homer.ucsd.edu/homer/configureHomer.pl | |
perl configureHomer.pl -install | |
# export PATH=$PATH:$PWD/bin/ | |
popd | |
# echo "^homer$" >> $PKG_PATH/.Rbuildignore | |
# Rscript -e 'install.packages("magick")' | |
- name: Install remotes | |
run: | | |
install.packages('remotes') | |
shell: Rscript {0} | |
- name: List package dependencies | |
run: | | |
saveRDS(remotes::dev_package_deps(pkgdir = "${{env.PKG_PATH}}", dependencies = TRUE, repos = c(getOption('repos'), BiocManager::repositories())), 'depends.Rds', version = 2) | |
shell: Rscript {0} | |
- name: Cache R packages | |
if: runner.os != 'Windows' && matrix.config.image == null | |
uses: actions/cache@v1 | |
with: | |
path: ${{ env.R_LIBS_USER }} | |
key: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }} | |
restore-keys: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}- | |
- name: Install system dependencies for Linux | |
if: runner.os == 'Linux' | |
env: | |
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
uses: r-lib/actions/setup-r-dependencies@v2 | |
with: | |
extra-packages: any::rcmdcheck | |
working-directory: '${{env.PKG_PATH}}' | |
pak-version: devel | |
- name: Install system dependencies for macOS | |
if: matrix.config.os == 'macOS-latest' | |
run: | | |
brew install harfbuzz | |
brew install fribidi | |
brew install --cask xquartz | |
- name: Install dependencies (R packages) | |
run: | | |
local_deps <- remotes::local_package_deps(pkgdir = "${{env.PKG_PATH}}", dependencies = TRUE) | |
deps <- remotes::dev_package_deps(pkgdir = "${{env.PKG_PATH}}", dependencies = TRUE, repos = BiocManager::repositories()) | |
BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpu = 2L) | |
remotes::install_cran('rcmdcheck', Ncpu = 2L) | |
shell: Rscript {0} | |
- name: Session info | |
run: | | |
options(width = 100) | |
pkgs <- installed.packages()[, "Package"] | |
sessioninfo::session_info(pkgs, include_base = TRUE) | |
shell: Rscript {0} | |
- name: Check | |
run: | | |
Sys.getenv("GITHUB_WORKSPACE") | |
Sys.setenv(MONALISA_HOMER = file.path(Sys.getenv("GITHUB_WORKSPACE"), "homer/bin")) | |
Sys.getenv("MONALISA_HOMER") | |
rcmdcheck::rcmdcheck(path = "${{env.PKG_PATH}}", | |
args = c("--no-build-vignettes","--no-manual","--timings"), | |
error_on = "warning", check_dir = "check") | |
shell: Rscript {0} | |
- name: BiocCheck | |
run: | | |
BiocManager::install("BiocCheck") | |
BiocCheck::BiocCheck(package = "${{env.PKG_PATH}}") | |
shell: Rscript {0} | |
- name: Check NEWS.md | |
run: | | |
BiocManager::install(c("commonmark", "xml2")) | |
tools:::.build_news_db_from_package_NEWS_md("monaLisa/NEWS.md") | |
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 failed) | |
if: failure() | |
uses: actions/upload-artifact@v4 | |
with: | |
name: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-results | |
path: check | |
- name: Test coverage | |
if: matrix.config.os == 'macOS-latest' | |
run: | | |
install.packages("covr") | |
covr::codecov(path = "${{env.PKG_PATH}}", token = "${{secrets.CODECOV_TOKEN}}") | |
shell: Rscript {0} | |
- name: Deploy | |
if: github.event_name == 'push' && github.ref == 'refs/heads/devel' && matrix.config.os == 'macOS-latest' | |
working-directory: ${{env.PKG_PATH}} | |
run: | | |
R CMD INSTALL . | |
Rscript -e "remotes::install_dev('pkgdown'); pkgdown::deploy_to_branch(new_process = FALSE)" | |