R-CMD-check #279
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on: | |
push: | |
pull_request: | |
branches: | |
- master | |
schedule: | |
- cron: '0 8 * * 5' | |
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: 'devel'} | |
- { os: macOS-latest, bioc: 'devel', curlConfigPath: '/usr/bin/'} | |
- { os: ubuntu-latest, bioc: 'devel'} | |
# - { os: ubuntu-latest, bioc: 'devel', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"} | |
- { os: ubuntu-latest, image: 'bioconductor/bioconductor_docker:devel'} | |
env: | |
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
CRAN: ${{ matrix.config.cran }} | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
CURL_CONFIG: ${{ matrix.config.curlConfigPath }}curl-config | |
steps: | |
- name: Check out repo | |
uses: actions/checkout@v2 | |
- 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: Set up pandoc | |
uses: r-lib/actions/setup-pandoc@v2 | |
if: matrix.config.image == null | |
- name: Install remotes | |
run: | | |
install.packages('remotes') | |
shell: Rscript {0} | |
- name: Query dependencies | |
run: | | |
saveRDS(remotes::dev_package_deps(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 | |
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 libglpk-dev libharfbuzz-dev libfribidi-dev | |
- name: Install system dependencies (macOS) | |
if: runner.os == 'macOS' | |
run: | | |
brew install cairo | |
brew install --cask xquartz | |
brew install harfbuzz | |
brew install fribidi | |
brew install fftw | |
# - name: Set up gfortran symlinks (macOS) | |
# if: runner.os == 'macOS' | |
# run: | | |
# set -x | |
# sudo ln -s /usr/local/Cellar/gcc@8/8.4.0_2/lib/gcc/8 /usr/local/gfortran/lib | |
# gfortran --version | |
- name: Install dependencies | |
run: | | |
local_deps <- remotes::local_package_deps(dependencies = TRUE) | |
deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpu = 2L) | |
BiocManager::install(c("GenomeInfoDbData", "GO.db"), Ncpu = 2L) | |
BiocManager::install("markdown") | |
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: Build, Install, Check | |
uses: grimbough/bioc-actions/build-install-check@v1 | |
- name: Run BiocCheck | |
uses: grimbough/bioc-actions/run-BiocCheck@v1 | |
with: | |
arguments: '--no-check-bioc-views --no-check-bioc-help' | |
error-on: 'error' | |
- name: Upload check results | |
if: failure() | |
uses: actions/upload-artifact@master | |
with: | |
name: ${{ runner.os }}-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: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-results | |
path: check | |
- name: Test coverage | |
if: matrix.config.os == 'macOS-latest' | |
run: | | |
install.packages("covr") | |
covr::codecov(token = "${{secrets.CODECOV_TOKEN}}") | |
shell: Rscript {0} | |
- name: Deploy | |
if: github.event_name == 'push' && github.ref == 'refs/heads/devel' && matrix.config.os == 'macOS-latest' | |
run: | | |
R CMD INSTALL . | |
Rscript -e "remotes::install_dev('pkgdown'); pkgdown::deploy_to_branch(new_process = FALSE)" |