update oncogene/TSG source #387
Workflow file for this run
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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.r }} - ${{ matrix.config.bioc }} - ${{ matrix.config.image }}) | |
strategy: | |
fail-fast: false | |
matrix: | |
config: | |
- { os: windows-latest, r: 'devel', bioc: 'devel'} | |
- { os: macOS-latest, r: 'release', bioc: '3.12'} | |
- { os: macOS-latest, r: 'devel', bioc: 'devel', curlConfigPath: '/usr/bin/'} | |
- { os: ubuntu-latest, r: 'release', 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 }} | |
steps: | |
- name: Check out repo | |
uses: actions/checkout@v2 | |
- name: Set up R | |
uses: r-lib/actions/setup-r@master | |
if: matrix.config.image == null | |
with: | |
r-version: ${{ matrix.config.r }} | |
- name: Set up pandoc | |
uses: r-lib/actions/setup-pandoc@master | |
if: matrix.config.image == null | |
- name: Install remotes | |
run: | | |
install.packages('remotes') | |
shell: Rscript {0} | |
- name: Set BiocManager version | |
if: matrix.config.image == null | |
run: | | |
install.packages('BiocManager') | |
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE) | |
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: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }} | |
restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}- | |
- name: Install system dependencies (macOS) | |
if: runner.os == 'macOS' | |
run: | | |
brew install harfbuzz | |
brew install fribidi | |
- name: Set up gfortran symlinks (macOS) | |
if: runner.os == 'macOS' | |
run: | | |
set -x | |
sudo ln -s /usr/local/Cellar/gcc@8/8.4.0_2/lib/gcc/8 /usr/local/gfortran/lib | |
gfortran --version | |
- name: Install system dependencies | |
if: runner.os == 'Linux' | |
env: | |
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
run: | | |
Rscript -e "remotes::install_github('r-hub/sysreqs')" | |
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | |
sudo -s eval "$sysreqs" | |
sudo apt-get update && sudo apt-get -y install libcurl4-openssl-dev | |
- name: Install dependencies | |
run: | | |
local_deps <- remotes::local_package_deps(dependencies = TRUE) | |
deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpu = 2L) | |
remotes::install_cran('rcmdcheck', Ncpu = 2L) | |
BiocManager::install("federicomarini/annoFuseData") | |
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: | | |
BiocManager::install("BiocCheck") | |
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-${{ matrix.config.bioc }}-results | |
path: check | |
# - name: Test coverage | |
# if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'release' | |
# run: | | |
# install.packages("covr") | |
# covr::codecov(token = "${{secrets.CODECOV_TOKEN}}") | |
# shell: Rscript {0} | |
# - name: Deploy | |
# if: github.event_name == 'push' && github.ref == 'refs/heads/master' && matrix.config.os == 'macOS-latest' && matrix.config.r == 'release' && matrix.config.bioc == 'devel' | |
# run: | | |
# R CMD INSTALL . | |
# Rscript -e "remotes::install_dev('pkgdown'); pkgdown::deploy_to_branch(new_process = FALSE)" |