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R-CMD-check.yml
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on: [push, pull_request]
name: R-CMD-check
# jobs:
# build:
# runs-on: ubuntu-18.04
# strategy:
# matrix:
# R: [ '3.5.3', '3.6.1' ]
# name: R ${{ matrix.R }} sample
# steps:
# - uses: actions/checkout@master
# - name: Setup R
# uses: r-lib/actions/setup-R@v1
# with:
# r-version: ${{ matrix.R }}
# - run: Rscript -e 'print("hello")'
jobs:
R-CMD-check:
if: "! contains(github.event.head_commit.message, '[ci skip]')"
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
strategy:
fail-fast: false
matrix:
config:
- { os: windows-latest, r: '3.5'}
- { os: windows-latest, r: '3.6'}
# - { os: macOS-latest, r: '3.6'}
# - { os: ubuntu-16.04, r: '3.5', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
# - { os: ubuntu-16.04, r: '3.6', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
CRAN: ${{ matrix.config.cran }}
steps:
- uses: actions/checkout@v1
- uses: r-lib/actions/setup-r@master
with:
r-version: ${{ matrix.config.r }}
- uses: r-lib/actions/setup-pandoc@master
# - run: Rscript -e 'print("hello")'
- run: Rscript -e "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager')"
- run: Rscript -e "if (!requireNamespace('DESeq2', quietly = TRUE)) BiocManager::install('DESeq2')"
- run: Rscript -e "if (!requireNamespace('dplyr', quietly = TRUE)) install.packages('dplyr')"
- run: Rscript -e "if (!requireNamespace('plotly', quietly = TRUE)) install.packages('plotly')"
- run: Rscript -e "if (!requireNamespace('shiny', quietly = TRUE)) BiocManager::install('shiny')"
- run: Rscript -e "if (!requireNamespace('tibble', quietly = TRUE)) install.packages('tibble')"
- run: Rscript -e "if (!requireNamespace('DT', quietly = TRUE)) install.packages('DT')"
- run: Rscript -e "if (!requireNamespace('shinyjs', quietly = TRUE)) BiocManager::install('shinyjs')"
# - name: Query dependencies
# run: Rscript -e "install.packages('remotes')" -e "saveRDS(remotes::dev_package_deps(dependencies = TRUE), 'depends.Rds', version = 2)"
# - name: "[Linux & macOS] Cache R packages"
# if: runner.os != 'Windows'
# uses: actions/cache@v1
# with:
# path: ${{ env.R_LIBS_USER }}
# key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }}
# restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
# - name: "[Linux] 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"
# - name: "[macOS] Install system dependencies"
# if: runner.os == 'macOS'
# run:
# brew cask install xquartz
# - name: Install dependencies
# run: Rscript -e "library(remotes)" -e "update(readRDS('depends.Rds'))" -e "remotes::install_cran('rcmdcheck')"
# - name: Check
# env:
# RGL_USE_NULL: TRUE
# DISPLAY: ":99"
# run: Rscript -e "rcmdcheck::rcmdcheck(args = c('--as-cran', '--no-manual'), error_on = 'warning', check_dir = 'check')"
# - name: Upload check results
# if: failure()
# uses: actions/upload-artifact@master
# with:
# name: ${{ runner.os }}-r${{ matrix.config.r }}-results
# path: check
# - name: Test coverage
# if: matrix.config.os == 'ubuntu-16.04' && matrix.config.r == '3.6'
# run: |
# Rscript -e "install.packages('covr')" -e 'covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")'