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R-CMD-check

R-CMD-check #306

Workflow file for this run

on:
push:
branches:
- master
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.r }} - ${{ matrix.config.bioc }} - ${{ matrix.config.image }})
strategy:
fail-fast: false
matrix:
config:
- { os: windows-latest, r: '4.1'}
- { os: macOS-latest, r: '4.1'}
- { os: ubuntu-16.04, r: '4.1', cran: "https://packagemanager.rstudio.com/all/__linux__/xenial/latest"}
# - { os: ubuntu-20.04, r: 'devel', cran: "https://packagemanager.rstudio.com/all/__linux__/focal/latest"}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
CRAN: ${{ matrix.config.cran }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- name: Install system libraries
if: ${{ runner.os == 'Linux' }}
run: |
sudo apt-get install libcurl4-openssl-dev libglpk-dev
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@master
with:
r-version: ${{ matrix.config.r }}
- uses: r-lib/actions/setup-pandoc@master
- name: Install remotes
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}
- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v1
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-1-
- name: Install dependencies
run: |
install.packages(c('BiocManager', 'rcmdcheck', 'covr'))
BiocManager::install(ask = FALSE, update = TRUE)
toInstall <- remotes::dev_package_deps(dependencies = TRUE)[,'package']
toInstall <- setdiff(toInstall, installed.packages()[,'Package'])
if(length(toInstall)) { BiocManager::install(toInstall, ask = FALSE) }
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-${{ matrix.config.bioc }}-results
path: check
- name: Test coverage
if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'release'
run: |
install.packages("covr")
covr::codecov(type = "all", token = "${{secrets.CODECOV_TOKEN}}")
shell: Rscript {0}