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R-CMD-check.yaml
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on:
push:
pull_request:
branches:
- main
schedule:
- cron: '0 9 * * 2'
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: macOS-latest, bioc: 'release', curlConfigPath: '/usr/bin/'}
- { os: windows-latest, bioc: 'release'}
- { os: ubuntu-latest, image: "bioconductor/bioconductor_docker:RELEASE_3_17", cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
_R_CHECK_FORCE_SUGGESTS_: false
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@v3
- 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 (Linux)
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 libharfbuzz-dev libfribidi-dev
- name: Install system dependencies (macOS)
if: runner.os == 'macOS'
run: |
brew install harfbuzz
brew install fribidi
brew install gcc
- 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)
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
id: build-install-check
uses: grimbough/bioc-actions/build-install-check@v1
- name: Upload install log if the build/install/check step fails
if: always() && (steps.build-install-check.outcome == 'failure')
uses: actions/upload-artifact@v3
with:
name: install-log
path: |
${{ steps.build-install-check.outputs.install-log }}
# - name: Run BiocCheck
# uses: grimbough/bioc-actions/run-BiocCheck@v1
# with:
# arguments: '--no-check-bioc-views --no-check-bioc-help'
# error-on: 'error'
- name: Show testthat output (windows)
if: always() && runner.os == 'Windows'
run: |
type ${{ steps.build-install-check.outputs.check-dir }}\tests\testthat.Rout
shell: cmd
- name: Show testthat output (non-windows)
if: always() && runner.os != 'Windows'
run: |
cat ${{ steps.build-install-check.outputs.check-dir }}/tests/testthat.Rout
shell: bash
- name: Upload check results
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-results
path: ${{ steps.build-install-check.outputs.check-dir }}
- name: Test coverage
if: matrix.config.os == 'macOS-latest'
run: |
install.packages("covr")
covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")
shell: Rscript {0}
- name: Deploy
if: github.event_name == 'push' && github.ref == 'refs/heads/main' && matrix.config.os == 'macOS-latest'
run: |
R CMD INSTALL .
Rscript -e "remotes::install_dev('pkgdown'); pkgdown::deploy_to_branch(new_process = FALSE)"