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R-CMD-check.yaml
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on:
push:
pull_request:
branches:
- master
- main
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: 'devel', bioc: 'devel', curlConfigPath: '/usr/bin/'}
- { os: ubuntu-latest, r: 'devel', bioc: 'devel'}
# - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
- { os: ubuntu-latest, r: 'devel', 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-${{ matrix.config.bioc }}-
- name: Install system dependencies
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
Rscript -e "remotes::install_github('r-hub/sysreqs')"
sysreqs=$(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)
BiocManager::install("icbi-lab/immunedeconv")
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: 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-${{ matrix.config.bioc }}-results
path: check
- name: Test coverage
if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'devel'
run: |
install.packages("covr")
covr::codecov(token = "${{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)"