GitHub Action - Build-Check-Install R Package¶
Source: r.pkg.template/build-check-install.yaml at main · insightsengineering/r.pkg.template (github.com)
name: R CMD Check 🧬
on:
push:
tags:
- "v*"
branches:
- main
- pre-release
pull_request:
branches:
- main
- pre-release
workflow_call:
secrets:
REPO_GITHUB_TOKEN:
description: |
Github token with read access to repositories, required for staged.dependencies installation
required: false
inputs:
install-system-dependencies:
description: Check for and install system dependencies
required: false
default: false
type: boolean
enable-staged-dependencies-check:
description: Enable staged dependencies YAML check
required: false
default: true
type: boolean
R_CHECK_FORCE_SUGGESTS:
description: If true, give an error if suggested packages are not available
required: false
default: true
type: boolean
jobs:
build-install-check:
strategy:
fail-fast: false
matrix:
config:
- image: ghcr.io/insightsengineering/rstudio_4.1.2_bioc_3.14
tag: latest
name: ${{ matrix.config.image }}, version ${{ matrix.config.tag }}
runs-on: ubuntu-latest
if: "! contains(github.event.commits[0].message, '[skip r-cmd]')"
container:
image: ${{ matrix.config.image }}:${{ matrix.config.tag }}
steps:
- name: Get branch names 🌿
id: branch-name
uses: tj-actions/branch-names@v5
- name: Checkout repo 🛎
uses: actions/checkout@v2
with:
ref: ${{ steps.branch-name.outputs.head_ref_branch }}
path: ${{ github.event.repository.name }}
- name: Run Staged dependencies 🎦
uses: insightsengineering/staged-dependencies-action@v1
with:
run-system-dependencies: ${{ inputs.install-system-dependencies }}
env:
GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }}
SD_REPO_PATH: ${{ github.event.repository.name }}
SD_ENABLE_CHECK: ${{ inputs.enable-staged-dependencies-check }}
- name: Show session info and installed packages ℹ
run: |
sessionInfo()
as.data.frame(installed.packages()[, c("LibPath", "Version")])
shell: Rscript {0}
- name: Build R package 🏗
run: |
R CMD build ${{ github.event.repository.name }}
echo "PKGBUILD=$(echo *.tar.gz)" >> $GITHUB_ENV
shell: bash
- name: Set TESTING_DEPTH ⚙
env:
COMMIT_NEWEST_MESSAGE: ${{ github.event.head_commit.message }}
COMMIT_OLDEST_MESSAGE: ${{ github.event.commits[0].message }}
run: |
cd ${{ github.event.repository.name }}
# set TESTING_DEPTH for PR
if [[ ! -z "${GITHUB_HEAD_REF}" ]]; then
TESTING_DEPTH=3
echo "TESTING_DEPTH=3" >> $GITHUB_ENV
COMMIT_NEWEST_MESSAGE=$(git log --format=%B -n 1 ${{ github.event.after }})
fi
if [[ $COMMIT_NEWEST_MESSAGE == *"[skip tests]"* ]]; then
echo "NO_TESTS=1" >> $GITHUB_ENV
fi
# default TESTING_DEPTH
if [[ -z "${TESTING_DEPTH}" ]]; then
echo "TESTING_DEPTH=1" >> $GITHUB_ENV
fi
shell: bash
- name: Run R CMD check 🏁
run: |
if [[ -z "${{ env.NO_TESTS }}" ]]; then
R CMD check ${{ env.PKGBUILD }}
else
R CMD check --no-tests ${{ env.PKGBUILD }}
fi
shell: bash
continue-on-error: true
env:
_R_CHECK_TESTS_NLINES_: 0
_R_CHECK_VIGNETTES_NLINES_: 0
_R_CHECK_FORCE_SUGGESTS_: ${{ inputs.R_CHECK_FORCE_SUGGESTS }}
- name: Check whether JUnit XML report exists 🚦
id: check-junit-xml
uses: andstor/file-existence-action@v1
with:
files: "${{ github.event.repository.name }}.Rcheck/tests/testthat/junit-result.xml"
- name: Publish Unit Test Summary 📑
uses: EnricoMi/publish-unit-test-result-action@v1
if: steps.check-junit-xml.outputs.files_exists == 'true' && github.event_name == 'pull_request'
with:
check_name: Unit Tests Summary
files: "${{ github.event.repository.name }}.Rcheck/tests/testthat/junit-result.xml"
- name: Catch warnings in R CMD check output 🗳
id: catch-errors
run: |
cat("Refer to the 'Run R CMD check 🏁' step to troubleshoot failures reported in this step\n")
cat("--------------------------------------------\n")
x <- tail(readLines("${{ github.event.repository.name }}.Rcheck/00check.log"), 1)
if (!grepl("^Status", x)) stop("☠ No status line found in R CMD check log")
if (grepl("ERROR", x)) stop("❌ R CMD check has errors")
if (grepl("WARNING", x)) stop("⚠ R CMD check has warnings")
shell: Rscript {0}
- name: Upload check results ⤴
if: failure()
uses: actions/upload-artifact@v2
with:
name: ${{ matrix.config.tag }}-results
path: ${{ github.event.repository.name }}.Rcheck/00check.log
- name: Install R package 🚧
run: R CMD INSTALL ${{ env.PKGBUILD }}
shell: bash
- name: Upload package build ⤴
if: startsWith(github.ref, 'refs/tags/v')
uses: actions/upload-artifact@v2
with:
path: ${{ env.PKGBUILD }}
name: ${{ env.PKGBUILD }}
upload-release-assets:
name: Upload build tar.gz
needs: build-install-check
runs-on: ubuntu-latest
if: "startsWith(github.ref, 'refs/tags/v') && (! contains(github.event.commits[0].message, '[skip r-cmd]'))"
steps:
- name: Checkout repo 🛎
uses: actions/checkout@v2
- name: Wait for release to succeed ⏳
timeout-minutes: 2
uses: lewagon/wait-on-check-action@v1.1.1
with:
ref: ${{ github.ref }}
check-name: "Release 🚀"
repo-token: ${{ secrets.GITHUB_TOKEN }}
wait-interval: 10
- name: Set release version and package build filename 📐
run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/v}" >> $GITHUB_ENV
- name: Get package build filename 📦
run: echo "PKGBUILD=${{ github.event.repository.name }}_${{ env.RELEASE_VERSION }}.tar.gz" >> $GITHUB_ENV
- name: Download artifact ⏬
uses: actions/download-artifact@v2
with:
name: ${{ env.PKGBUILD }}
- name: Upload binaries to release 🔼
uses: svenstaro/upload-release-action@v2
with:
repo_token: ${{ secrets.GITHUB_TOKEN }}
file: ${{ env.PKGBUILD }}
asset_name: ${{ env.PKGBUILD }}
tag: ${{ github.ref }}
overwrite: false
Appendix: Links¶
Backlinks:
list from [[GitHub Action - Build-Check-Install R Package]] AND -"Changelog"