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Initialize revdepcheck action #1194

Initialize revdepcheck action

Initialize revdepcheck action #1194

---
name: R CMD Check 🧬
on:
push:
tags:
- "v*"
branches:
- main
pull_request:
types:
- opened
- synchronize
- reopened
- ready_for_review
branches:
- main
workflow_dispatch:
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: false
type: boolean
R_CHECK_FORCE_SUGGESTS:
description: If true, give an error if suggested packages are not available
required: false
default: true
type: boolean
skip-r-cmd-check:
description: Skip the R CMD check step in this workflow
required: false
default: false
type: boolean
skip-r-cmd-install:
description: Skip the R CMD INSTALL step in this workflow
required: false
default: true
type: boolean
enforce-note-blocklist:
description: Whether to check for specific NOTEs via regexes that should cause the pipeline to fail
required: false
default: false
type: boolean
note-blocklist:
description: |
List of regular expressions appearing in NOTEs that should cause the pipeline to fail.
Example usage:
note-blocklist: |
checking package dependencies ... NOTE( )+Depends: includes the non-default packages
checking R code for possible problems ... NOTE( )+.*: no visible global function definition for
checking for unstated dependencies in vignettes ... NOTE( )+\'.*\' import not declared from
checking dependencies in R code ... NOTE( )+Namespace in Imports field not imported from
checking installed package size ... NOTE( )+installed size is
required: false
default: ""
type: string
additional-r-cmd-check-params:
description: Additional flags or parameters to add to R CMD check
required: false
default: ""
type: string
disable-unit-test-reports:
description: Do not produce unit test reports
required: false
default: false
type: boolean
additional-env-vars:
description: |
Extra environment variables, as a 'key=value' pair, with each pair on a new line.
Example usage:
additional-env-vars: |
ABC=123
XYZ=456
required: false
default: ""
type: string
junit-xml-storage:
description: Branch name to store JUnit XML reports
required: false
default: "_junit_xml_reports"
type: string
junit-xml-diff-branch:
description: Against which branch should the JUnit XML report from the current branch be compared?
required: false
default: main
type: string
junit-xml-comparison:
description: Turn on JUnit XML comparison
required: false
default: true
type: boolean
junit-xml-negative-threshold:
description: |
If time difference during JUnit XML comparison is between negative-threshold and 0: it's treated as 0.
This means that if test suite/case executes up to negative-threshold seconds faster,
this time difference is ignored as insignificant, and test suite/case is not shown in the table
required: false
default: 1.0
type: string
junit-xml-positive-threshold:
description: |
If time difference during JUnit XML comparison is between 0 and positive-threshold: it's treated as 0.
This means that if test suite/case executes up to positive-threshold seconds slower,
this time difference is ignored as insignificant, and test suite/case is not shown in the table
required: false
default: 1.0
type: string
sd-direction:
description: The direction to use to install staged dependencies. Choose between 'upstream', 'downstream' and 'all'
required: false
type: string
default: upstream
install-deps-from-package-repositories:
description: |
Set this to a comma-separated named list of R packages repositories to use for installing dependencies.
Example: "R-universe=https://insightsengineering.r-universe.dev/,CRAN=https://cloud.r-project.org/"
required: false
type: string
default: ""
unit-test-report-brand:
description: Image URL to use in unit test report for branding. If empty, the default xunit-viewer brand will be used.
required: false
type: string
default: ""
publish-unit-test-report-gh-pages:
description: Publish HTML unit test report to GitHub Pages alongside pkgdown docs.
required: false
type: boolean
default: true
latest-tag-alt-name:
description: |
The name of directory to store unit test report when running for latest tag.
The variable is named this way to keep it consistent with r-pkgdown-multiversion input name.
required: false
type: string
default: "latest-tag"
release-candidate-alt-name:
description: |
The name of directory to store unit test report when running for rc tag.
The variable is named this way to keep it consistent with r-pkgdown-multiversion input name.
required: false
type: string
default: "release-candidate"
package-subdirectory:
description: Subdirectory in the repository, where the R package is located.
required: false
type: string
default: ""
additional-caches:
description: |
Additional cache directories. One cache path per new line.
Example usage:
additional-caches: |
~/awesome-cache
/tmp/some-cache
required: false
type: string
default: ""
concurrency-group:
description: |
Concurrency group name in case a calling workflow would like to use multiple instances of this workflow simultaneously.
required: false
type: string
default: ""
enable-sd:
description: |
Whether the installation of package dependencies via staged.dependencies should be enabled.
required: false
type: boolean
default: true
update-r-packages:
description: |
Whether R packages installed in the container should be updated to their latest version from CRAN/BioC.
required: false
type: boolean
default: false
concurrency:
group: r-cmd-${{ inputs.concurrency-group }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
jobs:
build-install-check:
strategy:
fail-fast: false
matrix:
config:
- image: ghcr.io/insightsengineering/rstudio
tag: latest
name: ${{ matrix.config.image }}, version ${{ matrix.config.tag }}
runs-on: ubuntu-latest
if: >
!contains(github.event.commits[0].message, '[skip r-cmd]')
&& github.event.pull_request.draft == false
container:
image: ${{ matrix.config.image }}:${{ matrix.config.tag }}
outputs:
publish-unit-test-html-report: ${{ steps.junit-output.outputs.junit-upload }}
current-branch-or-tag: ${{ steps.current-branch-or-tag.outputs.ref-name }}
is-latest-tag: ${{ steps.current-branch-or-tag.outputs.is-latest-tag }}
is-rc-tag: ${{ steps.current-branch-or-tag.outputs.is-rc-tag }}
multiversion-docs: ${{ steps.current-branch-or-tag.outputs.multiversion-docs }}
steps:
- name: Setup token 🔑
id: github-token
run: |
if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then
echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN."
echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
else
echo "Using REPO_GITHUB_TOKEN."
echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
fi
shell: bash
- name: Get branch names 🌿
id: branch-name
uses: tj-actions/branch-names@v7
- name: Checkout repo (PR) 🛎
uses: actions/[email protected]
if: github.event_name == 'pull_request'
with:
ref: ${{ steps.branch-name.outputs.head_ref_branch }}
path: ${{ github.event.repository.name }}
repository: ${{ github.event.pull_request.head.repo.full_name }}
fetch-depth: 0
- name: Checkout repo 🛎
uses: actions/[email protected]
if: github.event_name != 'pull_request'
with:
ref: ${{ steps.branch-name.outputs.head_ref_branch }}
path: ${{ github.event.repository.name }}
- name: Check commit message 💬
run: |
git config --global --add safe.directory $(pwd)
export head_commit_message="$(git show -s --format=%B | tr '\r\n' ' ' | tr '\n' ' ')"
echo "head_commit_message = $head_commit_message"
if [[ $head_commit_message == *"$SKIP_INSTRUCTION"* ]]; then
echo "Skip instruction detected - cancelling the workflow."
exit 1
fi
shell: bash
working-directory: ${{ github.event.repository.name }}
env:
SKIP_INSTRUCTION: "[skip r-cmd]"
- name: Checkout gh-pages 🛎
if: >-
inputs.publish-unit-test-report-gh-pages == true
&& github.event_name != 'pull_request'
id: checkout-gh-pages
uses: actions/[email protected]
with:
ref: gh-pages
path: gh-pages
repository: ${{ github.event.pull_request.head.repo.full_name }}
continue-on-error: true
- name: Get current branch or tag 🏷️
if: >-
inputs.publish-unit-test-report-gh-pages == true
&& github.event_name != 'pull_request'
id: current-branch-or-tag
run: |
if [ "${{ steps.branch-name.outputs.is_tag }}" == "true" ]; then
echo "Current tag: ${{ steps.branch-name.outputs.tag }}"
echo "ref-name=${{ steps.branch-name.outputs.tag }}" >> $GITHUB_OUTPUT
current_tag="${{ steps.branch-name.outputs.tag }}"
if [ "$(echo "$current_tag" | grep -E "^v([0-9]+\.)?([0-9]+\.)?([0-9]+)$")" != "" ]; then
echo "Running for latest-tag."
echo "is-latest-tag=true" >> $GITHUB_OUTPUT
elif [ "$(echo "$current_tag" | grep -E "^v([0-9]+\.)?([0-9]+\.)?([0-9]+)(-rc[0-9]+)$")" != "" ]; then
echo "Running for rc-tag."
echo "is-rc-tag=true" >> $GITHUB_OUTPUT
fi
else
echo "Current branch: ${{ steps.branch-name.outputs.current_branch }}"
echo "ref-name=${{ steps.branch-name.outputs.current_branch }}" >> $GITHUB_OUTPUT
fi
# Check if pkgdown multiversion docs are used at all.
if [ $(grep -rl '<!-- start dropdown for versions -->' gh-pages | wc -l) -gt 0 ]; then
echo "multiversion-docs=true" >> $GITHUB_OUTPUT
else
echo "multiversion-docs=false" >> $GITHUB_OUTPUT
fi
shell: bash
- name: Normalize variables 📏
run: |
junit_xml_storage_input="${{ inputs.junit-xml-storage }}"
junit_xml_diff_branch_input="${{ inputs.junit-xml-diff-branch }}"
junit_xml_comparison_input="${{ inputs.junit-xml-comparison }}"
junit_xml_positive_threshold="${{ inputs.junit-xml-positive-threshold }}"
junit_xml_negative_threshold="${{ inputs.junit-xml-negative-threshold }}"
enable_sd="${{ inputs.enable-sd }}"
echo "junit_xml_storage=${junit_xml_storage_input:-_junit_xml_reports}" >> $GITHUB_ENV
echo "junit_xml_diff_branch=${junit_xml_diff_branch_input:-main}" >> $GITHUB_ENV
echo "junit_xml_comparison=${junit_xml_comparison_input:-true}" >> $GITHUB_ENV
echo "junit_xml_positive_threshold=${junit_xml_positive_threshold:-1.0}" >> $GITHUB_ENV
echo "junit_xml_negative_threshold=${junit_xml_negative_threshold:-1.0}" >> $GITHUB_ENV
echo "enable_sd=${enable_sd:-true}" >> $GITHUB_ENV
shell: bash
- name: Restore npm cache 💰
if: >-
inputs.publish-unit-test-report-gh-pages == true
&& github.event_name != 'pull_request'
uses: actions/cache@v4
with:
key: npm-${{ runner.os }}-${{ github.job }}
restore-keys: |
npm-${{ runner.os }}-
path: node_modules
- name: Setup NodeJS ☊
if: >-
inputs.publish-unit-test-report-gh-pages == true
&& github.event_name != 'pull_request'
uses: actions/setup-node@v4
id: npm-cache
with:
node-version: 20
- name: Install xunit-viewer ⚙️
if: >-
steps.npm-cache.outputs.cache-hit != 'true'
&& inputs.publish-unit-test-report-gh-pages == true
&& github.event_name != 'pull_request'
run: npm i -g xunit-viewer
shell: bash
- name: Restore SD cache 💰
if: inputs.install-deps-from-package-repositories == ''
uses: actions/cache@v4
with:
key: sd-${{ runner.os }}-${{ github.event.repository.name }}
path: ~/.staged.dependencies
- name: Update R packages 🗓️
if: >-
inputs.update-r-packages == true
run: |
update.packages()
shell: Rscript {0}
- name: Run Staged dependencies 🎦
if: >-
env.enable_sd == 'true'
&& inputs.install-deps-from-package-repositories == ''
uses: insightsengineering/staged-dependencies-action@v1
env:
GITHUB_PAT: ${{ steps.github-token.outputs.token }}
with:
path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
enable-check: ${{ inputs.enable-staged-dependencies-check }}
run-system-dependencies: ${{ inputs.install-system-dependencies }}
direction: ${{ inputs.sd-direction }}
- name: Install dependencies from package repositories 🗄️
if: inputs.install-deps-from-package-repositories != ''
run: |
split_to_map <- function(args) {
tmp <- strsplit(x = unlist(strsplit(args, ",")), "=")
content <- unlist(lapply(tmp, function(x) x[2]))
names(content) <- unlist(lapply(tmp, function(x) x[1]))
return(content)
}
devtools::install_dev_deps(".", repos = split_to_map("${{ inputs.install-deps-from-package-repositories }}"))
shell: Rscript {0}
working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
- name: Show session info and installed packages ℹ
run: |
sessionInfo()
as.data.frame(installed.packages()[, c("LibPath", "Version")])
if (grepl("--as-cran", "${{ inputs.additional-r-cmd-check-params }}", fixed = TRUE)) {
x <- desc::desc_del("Remotes")
}
if ("${{ inputs.disable-unit-test-reports }}" != "true") {
x <- desc::desc_set_dep("xml2", "Suggests")
}
shell: Rscript {0}
working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
- name: Get package name 📦
run: |
echo "PKGBUILD=$(echo $(awk -F: '/Package:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION)_"\
"$(awk -F: '/Version:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION).tar.gz)" >> $GITHUB_ENV
echo "PKGNAME=$(echo $(awk -F: '/Package:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION))" >> $GITHUB_ENV
shell: bash
working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
- name: Replace testthat.R for test reporting 🎚
if: inputs.disable-unit-test-reports != 'true'
run: |
if [ -f "tests/testthat.R" ]; then {
# Overwrite testthat.R for JUnit XML reporting
cat > tests/testthat.R <<EOF
pkg_name <- "${{ env.PKGNAME }}"
if (requireNamespace("testthat", quietly = TRUE)) {
library(testthat)
reporter <- MultiReporter\$new(list(
CheckReporter\$new(),
JunitReporter\$new(file = "junit-result.xml")
))
test_check(pkg_name, reporter = reporter)
}
EOF
}
cat tests/testthat.R
fi
shell: bash
working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
- name: Restore any additional caches 📥
if: inputs.additional-caches != ''
uses: actions/cache@v4
with:
path: "${{ inputs.additional-caches }}"
key: additional-caches-${{ runner.os }}
- name: Build R package 🏗
run: |
if [ "${{ inputs.additional-env-vars }}" != "" ]
then {
echo -e "${{ inputs.additional-env-vars }}" > /tmp/dotenv.env
export $(tr '\n' ' ' < /tmp/dotenv.env)
}
fi
R CMD build ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
shell: bash
- name: Run R CMD check 🏁
run: |
if [ "${{ inputs.skip-r-cmd-check }}" == "true" ]
then {
echo "Skipping R CMD check as 'skip-r-cmd-check' was set to 'true'"
exit 0
}
fi
if [ "${{ inputs.R_CHECK_FORCE_SUGGESTS }}" == "" ]
then {
_R_CHECK_FORCE_SUGGESTS_="FALSE"
}
fi
ADDITIONAL_PARAMS=${{ inputs.additional-r-cmd-check-params }}
if [[ ! -z "${{ env.NO_TESTS }}" ]]
then {
ADDITIONAL_PARAMS="${ADDITIONAL_PARAMS} --no-tests"
}
fi
if [ "${{ inputs.additional-env-vars }}" != "" ]
then {
echo -e "${{ inputs.additional-env-vars }}" > /tmp/dotenv.env
export $(tr '\n' ' ' < /tmp/dotenv.env)
}
fi
Rscript - <<EOF
if ("${{ inputs.disable-unit-test-reports }}" != "true") {
if (!require("xml2")) {
install.packages("xml2", repos = "https://cloud.r-project.org", quiet = TRUE)
}
}
EOF
R CMD check ${ADDITIONAL_PARAMS} ${{ env.PKGBUILD }}
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: Fetch report from ${{ env.junit_xml_storage }} ⤵️
if: env.junit_xml_comparison == 'true'
uses: actions/[email protected]
with:
path: ${{ env.junit_xml_storage }}
fetch-depth: 0
- name: Initialize storage branch ${{ env.junit_xml_storage }} 🗄️
if: env.junit_xml_comparison == 'true'
working-directory: ${{ env.junit_xml_storage }}
run: |
git config --global --add safe.directory ${PWD}
git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
git config --global user.name "github-actions[bot]"
# Switch to the branch if it already exists
git switch ${{ env.junit_xml_storage }} || true
git pull origin ${{ env.junit_xml_storage }} || true
# Create the branch if it doesn't exist yet
git checkout --orphan ${{ env.junit_xml_storage }} || true
# Ensure that the bare minimum components exist in the branch
mkdir -p data
touch README.md data/.gitkeep
# Copy necessary files and folders to a temporary location
mkdir -p /tmp/${{ github.sha }}
echo "Copying data to /tmp/${{ github.sha }}"
cp -r .git README.md data /tmp/${{ github.sha }}
# Remove everything else
# Attribution: https://unix.stackexchange.com/a/77313
rm -rf ..?* .[!.]* *
# Restore files from the temporary location
echo "Copying data from /tmp/${{ github.sha }}"
cp -r /tmp/${{ github.sha }}/.git /tmp/${{ github.sha }}/README.md /tmp/${{ github.sha }}/data .
rm -rf /tmp/${{ github.sha }}
git add --all -f
git commit -m "Update storage branch: $(date)" || true
shell: bash
- name: Push storage branch ${{ env.junit_xml_storage }} 🗄️
if: env.junit_xml_comparison == 'true'
uses: ad-m/github-push-action@master
with:
github_token: ${{ steps.github-token.outputs.token }}
branch: ${{ env.junit_xml_storage }}
directory: ${{ env.junit_xml_storage }}
force: true
continue-on-error: true
- name: Check whether JUnit XML report exists 🚦
id: check-junit-xml
uses: andstor/file-existence-action@v3
with:
files: "${{ env.PKGNAME }}.Rcheck/tests/testthat/junit-result.xml"
- name: Convert JUnit XML to HTML 📝
if: >-
steps.check-junit-xml.outputs.files_exists == 'true'
&& inputs.publish-unit-test-report-gh-pages == true
&& github.event_name != 'pull_request'
run: |
brand_option=""
if [ "${{ inputs.unit-test-report-brand }}" != "" ]; then
brand_option='--brand ${{ inputs.unit-test-report-brand }}'
fi
xunit-viewer -r "${{ env.PKGNAME }}.Rcheck/tests/testthat/junit-result.xml" \
-o index.html \
-f "https://www.clipboardmaster.com/favicon.ico" \
-t "${{ env.PKGNAME }} Unit Test Results" \
$brand_option
shell: bash
- name: Publish JUnit XML as artifact 📰
if: >-
steps.check-junit-xml.outputs.files_exists == 'true'
&& inputs.publish-unit-test-report-gh-pages == true
&& github.event_name != 'pull_request'
uses: actions/upload-artifact@v4
with:
name: unit-test-report
path: "index.html"
- name: Set output ⚙️
id: junit-output
if: >-
steps.check-junit-xml.outputs.files_exists == 'true'
&& inputs.publish-unit-test-report-gh-pages == true
&& github.event_name != 'pull_request'
run: echo "junit-upload=true" >> $GITHUB_OUTPUT
- name: Publish Unit Test Summary 📑
uses: EnricoMi/publish-unit-test-result-action@v2
id: test-results
# Second line of the condition skips the step if workflow is running in a fork.
if: |
steps.check-junit-xml.outputs.files_exists == 'true' && github.event_name == 'pull_request' &&
github.event.pull_request.head.repo.full_name == github.event.pull_request.base.repo.full_name
with:
check_name: Unit Tests Summary
junit_files: "${{ env.PKGNAME }}.Rcheck/tests/testthat/junit-result.xml"
- name: Fetch JUnit XML reports from ${{ env.junit_xml_storage }} ⤵️
if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
uses: actions/[email protected]
with:
path: ${{ env.junit_xml_storage }}
fetch-depth: 0
- name: Set up ${{ env.junit_xml_storage }} branch for reports 🗃️
if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
run: |
BRANCH=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}
echo "diff_storage_branch=$BRANCH" >> $GITHUB_ENV
mkdir -p ${{ env.junit_xml_storage }}/data/${BRANCH}
shell: bash
- name: Commit JUnit XML report 📄
if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
working-directory: ${{ env.junit_xml_storage }}/data
run: |
git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
git config --global user.name "github-actions[bot]"
git switch ${{ env.junit_xml_storage }} || true
git config pull.rebase false
git pull origin ${{ env.junit_xml_storage }} || true
cp ../../${{ env.PKGNAME }}.Rcheck/tests/testthat/junit-result.xml \
'./${{ env.diff_storage_branch }}/junit-result.xml'
git add -f '${{ env.diff_storage_branch }}/junit-result.xml'
git commit -m "Add/Update JUnit report: ${{ github.sha }}" || true
shell: bash
- name: Push JUnit XML report to ${{ env.junit_xml_storage }} 📄
if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
uses: ad-m/github-push-action@master
with:
github_token: ${{ steps.github-token.outputs.token }}
branch: ${{ env.junit_xml_storage }}
directory: ${{ env.junit_xml_storage }}/data
continue-on-error: true
- name: Run XML comparison 🔍
if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
run: |
cp '${{ env.junit_xml_storage }}/data/${{ env.diff_storage_branch }}/junit-result.xml' new.xml
if [ ! -f ${{ env.junit_xml_storage }}/data/${{ env.junit_xml_diff_branch }}/junit-result.xml ]; then
# If XML for the branch against which we're comparing doesn't exist, we're skipping the comparison.
echo "JUnit report for branch \`${{ env.junit_xml_diff_branch }}\` " \
"doesn't exist on \`${{ env.junit_xml_storage }}\` branch yet." > output.md
echo "Once this workflow runs on \`${{ env.junit_xml_diff_branch }}\` branch, " \
"you'll see comparison of tests performance between \`${{ env.junit_xml_diff_branch }}\` " \
"and \`${{ env.diff_storage_branch }}\` as a PR comment." >> output.md
else
cp ${{ env.junit_xml_storage }}/data/${{ env.junit_xml_diff_branch }}/junit-result.xml old.xml
wget https://github.com/insightsengineering/junit-xml-diff/releases/download/v0.4.0/junit-xml-diff_0.4.0_linux_amd64.tar.gz \
-O junit-xml-diff.tar.gz
tar xzf junit-xml-diff.tar.gz
./junit-xml-diff old.xml new.xml output.md '${{ env.junit_xml_diff_branch }}' \
'${{ env.junit_xml_positive_threshold }}' '${{ env.junit_xml_negative_threshold }}'
if [ "$(du -b output.md | awk '{print $1}')" != "0" ]; then
# Non-empty output which means that there is at least one test suite/case in the table.
# Empty table won't be published since junit_xml_comparison_result_method won't be set.
echo "junit_xml_comparison_result_method=comment" >> $GITHUB_ENV
echo "" >> output.md
echo "Results for commit ${{ github.sha }}" >> output.md
echo "" >> output.md
echo "♻️ This comment has been updated with latest results." >> output.md
cp output.md output-artifact.md
echo "Size of markdown: $(du -b output.md | awk '{print $1}') bytes"
if [ "$(du -b output.md | awk '{print $1}')" -ge "60000" ]; then
echo "The result of JUnit XML file comparison exceeded maximum size. " \
"The report has therefore been uploaded as an R CMD check workflow artifact." > output.md
echo "junit_xml_comparison_result_method=artifact" >> $GITHUB_ENV
fi
echo "Markdown output:"
cat output.md
else
echo "No test suites/cases in JUnit XML file difference."
fi
fi
- name: Post JUnit XML comparison as comment 💬
if: >
steps.check-junit-xml.outputs.files_exists == 'true' &&
env.junit_xml_comparison == 'true' &&
env.junit_xml_comparison_result_method == 'comment' &&
!github.event.pull_request.head.repo.fork &&
github.event_name == 'pull_request'
uses: marocchino/sticky-pull-request-comment@v2
with:
header: markdown-table
path: output.md
continue-on-error: true
- name: Upload JUnit XML comparison ⤴
if: >
steps.check-junit-xml.outputs.files_exists == 'true' &&
env.junit_xml_comparison == 'true' &&
env.junit_xml_comparison_result_method == 'artifact' &&
!github.event.pull_request.head.repo.fork &&
github.event_name == 'pull_request'
uses: actions/upload-artifact@v4
with:
path: output-artifact.md
name: junit-xml-report-comparison
continue-on-error: true
- name: Show R CMD check logs 🔎
if: inputs.skip-r-cmd-check != true
run: |
find ${{ env.PKGNAME }}.Rcheck -type f -regextype posix-egrep \
-regex '.*00install.out|.*00check.log|.*00build.out' -print0 | while IFS= read -r -d $'\0' file; do
printf "==================================\n$file\n==================================\n"
cat $file
done
shell: bash
- name: Catch warnings in R CMD check output 🗳
id: catch-errors
run: |
check_log <- "${{ env.PKGNAME }}.Rcheck/00check.log"
if (file.exists(check_log)) {
x <- tail(readLines(check_log), 1)
if (grepl("ERROR", x)) {
writeLines(readLines(check_log))
stop("❌ R CMD check has errors. Please refer to the 'Show R CMD check logs 🔎' step above.")
}
if (grepl("WARNING", x)) {
writeLines(readLines(check_log))
stop("⚠ R CMD check has warnings. Please refer to the 'Show R CMD check logs 🔎' step above.")
}
if ("${{ inputs.enforce-note-blocklist }}" == "true") {
print("Checking notes...")
regexes <- "${{ inputs.note-blocklist }}"
regexes <- unlist(strsplit(regexes, split = "\n"))
lines <- paste(readLines(check_log), collapse = "\n")
notes_result <- vapply(
regexes,
function(r){
if (grepl(paste0(r, "\n"), lines, perl=T)) {
print(r)
return(TRUE)
}
return(FALSE)
},
logical(1)
)
if (any(notes_result)) {
stop("NOTEs on the blocklist were found. Please refer to the 'Run R CMD check 🏁' step above.")
}
}
}
shell: Rscript {0}
- name: Install R package 🚧
run: |
if [ "${{ inputs.skip-r-cmd-install }}" == "true" ]
then {
echo "Skipping R CMD INSTALL as 'skip-r-cmd-install' was set to 'true'"
exit 0
}
fi
if [ "${{ inputs.additional-env-vars }}" != "" ]
then {
echo -e "${{ inputs.additional-env-vars }}" > /tmp/dotenv.env
export $(tr '\n' ' ' < /tmp/dotenv.env)
}
fi
R CMD INSTALL ${{ env.PKGBUILD }}
shell: bash
- name: Rebuild R package 🏗
if: >
(inputs.disable-unit-test-reports != 'true' ||
startsWith(github.ref, 'refs/tags/v')) &&
github.event_name != 'pull_request'
run: |
# Undo changes to DESCRIPTION and tests/testthat.R
git checkout DESCRIPTION
if [ -f "tests/testthat.R" ]; then
git checkout tests/testthat.R
fi
if [ "${{ inputs.additional-env-vars }}" != "" ]
then {
echo -e "${{ inputs.additional-env-vars }}" > /tmp/dotenv.env
export $(tr '\n' ' ' < /tmp/dotenv.env)
}
fi
R CMD build .
shell: bash
working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
- name: Upload package build ⤴
if: startsWith(github.ref, 'refs/tags/v')
uses: actions/upload-artifact@v4
with:
path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/${{ env.PKGBUILD }}
name: ${{ env.PKGBUILD }}
publish-junit-html-report:
name: Publish JUnit HTML report 📰
runs-on: ubuntu-latest
needs: build-install-check
if: >
needs.build-install-check.outputs.publish-unit-test-html-report == 'true'
&& github.event_name != 'pull_request'
# Only one job can publish to gh-pages branch concurrently.
concurrency:
group: ghpages
steps:
- name: Setup token 🔑
id: github-token
run: |
if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then
echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN."
echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
else
echo "Using REPO_GITHUB_TOKEN."
echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
fi
shell: bash
- name: Download JUnit HTML report as artifact ⤵️
uses: actions/download-artifact@v4
with:
name: unit-test-report
path: unit-test-report
- name: Upload JUnit HTML report to GitHub pages 🗞️
if: needs.build-install-check.outputs.multiversion-docs == 'true'
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ steps.github-token.outputs.token }}
publish_dir: ./unit-test-report
destination_dir: ${{ needs.build-install-check.outputs.current-branch-or-tag }}/unit-test-report
- name: Upload JUnit HTML report to GitHub pages (latest-tag) 🏷️
if: >
needs.build-install-check.outputs.is-latest-tag == 'true'
&& needs.build-install-check.outputs.multiversion-docs == 'true'
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ steps.github-token.outputs.token }}
publish_dir: ./unit-test-report
destination_dir: ${{ inputs.latest-tag-alt-name }}/unit-test-report
- name: Upload JUnit HTML report to GitHub pages (release-candidate) 🏷️
if: >
needs.build-install-check.outputs.is-rc-tag == 'true'
&& needs.build-install-check.outputs.multiversion-docs == 'true'
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ steps.github-token.outputs.token }}
publish_dir: ./unit-test-report
destination_dir: ${{ inputs.release-candidate-alt-name }}/unit-test-report
- name: Upload JUnit HTML report to GitHub pages (non-multiversion) 🗞️
if: needs.build-install-check.outputs.multiversion-docs == 'false'
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ steps.github-token.outputs.token }}
publish_dir: ./unit-test-report
destination_dir: unit-test-report
upload-release-assets:
name: Upload build tar.gz
needs: build-install-check
runs-on: ubuntu-latest
if: >
startsWith(github.ref, 'refs/tags/v')
&& (!contains(github.event.commits[0].message, '[skip r-cmd]'))
&& github.event.pull_request.draft == false
steps:
- name: Checkout repo 🛎
uses: actions/[email protected]
- name: Get package build filename 📦
run: |
echo "PKGBUILD=$(echo $(awk -F: '/Package:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION)_"\
"$(awk -F: '/Version:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION).tar.gz)" >> $GITHUB_ENV
shell: bash
- name: Download artifact ⏬
uses: actions/download-artifact@v4
with:
name: ${{ env.PKGBUILD }}
- name: Check if release exists
id: check-if-release-exists
uses: insightsengineering/release-existence-action@v1
- name: Upload binaries to release 🔼
if: >-
steps.check-if-release-exists.outputs.release-exists == 'true'
uses: svenstaro/upload-release-action@v2
with:
repo_token: ${{ secrets.GITHUB_TOKEN }}
file: ${{ env.PKGBUILD }}
asset_name: ${{ env.PKGBUILD }}
tag: ${{ github.ref }}
overwrite: true