Dynamic allocation of logging toggles #468
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# NOTE: This script is a modification of the r-lib/actions standard cehcking script and the public-private sync script, on which it piggybacks to detect when it's in a private repo and can therefore skip some or even all tests. It also builds and uploads binaries for Windows and MacOS. | |
# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | |
# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | |
# Each entry in the config matrix must have the following keys: | |
# | |
# os: windows-latest, macOS-latest, ubuntu-20.04, etc. (as of this writing) | |
# | |
# r: devel or release | |
# | |
# rspm: Linux only, just leave it alone. | |
# | |
# timeout: in minutes | |
# | |
# flags: a comma (or some other aesthetically pleasing and | |
# non-forbidden symbol) separated list of flags. Currently | |
# supported: | |
# | |
# binaries: build and upload as an artefact a binary version (particularly for MacOS and Windows). | |
# | |
# full: run with ENABLE_statnet_TESTS. | |
# | |
# vignettes: build vignettes and manuals; otherwise ignore. | |
# | |
# ubsan: compile with -fsanitize=undefined and fail on any errors identified. | |
# | |
# debug: compile package with -DDEBUG and -UNDEBUG | |
# | |
# covr: run in covr mode may be used with 'full' but probably not with others. | |
# | |
# | |
# Typical public, private, and release configurations are provided in the variables below. | |
on: [push, pull_request] | |
name: R-CMD-check | |
# Set public and private repositories (i.e., USER/PKG). Leave blank to autodetect. | |
env: | |
PUBLIC: '' | |
PRIVATE: '' | |
PUBLIC_CONFIG: '{"config":[ | |
{"os":"windows-latest", "r":"release", "timeout":360, "flags":"binaries"}, | |
{"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries, ubsan"}, | |
{"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, ubsan, debug"}, | |
{"os":"ubuntu-latest", "r":"devel", "timeout":360, "flags":"vignettes, remote"}, | |
{"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, covr"}]}' | |
RELEASE_CONFIG: '{"config":[ | |
{"os":"windows-latest", "r":"release", "timeout":360, "flags":"binaries, vignettes, remote, strict"}, | |
{"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries, ubsan, vignettes, remote, strict"}, | |
{"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, ubsan, debug, strict"}, | |
{"os":"ubuntu-latest", "r":"devel", "timeout":360, "flags":"vignettes, remote, strict"}, | |
{"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, covr, strict"}]}' | |
PRIVATE_CONFIG: '{"config":[ | |
{"os":"ubuntu-latest", "r":"release", "timeout":10, "flags":"none"} | |
]}' | |
jobs: | |
Set-Matrix-Private: | |
runs-on: ubuntu-latest | |
outputs: | |
matrix: ${{ steps.set-matrix.outputs.matrix }} | |
steps: | |
- name: check-config # Make sure either neither or both are set; abort if not. | |
if: (env.PUBLIC == '') != (env.PRIVATE == '') | |
run: | | |
echo "Configuration problem: only one of the repositories is set." | |
exit 1 | |
- name: detect-repos | |
if: env.PUBLIC == '' && env.PRIVATE == '' # Autodetect always. | |
run: | | |
if [[ "${{ github.repository }}" == *-private ]] | |
then # Current repo is private. | |
IAM="private" | |
PRIVATE="${{ github.repository }}" | |
PUBLIC="${PRIVATE%-private}" | |
else # Current repo is public. | |
IAM="public" | |
PUBLIC="${{ github.repository }}" | |
PRIVATE="$PUBLIC-private" | |
fi | |
echo "IAM=$IAM" >> $GITHUB_ENV | |
echo "PRIVATE=$PRIVATE" >> $GITHUB_ENV | |
echo "PUBLIC=$PUBLIC" >> $GITHUB_ENV | |
- name: public-check # Check if the branch/tag exists in the public repository. | |
if: env.IAM == 'private' # Only check if from private repo. | |
run: | | |
set +e | |
git ls-remote --exit-code https://github.com/${{ env.PUBLIC }} ${{ github.ref }} | |
echo "FOUND_PUBLIC=$?" >> $GITHUB_ENV | |
- name: set-matrix | |
id: set-matrix | |
run: | | |
if [[ "${{ env.IAM }}" == 'public' ]] # Public: full set. | |
then | |
config='${{ env.PUBLIC_CONFIG }}' | |
elif [[ "${{ env.FOUND_PUBLIC }}" != '0' ]] # Private with no public analogue: reduced set. | |
then | |
config='${{ env.PRIVATE_CONFIG }}' | |
else # Private with public analogue: no checking. | |
config='' | |
fi | |
config="${config//$'\r'/' '}" | |
config="${config//$'\n'/' '}" | |
echo "matrix=$config" >> $GITHUB_OUTPUT | |
R-CMD-check: | |
needs: Set-Matrix-Private | |
if: needs.Set-Matrix-Private.outputs.matrix != '' | |
runs-on: ${{ matrix.config.os }} | |
name: ${{ matrix.config.os }} (r ${{ matrix.config.r }}, flags ${{ matrix.config.flags }}) | |
strategy: | |
fail-fast: false | |
matrix: ${{fromJson(needs.Set-Matrix-Private.outputs.matrix)}} | |
env: | |
HOMEBREW_NO_INSTALL_CLEANUP: 1 | |
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
steps: | |
- name: If available, use the Janitor's key rather than the repository-specific key. | |
id: set-pat | |
run: | | |
if [[ -n "${{ secrets.JANITORS_GITHUB_PAT }}" ]] | |
then | |
echo "GITHUB_PAT=${{ secrets.JANITORS_GITHUB_PAT }}" >> $GITHUB_ENV | |
else | |
echo "GITHUB_PAT=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_ENV | |
fi | |
shell: bash | |
- uses: actions/checkout@v4 | |
- uses: r-lib/actions/setup-r@v2 | |
with: | |
use-public-rspm: true | |
r-version: ${{ matrix.config.r }} | |
- name: Install tidy (on Linux if running vignettes) | |
if: runner.os == 'Linux' && contains(matrix.config.flags, 'vignettes') | |
run: | | |
/usr/bin/sudo DEBIAN_FRONTEND=noninteractive apt-get install -y tidy | |
shell: bash | |
- uses: r-lib/actions/setup-pandoc@v2 | |
- name: Install tinytex (system) | |
if: contains(matrix.config.flags, 'vignettes') | |
uses: r-lib/actions/setup-tinytex@v2 | |
- uses: r-lib/actions/setup-r-dependencies@v2 | |
with: | |
extra-packages: | | |
any::rcmdcheck | |
any::covr | |
any::V8 | |
any::xml2 | |
needs: | | |
check | |
coverage | |
- name: Install tinytex (R) | |
if: contains(matrix.config.flags, 'vignettes') | |
run: | | |
if(!requireNamespace("tinytex", quietly = TRUE)) pak::pkg_install("tinytex") | |
tinytex:::install_yihui_pkgs() | |
tinytex::tlmgr_install("makeindex") | |
shell: Rscript {0} | |
- name: Build | |
if: contains(matrix.config.flags, 'binaries') | |
run: | | |
dir.create("binaries", FALSE) | |
pkgbuild::build(binary=TRUE, vignettes=FALSE, dest_path = "binaries") | |
shell: Rscript {0} | |
- name: Upload build results | |
if: contains(matrix.config.flags, 'binaries') && !failure() | |
uses: actions/upload-artifact@v4 | |
with: | |
name: ${{ runner.os }}-r${{ matrix.config.r }}-binaries | |
path: binaries | |
- name: Clean up build results | |
if: contains(matrix.config.flags, 'binaries') | |
run: rm -rf binaries | |
shell: bash | |
- name: Check | |
if: contains(matrix.config.flags, 'covr') == false | |
timeout-minutes: ${{ matrix.config.timeout }} | |
env: | |
_R_CHECK_CRAN_INCOMING_REMOTE_: ${{ contains(matrix.config.flags, 'remote') }} | |
_R_CHECK_FORCE_SUGGESTS_: false | |
ENABLE_statnet_TESTS: ${{ contains(matrix.config.flags, 'full') }} | |
R_VIGNETTES: ${{ contains(matrix.config.flags, 'vignettes') }} | |
FAIL_ON_WARN: ${{ contains(matrix.config.flags, 'strict') }} | |
USE_UBSAN: ${{ contains(matrix.config.flags, 'ubsan') }} | |
SET_DEBUG: ${{ contains(matrix.config.flags, 'debug') }} | |
run: | | |
if(Sys.getenv("R_VIGNETTES") == "true"){ | |
check_args <- c("--as-cran") | |
build_args <- c("--compact-vignettes=gs+qpdf") | |
}else{ | |
check_args <- c("--no-manual", "--as-cran", "--ignore-vignettes") | |
build_args <- c("--no-manual", "--no-build-vignettes") | |
} | |
if(Sys.getenv("ENABLE_statnet_TESTS") == "true"){ | |
check_args <- c(check_args, "--run-donttest") | |
} | |
error_on <- if(Sys.getenv("FAIL_ON_WARN") == "true") "warning" else "error" | |
extra_flags <- c() | |
if(Sys.getenv("USE_UBSAN") == "true"){ | |
extra_flags <- c(extra_flags, "-fsanitize=undefined") | |
Sys.setenv(UBSAN_OPTIONS=paste(Sys.getenv("UBSAN_OPTIONS"), "print_stacktrace=1")) | |
} | |
if(Sys.getenv("SET_DEBUG") == "true") extra_flags <- c(extra_flags, "-UNDEBUG", "-DDEBUG") | |
# Before R 4.3.0, R itself was not compliant. | |
if(getRversion() >= "4.3") extra_flags <- c(extra_flags, "-Wstrict-prototypes") | |
Sys.setenv(PKG_LIBS=paste(c(Sys.getenv("PKG_LIBS"), extra_flags), collapse=" "), | |
PKG_CXXFLAGS=paste(c(Sys.getenv("PKG_CXXFLAGS"), extra_flags), collapse=" "), | |
PKG_CFLAGS=paste(c(Sys.getenv("PKG_CFLAGS"), extra_flags), collapse=" ")) | |
rcmdcheck::rcmdcheck(args = check_args, build_args = build_args, error_on = error_on, check_dir = "check") | |
shell: Rscript {0} | |
- name: Check UBSAN output | |
if: contains(matrix.config.flags, 'ubsan') | |
# NB: xargs -r only works in GNU, so not on MacOS. | |
run: | | |
find check/ -name '*.Rout' -print0 > check/Rout.list | |
if [ -s check/Rout.list ] | |
then | |
cat check/Rout.list | xargs -0 grep -E '\.[hc]:[0-9]+:[0-9]+: +runtime error:' > check/ubsan.err || true | |
if [ -s check/ubsan.err ] | |
then | |
echo "UBSAN errors:" >&2 | |
cat check/ubsan.err >&2 | |
exit 1 | |
fi | |
fi | |
shell: bash | |
- name: Upload check results | |
if: contains(matrix.config.flags, 'covr') == false && failure() | |
uses: actions/upload-artifact@v4 | |
with: | |
name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
path: | | |
check | |
!check/*/00_pkg_src | |
- name: Test coverage | |
if: contains(matrix.config.flags, 'covr') | |
timeout-minutes: ${{ matrix.config.timeout }} | |
env: | |
_R_CHECK_CRAN_INCOMING_REMOTE_: false | |
_R_CHECK_FORCE_SUGGESTS_: ${{ runner.os != 'macOS' }} # Rmpi is not available on macOS. | |
ENABLE_statnet_TESTS: ${{ contains(matrix.config.flags, 'full') }} | |
run: | | |
cov <- covr::package_coverage( | |
type=c("tests", "examples"), | |
quiet = FALSE, | |
clean = FALSE, | |
install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | |
) | |
covr::to_cobertura(cov) | |
shell: Rscript {0} | |
- name: Upload coverage results | |
if: contains(matrix.config.flags, 'covr') | |
uses: codecov/codecov-action@v4 | |
with: | |
fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} | |
file: ./cobertura.xml | |
plugin: noop | |
disable_search: true | |
token: ${{ secrets.CODECOV_TOKEN }} |