From 4cbcc7117849e1dd396e483d51f6d0fd3ab4160a Mon Sep 17 00:00:00 2001 From: "Pavel N. Krivitsky" Date: Wed, 6 Nov 2024 21:47:43 +1100 Subject: [PATCH] Updated the GitHub workflows and/or the README file to the latest versions. --- .github/workflows/R-CMD-check.yaml | 166 ++++++++++++++++------------- 1 file changed, 93 insertions(+), 73 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 1a7e89f..2553f54 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -25,7 +25,12 @@ # # 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] @@ -35,19 +40,23 @@ name: R-CMD-check 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: -## Remove-Old-Artifacts: -## runs-on: ubuntu-latest -## timeout-minutes: 10 -## -## steps: -## - name: Remove old artifacts -## uses: c-hive/gha-remove-artifacts@v1.2.0 -## with: -## age: '1 month' -## skip-recent: 8 - Set-Matrix-Private: runs-on: ubuntu-latest outputs: @@ -85,24 +94,16 @@ jobs: run: | if [[ "${{ env.IAM }}" == 'public' ]] # Public: full set. then - config='{"config":[ - {"os":"windows-latest", "r":"release", "timeout":360, "flags":"binaries"}, - {"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries"}, - {"os":"ubuntu-20.04", "r":"release", "rspm":"https://packagemanager.rstudio.com/cran/__linux__/focal/latest", "timeout":360, "flags":"full, ubsan"}, - {"os":"ubuntu-20.04", "r":"devel", "rspm":"https://packagemanager.rstudio.com/cran/__linux__/focal/latest", "timeout":360, "flags":"vignettes"}, - {"os":"ubuntu-20.04", "r":"release", "rspm":"https://packagemanager.rstudio.com/cran/__linux__/focal/latest", "timeout":360, "flags":"full, covr"}]}' + config='${{ env.PUBLIC_CONFIG }}' elif [[ "${{ env.FOUND_PUBLIC }}" != '0' ]] # Private with no public analogue: reduced set. then - config='{"config":[ - {"os":"ubuntu-20.04", "r":"release", "rspm":"https://packagemanager.rstudio.com/cran/__linux__/focal/latest", "timeout":10, "flags":"none"} - ]}' + config='${{ env.PRIVATE_CONFIG }}' else # Private with public analogue: no checking. config='' fi - config="${config//'%'/'%25'}" - config="${config//$'\n'/'%0A'}" - config="${config//$'\r'/'%0D'}" - echo "::set-output name=matrix::$config" + config="${config//$'\r'/' '}" + config="${config//$'\n'/' '}" + echo "matrix=$config" >> $GITHUB_OUTPUT R-CMD-check: needs: Set-Matrix-Private @@ -118,8 +119,8 @@ jobs: matrix: ${{fromJson(needs.Set-Matrix-Private.outputs.matrix)}} env: + HOMEBREW_NO_INSTALL_CLEANUP: 1 R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} steps: - name: If available, use the Janitor's key rather than the repository-specific key. @@ -133,60 +134,42 @@ jobs: fi shell: bash - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: + use-public-rspm: true r-version: ${{ matrix.config.r }} - - name: Install GhostScript (on Linux if running vignettes) + - name: Install tidy (on Linux if running vignettes) if: runner.os == 'Linux' && contains(matrix.config.flags, 'vignettes') run: | - /usr/bin/sudo DEBIAN_FRONTEND=noninteractive apt-get install -y ghostscript + /usr/bin/sudo DEBIAN_FRONTEND=noninteractive apt-get install -y tidy shell: bash - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-pandoc@v2 - name: Install tinytex (system) if: contains(matrix.config.flags, 'vignettes') - uses: r-lib/actions/setup-tinytex@v1 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} + uses: r-lib/actions/setup-tinytex@v2 - - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v2 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install system dependencies - if: runner.os == 'Linux' - run: | - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') - - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("pkgbuild") - remotes::install_cran("rcmdcheck") - remotes::install_cran("covr") - shell: Rscript {0} + extra-packages: | + any::rcmdcheck + any::covr + any::V8 + any::xml2 + needs: | + check + coverage - name: Install tinytex (R) if: contains(matrix.config.flags, 'vignettes') run: | - remotes::install_cran("tinytex") + if(!requireNamespace("tinytex", quietly = TRUE)) pak::pkg_install("tinytex") tinytex:::install_yihui_pkgs() + tinytex::tlmgr_install("makeindex") shell: Rscript {0} - name: Build @@ -198,7 +181,7 @@ jobs: - name: Upload build results if: contains(matrix.config.flags, 'binaries') && !failure() - uses: actions/upload-artifact@v2 + uses: actions/upload-artifact@v4 with: name: ${{ runner.os }}-r${{ matrix.config.r }}-binaries path: binaries @@ -212,12 +195,13 @@ jobs: if: contains(matrix.config.flags, 'covr') == false timeout-minutes: ${{ matrix.config.timeout }} env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false + _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") @@ -227,32 +211,51 @@ jobs: 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"){ - Sys.setenv(PKG_LIBS="-fsanitize=undefined", - PKG_CFLAGS="-fsanitize=undefined", - UBSAN_OPTIONS="print_stacktrace=1") + 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 | xargs -r -0 grep -E '\.[hc]:[0-9]+:[0-9]+: +runtime error:' > check/ubsan.err || true - if [ -s check/ubsan.err ] + find check/ -name '*.Rout' -print0 > check/Rout.list + if [ -s check/Rout.list ] then - echo "UBSAN errors:" >&2 - cat check/ubsan.err >&2 - exit 1 + 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@v2 + uses: actions/upload-artifact@v4 with: name: ${{ runner.os }}-r${{ matrix.config.r }}-results path: | @@ -266,5 +269,22 @@ jobs: _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: covr::codecov(type=c("tests","examples")) + 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 }}