Moved sginv() and xTAx_seigen() into statnet.common and bumped the re… #1260
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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. | |
| on: [push, pull_request] | |
| name: R-CMD-check | |
| # Set public and private repositories (i.e., USER/PKG). Leave blank to autodetect. | |
| env: | |
| PUBLIC: '' | |
| PRIVATE: '' | |
| 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='{"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"}]}' | |
| elif [[ "${{ env.FOUND_PUBLIC }}" != '0' ]] # Private with no public analogue: reduced set. | |
| then | |
| config='{"config":[ | |
| {"os":"ubuntu-latest", "r":"release", "timeout":10, "flags":"none"} | |
| ]}' | |
| else # Private with public analogue: no checking. | |
| config='' | |
| fi | |
| config="${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@v3 | |
| - 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 | |
| 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@v3 | |
| 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@v3 | |
| 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: covr::codecov(type=c("tests","examples")) | |
| shell: Rscript {0} |