regenerate github action

Author: LabAsim

.github/workflows/R-CMD-check._old.yaml

@@ -0,0 +1,285 @@
+# 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:
+## 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:
+      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, vignettes"},
+            {"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries, ubsan, vignettes"},
+            {"os":"ubuntu-20.04", "r":"release", "rspm":"https://packagemanager.rstudio.com/cran/__linux__/focal/latest", "timeout":360, "flags":"full, ubsan, debug"},
+            {"os":"ubuntu-20.04", "r":"devel", "rspm":"https://packagemanager.rstudio.com/cran/__linux__/focal/latest", "timeout":360, "flags":"vignettes, remote"},
+            {"os":"ubuntu-20.04", "r":"release", "rspm":"https://packagemanager.rstudio.com/cran/__linux__/focal/latest", "timeout":360, "flags":"full, covr"}]}'
+          elif [[ "${{ env.FOUND_PUBLIC }}" != '0' ]] # Private with no public analogue: reduced set.
+          then
+            config='{"config":[
+            {"os":"ubuntu-20.04", "r":"release", "rspm":"https://packagemanager.rstudio.com/cran/__linux__/focal/latest", "timeout":10, "flags":"none"}
+            ]}'
+          else # Private with public analogue: no checking.
+            config=''
+          fi
+          config="${config//'%'/'%25'}"
+          config="${config//$'\n'/'%0A'}"
+          config="${config//$'\r'/'%0D'}"
+          echo "::set-output name=matrix::$config"
+
+  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:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+
+    steps:
+      - name: If available, use the Janitor's key rather than the repository-specific key.
+        id: set-pat
+        run: |
+          if [[ -n "${{ 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@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - name: Install GhostScript (on Linux if running vignettes)
+        if: runner.os == 'Linux' && contains(matrix.config.flags, 'vignettes')
+        run: |
+          /usr/bin/sudo DEBIAN_FRONTEND=noninteractive apt-get install -y ghostscript
+        shell: bash
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Install tinytex (system)
+        if: contains(matrix.config.flags, 'vignettes')
+        uses: r-lib/actions/setup-tinytex@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v4
+        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}
+
+      - name: Install tinytex (R)
+        if: contains(matrix.config.flags, 'vignettes')
+        run: |
+          remotes::install_cran("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"
+
+          if(Sys.getenv("USE_UBSAN") == "true"){
+            Sys.setenv(PKG_LIBS=paste(Sys.getenv("PKG_LIBS"), "-fsanitize=undefined"),
+                       PKG_CFLAGS=paste(Sys.getenv("PKG_CFLAGS"), "-fsanitize=undefined"),
+                       PKG_CXXFLAGS=paste(Sys.getenv("PKG_CXXFLAGS"), "-fsanitize=undefined"),
+                       UBSAN_OPTIONS=paste(Sys.getenv("UBSAN_OPTIONS"), "print_stacktrace=1"))
+          }
+
+          if(Sys.getenv("SET_DEBUG") == "true"){
+            Sys.setenv(PKG_LIBS=paste(Sys.getenv("PKG_LIBS"), "-UNDEBUG -DDEBUG"),
+                       PKG_CXXFLAGS=paste(Sys.getenv("PKG_CXXFLAGS"), "-UNDEBUG -DDEBUG"),
+                       PKG_CFLAGS=paste(Sys.getenv("PKG_CFLAGS"), "-UNDEBUG -DDEBUG"))
+          }
+
+          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')
+        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 ]
+          then
+            echo "UBSAN errors:" >&2
+            cat check/ubsan.err >&2
+            exit 1
+          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: covr::codecov(type=c("tests","examples"))
+        shell: Rscript {0}