Pull request #15: Add ASAN/UBSAN pipeline

Merge in STAT/prestogp from build-workflow to to-git Squashed commit of the following: commit 2c9c2ed Merge: 6af43f4 56cdbf2 Author: sciome-bot <software.tools@sciome.com> Date: Thu Dec 28 13:11:14 2023 -0500 Merge branch 'to-git' of ssh://sciome-bot/stat/prestogp into build-workflow commit 6af43f4 Merge: e530819 17f5284 Author: sciome-bot <software.tools@sciome.com> Date: Thu Dec 28 13:07:50 2023 -0500 Merge branch 'master' of ssh://sciome-bot/stat/prestogp into build-workflow commit e530819 Author: sciome-bot <software.tools@sciome.com> Date: Thu Dec 28 13:06:21 2023 -0500 Add USAN/ASAN pipeline commit 17f5284 Merge: ea78ffa 895100d Author: Eric Bair <eric.bair@sciome.com> Date: Fri Dec 1 10:49:09 2023 -0500 Pull request #12: Testing Merge in STAT/prestogp from testing to master * commit '895100db78d89c5082ddfcf1411dad69bdf1b6c5': Fixed another sparseNN bug and updated tests Fixed a bug in SparseNN Added more likelihood and maxmin ordering tests commit 895100d Merge: 7f3ca3c fb060ff Author: Eric Bair <eric.bair@sciome.com> Date: Wed Nov 29 17:02:10 2023 -0500 Merge branch 'to-git' of http://192.168.167.103:7990/bitbucket/scm/stat/prestogp into testing Conflicts: DESCRIPTION man/prestogp_fit-PrestoGPModel-method.Rd tests/testthat/test-Log_Likelihood.R Fixed merge conflicts. commit 7f3ca3c Author: Eric Bair <eric.bair@sciome.com> Date: Wed Nov 29 16:43:40 2023 -0500 Fixed another sparseNN bug and updated tests commit 1ca9586 Author: Eric Bair <eric.bair@sciome.com> Date: Tue Nov 28 18:40:36 2023 -0500 Fixed a bug in SparseNN commit 80a9818 Author: Eric Bair <eric.bair@sciome.com> Date: Tue Nov 21 17:49:19 2023 -0500 Added more likelihood and maxmin ordering tests commit 4822fbc Author: sciome-bot <software.tools@sciome.com> Date: Mon Nov 20 15:01:37 2023 -0500 Add UBSAN/ASAN sanitizers commit ea78ffa Merge: 286ba5d 53e2b0d Author: sciome-bot <software.tools@sciome.com> Date: Mon Nov 20 12:41:08 2023 -0500 Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP commit 286ba5d Merge: f52ebbb 84fd72f Author: sciome-bot <software.tools@sciome.com> Date: Tue Nov 14 13:11:48 2023 -0500 Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP commit f52ebbb Merge: 4e0e1ec 2dd74a2 Author: Eric Bair <eric.bair@sciome.com> Date: Tue Nov 14 13:10:51 2023 -0500 Pull request #9: Testing * commit '2dd74a21380be960918b6067abec8ec163721853': Added a simulation file for testing Fixed likelihood function and added additional tests Fixed likelihood function and added additional test commit 2dd74a2 Author: Eric Bair <eric.bair@sciome.com> Date: Mon Nov 13 19:17:43 2023 -0500 Added a simulation file for testing commit 6c17318 Author: Eric Bair <eric.bair@sciome.com> Date: Mon Nov 13 19:16:32 2023 -0500 Fixed likelihood function and added additional tests commit f90ce5e Author: Eric Bair <eric.bair@sciome.com> Date: Mon Nov 13 19:10:57 2023 -0500 Fixed likelihood function and added additional test commit 4e0e1ec Merge: 0d13ba9 a6d1d1b Author: Eric Bair <eric.bair@sciome.com> Date: Tue Nov 7 15:38:43 2023 -0500 Pull request #7: Testing Merge in STAT/prestogp from testing to master * commit 'a6d1d1b06e9f640140bad7f03746d14ef0629af4': Added new testing files Added new testthat tests
NIEHS · Dec 28, 2023 · 1e4361d · 1e4361d
1 parent ae3d17b
commit 1e4361d
Showing 1 changed file with 170 additions and 0 deletions.
diff --git a/.github/workflows/sanitizers.yaml b/.github/workflows/sanitizers.yaml
@@ -0,0 +1,170 @@
+name: UBSAN/ASAN Checks
+
+on:
+  pull_request:
+    branches: [ "main" ]
+  push:
+    branches: [ "build-workflow" ]
+  workflow_dispatch: 
+
+
+permissions:
+  contents: read
+
+jobs:
+  sanitizer-check-asan:
+    runs-on: ubuntu-latest
+    env:
+      CC: clang
+      CXX: clang++
+      CXXFLAGS: "-fsanitize=address"
+      LINK: clang++
+      ASAN: true
+      UBSAN: true
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      ## R CMD check
+      _R_CHECK_CRAN_INCOMING_: false
+      _R_CHECK_LENGTH_1_CONDITION_: true
+      _R_CHECK_LENGTH_1_LOGIC2_: true
+      _R_CHECK_MATRIX_DATA_: true
+      ## Specific to package
+      _R_CHECK_USE_VALGRIND_: true
+      UBSAN_OPTIONS: "print_stacktrace=1"
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Clang
+        uses: egor-tensin/setup-clang@v1
+        with:
+            version: latest
+            platform: x64
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v3
+        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
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Check with ASAN
+        run: rcmdcheck::rcmdcheck(build_args = "--no-build-vignettes", args = c("--no-codoc", "--no-examples", "--no-manual", "--ignore-vignettes"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: ${{ runner.os }}-asan-rrelease-results
+          path: check
+  sanitizer-check-usan:
+    runs-on: ubuntu-latest
+    env:
+      CC: clang
+      CXX: clang++
+      CXXFLAGS: "-fsanitize=undefined"
+      LINK: clang++
+      ASAN: true
+      UBSAN: true
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      ## R CMD check
+      _R_CHECK_CRAN_INCOMING_: false
+      _R_CHECK_LENGTH_1_CONDITION_: true
+      _R_CHECK_LENGTH_1_LOGIC2_: true
+      _R_CHECK_MATRIX_DATA_: true
+      ## Specific to package
+      _R_CHECK_USE_VALGRIND_: true
+      UBSAN_OPTIONS: "print_stacktrace=1"
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Clang
+        uses: egor-tensin/setup-clang@v1
+        with:
+            version: latest
+            platform: x64
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v3
+        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
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Check with UBSAN
+        run: rcmdcheck::rcmdcheck(build_args = "--no-build-vignettes", args = c("--no-codoc", "--no-examples", "--no-manual", "--ignore-vignettes"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: ${{ runner.os }}-ubsan-rrelease-results
+          path: check