Merge pull request #958 from stan-dev/fix-rtools44

Fix Github Workflows
stan-dev · Apr 29, 2024 · cd3da48 · cd3da48
2 parents 9580b06 + 6c67158
commit cd3da48
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Showing 4 changed files with 34 additions and 120 deletions.
diff --git a/.github/workflows/R-CMD-check-wsl.yaml b/.github/workflows/R-CMD-check-wsl.yaml
@@ -40,20 +40,9 @@ jobs:
       - uses: r-lib/actions/setup-r@v2.8.7
       - uses: r-lib/actions/setup-pandoc@v2.8.7
 
-      - 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: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_local(path = ".", INSTALL_opts = "--no-test-load")
-          install.packages("curl")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2.8.7
+        with:
+          extra-packages: any::rcmdcheck, local::.
 
       - uses: Vampire/setup-wsl@v3
         with:
@@ -82,11 +71,9 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Check
+      - uses: r-lib/actions/check-r-package@v2.8.7
         env:
           _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
 
       - name: Show testthat output
         if: always()

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -25,12 +25,12 @@ jobs:
         config:
           - {os: macOS-latest, r: 'devel', rtools: ''}
           - {os: macOS-latest, r: 'release', rtools: ''}
-          - {os: windows-latest, r: 'devel', rtools: ''}
-          - {os: windows-latest, r: 'release', rtools: ''}
-          - {os: windows-latest, r: 'oldrel', rtools: '42'}
-          - {os: ubuntu-20.04, r: 'devel', rtools: ''}
-          - {os: ubuntu-20.04, r: 'release', rtools: ''}
-          - {os: ubuntu-20.04, r: 'oldrel', rtools: ''}
+          - {os: windows-latest, r: 'devel', rtools: '44'}
+          - {os: windows-latest, r: 'release', rtools: '44'}
+          - {os: windows-latest, r: 'oldrel', rtools: '43'}
+          - {os: ubuntu-latest, r: 'devel', rtools: ''}
+          - {os: ubuntu-latest, r: 'release', rtools: ''}
+          - {os: ubuntu-latest, r: 'oldrel', rtools: ''}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -49,42 +49,16 @@ jobs:
 
       - uses: actions/checkout@v4
 
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y libcurl4-openssl-dev || true
-          sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true
-
       - uses: r-lib/actions/setup-r@v2.8.7
         with:
           r-version: ${{ matrix.config.r }}
           rtools-version: ${{ matrix.config.rtools }}
-      - uses: r-lib/actions/setup-pandoc@v2.8.7
 
-      - 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-pandoc@v2.8.7
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v4
+      - uses: r-lib/actions/setup-r-dependencies@v2.8.7
         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 dependencies
-        run: |
-          Sys.setenv("MAKEFLAGS"="-j2")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_local(path = ".")
-          install.packages("curl")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck, local::.
 
       - name: Install cmdstan
         run: |
@@ -99,11 +73,9 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Check
+      - uses: r-lib/actions/check-r-package@v2.8.7
         env:
           _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
 
       - name: Show testthat output
         if: always()

diff --git a/.github/workflows/Test-coverage.yaml b/.github/workflows/Test-coverage.yaml
@@ -13,10 +13,18 @@ name: Test coverage
       - master
 
 jobs:
-  test-coverage-ubuntu:
-    name: "Linux"
+  test-coverage:
     if: "! contains(github.event.head_commit.message, '[ci skip]')"
-    runs-on: ubuntu-20.04
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: windows-latest }
+          - { os: ubuntu-latest }
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       NOT_CRAN: true
@@ -37,76 +45,23 @@ jobs:
       - uses: r-lib/actions/setup-r@v2.8.7
       - uses: r-lib/actions/setup-pandoc@v2.8.7
 
-      - name: Install Ubuntu dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y libcurl4-openssl-dev
-          sudo apt-get install -y openmpi-bin openmpi-common openmpi-doc libopenmpi-dev
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v4
+      - uses: r-lib/actions/setup-r-dependencies@v2.8.7
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ubuntu-r-4.0-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ubuntu-r-4.0-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "curl"), dependencies = TRUE)
-          remotes::install_local(path = ".", INSTALL_opts = "--no-test-load")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-          remotes::install_cran("gridExtra")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck, local::., any::covr, any::gridExtra
 
       - name: Install cmdstan
         run: |
           cmdstanr::check_cmdstan_toolchain(fix = TRUE)
           cmdstanr::install_cmdstan(cores = 2)
         shell: Rscript {0}
 
-      - name: Test coverage
+      - name: Test coverage (Linux)
+        if: runner.os == 'Linux'
         run: covr::codecov(type = "tests")
         shell: Rscript {0}
 
-  test-coverage-windows:
-    name: "Windows"
-    if: "! contains(github.event.head_commit.message, '[ci skip]')"
-    runs-on: windows-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      NOT_CRAN: true
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-r@v2.8.7
-
-      - uses: r-lib/actions/setup-pandoc@v2.8.7
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "curl"), dependencies = TRUE)
-          remotes::install_local(path = ".")
-          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
-          cmdstanr::install_cmdstan(cores = 2, overwrite = TRUE)
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-          remotes::install_cran("gridExtra")
-        shell: Rscript {0}
-
-      - name: Test coverage
+      - name: Test coverage (Windows)
+        if: runner.os == 'Windows'
         run: |
           options(covr.gcov = 'C:/rtools40/mingw64/bin/gcov.exe');
           covr::codecov(type = "tests", function_exclusions = "sample_mpi")

diff --git a/tests/testthat/test-install.R b/tests/testthat/test-install.R
@@ -98,7 +98,7 @@ test_that("install_cmdstan() works with version and release_url", {
   expect_message(
     expect_output(
       install_cmdstan(dir = dir, overwrite = TRUE, cores = 4,
-                      release_url = "https://github.com/stan-dev/cmdstan/releases/download/v2.26.1/cmdstan-2.26.1.tar.gz",
+                      release_url = "https://github.com/stan-dev/cmdstan/releases/download/v2.33.0/cmdstan-2.33.0.tar.gz",
                       wsl = os_is_wsl()),
       "Compiling, linking C++ code",
       fixed = TRUE
@@ -110,7 +110,7 @@ test_that("install_cmdstan() works with version and release_url", {
     expect_message(
       expect_output(
         install_cmdstan(dir = dir, overwrite = TRUE, cores = 4,
-                        version = "2.27.0",
+                        version = "2.33.0",
                         # the URL is intentionally invalid to test that the version has higher priority
                         release_url = "https://github.com/stan-dev/cmdstan/releases/download/v2.27.3/cmdstan-2.27.3.tar.gz",
                         wsl = os_is_wsl()),
@@ -123,7 +123,7 @@ test_that("install_cmdstan() works with version and release_url", {
     "version and release_url shouldn't both be specified",
     fixed = TRUE
   )
-  expect_true(dir.exists(file.path(dir, "cmdstan-2.27.0")))
+  expect_true(dir.exists(file.path(dir, "cmdstan-2.33.0")))
   set_cmdstan_path(cmdstan_default_path())
 })