update github ci

* update github ci
prioritizr · Aug 4, 2022 · 40e8e79 · 40e8e79
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commit 40e8e79
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diff --git a/.github/workflows/R-CMD-check-macos.yaml b/.github/workflows/R-CMD-check-macos.yaml
@@ -37,42 +37,28 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@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-
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
       - name: Install system dependencies
         run: |
           brew install gmp
           brew install mpfr
+          brew install automake
           brew install gdal
-          brew upgrade --cask chromedriver
 
-      - name: Install dependencies
-        run: |
-          options("install.packages.compile.from.source" = "never")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("covr")
-          remotes::install_cran("curl", pkgType = "source")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 4
+          extra-packages: |
+            any::rcmdcheck
+            any::XML
+          needs: |
+            check
 
       - name: Session information
         run: |
@@ -81,19 +67,11 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Check
-        run: |
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-build-vignettes"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
 
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
diff --git a/.github/workflows/R-CMD-check-ubuntu.yaml b/.github/workflows/R-CMD-check-ubuntu.yaml
@@ -18,14 +18,14 @@ jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }}) (${{ matrix.config.pkgs }} packages)
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
     strategy:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-20.04, r: 'release', pkgs: 'all'}
-          - {os: ubuntu-20.04, r: 'devel', pkgs: 'all'}
+          - {os: ubuntu-20.04, r: 'release'}
+          - {os: ubuntu-20.04, r: 'devel'}
           - {os: ubuntu-20.04, r: 'devel', pkgs: 'depends only'}
 
     env:
@@ -39,42 +39,28 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@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@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: |
-          sudo apt-get -y install libcurl4-openssl-dev libmpfr-dev libgmp3-dev libudunits2-dev libgdal-dev libgeos-dev libproj-dev
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
+          cache-version: 4
+          extra-packages: |
+            any::covr
+            any::rcmdcheck
+            any::XML
+            prepr=?ignore
+          needs: |
+            check
+            coverage
+
+      - name: Install spatial R packages
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("covr")
-          remotes::install_cran("urlchecker")
+          pak::pkg_install("dickoa/prepr")
         shell: Rscript {0}
 
       - name: Session information
@@ -84,22 +70,15 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Set environmental variables for package checks
+      - name: Environmental variables
         if: matrix.config.pkgs == 'depends only'
         run: |
           echo "_R_CHECK_DEPENDS_ONLY_=true" >> $GITHUB_ENV
 
-      - name: Check
-        run: |
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-build-vignettes"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          args: 'c("--no-manual", "--as-cran", "--no-build-vignettes")'
+          upload-snapshots: true
 
       - name: Show testthat output
         if: always()
@@ -110,13 +89,3 @@ jobs:
         if: runner.os == 'Linux' && matrix.config.r == 'release'
         run: covr::codecov()
         shell: Rscript {0}
-
-      - name: Check URLs
-        if: runner.os == 'Linux' && matrix.config.r == 'release'
-        run: |
-          result <- urlchecker::url_check()
-          if (nrow(result) > 0) {
-            print(result)
-            stop("Invalid URLs detected")
-          }
-        shell: Rscript {0}
diff --git a/.github/workflows/R-CMD-check-windows.yaml b/.github/workflows/R-CMD-check-windows.yaml
@@ -35,27 +35,36 @@ jobs:
       CI: true
 
     steps:
+      # configure git to prevent it from automatically converting line-endings
+      # this is important to avoid WARNINGS during CRAN checks
+      # that are false-positives, see:
+      # https://msmith.de/2020/03/12/r-cmd-check-github-actions.html
+      - name: Configure git
+        run: git config --global core.autocrlf false
+
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@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-r-dependencies@v2
+        with:
+          cache-version: 4
+          extra-packages: |
+            any::rcmdcheck
+            any::XML
+            prepr=?ignore
+          needs: |
+            check
 
-      - name: Install dependencies
+      - name: Install spatial R packages
         run: |
-          options("install.packages.compile.from.source" = "never", pkgType = "binary")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("covr")
+          install.packages("remotes")
+          remotes::install_github("dickoa/prepr")
         shell: Rscript {0}
 
       - name: Session information
@@ -65,19 +74,11 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Check
-        run: |
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-build-vignettes"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
 
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml
@@ -37,44 +37,35 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
+      - name: Install system 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}
+          sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
+          sudo apt update
+          sudo apt-get install \
+            libgdal-dev libgeos-dev libproj-dev \
+            libgmp3-dev libmpfr-dev libudunits2-dev
 
-      - 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-
+          cache-version: 4
+          extra-packages: |
+            any::rcmdcheck
+            any::XML
+            any::urlchecker
+            prepr=?ignore
+          needs: |
+            check
 
-      - name: Install system dependencies
+      - name: Install spatial R packages
         run: |
-          sudo apt-get -y install \
-            libcurl4-openssl-dev coinor-libsymphony-dev coinor-libcbc-dev coinor-libclp-dev \
-            libudunits2-dev libgdal-dev libgeos-dev libproj-dev libglpk-dev
-          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("rcmdcheck")
-          remotes::install_cran("covr")
-          remotes::install_bioc("lpsymphony")
-          remotes::install_cran("urlchecker")
+          pak::pkg_install("dickoa/prepr")
         shell: Rscript {0}
 
       - name: Session information
@@ -84,11 +75,6 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Set environmental variables for package checks
-        if: matrix.config.pkgs == 'depends only'
-        run: |
-          echo "_R_CHECK_DEPENDS_ONLY_=true" >> $GITHUB_ENV
-
       - name: Check URLs
         if: runner.os == 'Linux' && matrix.config.r == 'release'
         run: |