Issue 316 gh action

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

@@ -5,8 +5,6 @@ on:
     branches:
       - main
       - master
-      - GitAction
-
   pull_request:
     branches:
       - main
@@ -24,21 +22,17 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macOS-latest, r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: 'oldrel'}
-
-         #- {os: macOS-latest,   r: 'devel'}
-          - {os: macOS-latest,   r: 'release'}
-
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          # - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
+      KMP_DUPLICATE_LIB_OK: TRUE
     steps:
       - uses: actions/checkout@v2
 
@@ -48,57 +42,78 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v1
 
+      - uses: r-lib/actions/setup-tinytex@master
+
+      - name: Install makeindex
+        run: tlmgr install makeindex
+
       - name: Query dependencies
         run: |
           setwd("DHARMa")
-          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")
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), "../.github/r-depends.rds")
         shell: Rscript {0}
 
-      - name: Cache R packages 
+      - name: Cache R packages
         if: runner.os != 'Windows'
         uses: actions/cache@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-
+          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
+
+      - name: Install curl for r-devel version
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install -y curl
+          sudo apt-get install -y texlive texlive-fonts-extra
 
       - name: Install system dependencies
         if: runner.os == 'Linux'
         run: |
-          cd DHARMa
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          setwd("DHARMa")
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
+        shell: Rscript {0}
 
       - name: Install dependencies
         run: |
           setwd("DHARMa")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install("rcmdcheck")
         shell: Rscript {0}
 
-      - name: Check_II
+      - name: Install Pkg
+        run: |
+          cd DHARMa
+          Rscript -e "pak::local_install()"
+
+      - name: Check I
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
           CI: true
         run: |
-          rcmdcheck::rcmdcheck("DHARMa", args = c("--no-multiarch", "--no-manual"), error_on = "warning", check_dir = "check")
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck("DHARMa", args = c("--no-multiarch", "--no-manual"), error_on = "error", check_dir = "check")
         shell: Rscript {0}
 
-      - name: Check
+      - name: testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Check II
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
           CI: true
         run: |
-          rcmdcheck::rcmdcheck("DHARMa", args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck("DHARMa", args = c("--no-manual", "--as-cran"), error_on = "note", check_dir = "check")
         shell: Rscript {0}
-
+        
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
+          path: check