UPDATE

uniofessex · Aug 18, 2024 · 651f0b4 · 651f0b4
1 parent 43ff96e
commit 651f0b4
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Showing 2 changed files with 45 additions and 17 deletions.
diff --git a/.github/workflows/mac_r.yml b/.github/workflows/mac_r.yml
@@ -30,9 +30,17 @@ jobs:
       - name: Install JAGS on macOS
         run: brew install jags
 
-      - name: Install gfortran for ARM (M1/M2)
+      - name: Install gcc (includes gfortran)
         run: brew install gcc
 
+      - name: Ensure gfortran is in PATH
+        run: |
+          echo "/opt/homebrew/bin" >> $GITHUB_PATH
+          echo "/opt/homebrew/opt/gcc/bin" >> $GITHUB_PATH
+
+      - name: Check gfortran installation
+        run: gfortran --version
+
       - name: Set up R ${{ matrix.r-version }}
         uses: r-lib/actions/setup-r@v2
         with:
@@ -43,34 +51,49 @@ jobs:
           Rscript -e "install.packages('tinytex')"
           Rscript -e "tinytex::install_tinytex()"
 
+      - name: Set CRAN mirror
+        run: |
+          Rscript -e "options(repos = c(CRAN = 'https://cloud.r-project.org/'))"
+        shell: Rscript {0}
+
       - name: Install remotes package
         run: |
           Rscript -e "install.packages('remotes')"
 
       - name: Install package dependencies
         run: |
-          Rscript -e "install.packages(c('smacof', 'ellipse', 'plyr', 'vegan'), dependencies=TRUE)"
+          Rscript -e "install.packages(c('smacof', 'vegan'), dependencies = TRUE)"
+        shell: Rscript {0}
 
       - name: Install basicspace from GitHub
         env:
-          GITHUB_PAT: ${{ secrets.MY_GITHUB_PAT }}
+          GITHUB_PAT: ${{ secrets.GITHUB_PAT }}
         run: |
           Rscript -e "remotes::install_github('cran/basicspace', force = TRUE)"
+        shell: Rscript {0}
 
-      - name: Set CRAN mirror and install other R package dependencies
-        env:
-          GITHUB_PAT: ${{ secrets.MY_GITHUB_PAT }}
+      - name: Install other R package dependencies
         run: |
-          Rscript -e "options(repos = c(CRAN = 'https://cloud.r-project.org/')); install.packages(c('rjags', 'ggplot2', 'knitr'));"
+          Rscript -e "install.packages(c('rjags', 'ggplot2', 'knitr'))"
+        shell: Rscript {0}
 
       - name: Install rcmdcheck package
         run: |
           Rscript -e "install.packages('rcmdcheck')"
+        shell: Rscript {0}
 
       - name: Check
         run: |
           Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'error')"
+        shell: Rscript {0}
 
       - name: Test (optional)
         run: |
           Rscript -e "devtools::test()"
+        shell: Rscript {0}
+
+    env:
+      R_LIBS_USER: /Users/runner/work/_temp/Library
+      TZ: UTC
+      _R_CHECK_SYSTEM_CLOCK_: FALSE
+      NOT_CRAN: true
diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml
@@ -14,7 +14,7 @@ on:
     branches: [ "master" ]
 
 permissions:
-  contents: read 
+  contents: read
 
 jobs:
   build:
@@ -34,52 +34,57 @@ jobs:
           choco install rtools
         shell: cmd
 
+      - name: Verify JAGS installation
+        run: jags --version
+        shell: cmd
+
       - name: Set up R ${{ matrix.r-version }}
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.r-version }}
 
       - name: Install remotes package
         run: |
-          Rscript -e \"install.packages('remotes')\"
+          Rscript -e "install.packages('remotes')"
         shell: cmd
 
-      - name: Install package dependencies
+      - name: Install CRAN packages including rjags
         run: |
-          Rscript -e \"install.packages(c('smacof', 'ellipse', 'plyr', 'vegan'))\"
+          Rscript -e "options(repos = 'https://cloud.r-project.org/')"
+          Rscript -e "install.packages('rjags')"
+          Rscript -e "install.packages(c('smacof', 'ellipse', 'plyr', 'vegan'), dependencies=TRUE)"
         shell: cmd
 
       - name: Install basicspace from GitHub
         env:
           GITHUB_PAT: ${{ secrets.MY_GITHUB_PAT }}
         run: |
-          Rscript -e \"remotes::install_github('cran/basicspace', force = TRUE)\"
+          Rscript -e "remotes::install_github('cran/basicspace', force = TRUE)"
         shell: cmd
 
       - name: Set CRAN mirror and install other R package dependencies
         env:
           GITHUB_PAT: ${{ secrets.MY_GITHUB_PAT }}
         run: |
-          Rscript -e \"options(repos = c(CRAN = 'https://cloud.r-project.org/')); install.packages(c('rjags', 'ggplot2', 'knitr'))\"
+          Rscript -e "options(repos = c(CRAN = 'https://cloud.r-project.org/')); install.packages(c('ggplot2', 'knitr'));"
         shell: cmd
 
       - name: Install rcmdcheck package
         run: |
-          Rscript -e \"install.packages('rcmdcheck')\"
+          Rscript -e "install.packages('rcmdcheck')"
         shell: cmd
 
       - name: Check
         run: |
-          Rscript -e \"rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'error')\"
+          Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'error')"
         shell: cmd
 
       - name: Test (optional)
         run: |
-          Rscript -e \"devtools::test() \"
+          Rscript -e "devtools::test()"
         shell: cmd
 
     env:
       TZ: UTC
       _R_CHECK_SYSTEM_CLOCK_: FALSE
       NOT_CRAN: true
-