changed R CMD check workflow etc

jr-leary7 · Nov 24, 2023 · d9483be · d9483be
1 parent 94cb5ba
commit d9483be
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Showing 3 changed files with 12 additions and 9 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -26,20 +26,16 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-
       - name: Checkout repo
         uses: actions/checkout@v3
-
       - name: Setup Pandoc
         uses: r-lib/actions/setup-pandoc@v2
-
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-
       - name: Setup dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -50,7 +46,10 @@ jobs:
         run: |
           install.packages("Matrix", type = "source", force = TRUE)
           install.packages("irlba", type = "source", force = TRUE)
-
+          install.packages("TMB", type = "source", force = TRUE)
+          install.packages("glmmTMB", type = "source", force = TRUE)
+        shell: Rscript {0}
+        working-directory: '.'
       - name: Check
         id: rcmdcheck
         run: |
@@ -60,7 +59,6 @@ jobs:
           check_results <- rcmdcheck::rcmdcheck(args = c("--no-vignettes", "--no-manual", "--as-cran"), build_args = c("--no-build-vignettes", "--no-manual"), check_dir = "check", error_on = "error")
         shell: Rscript {0}
         working-directory: '.'
-
       - name: Show testthat output
         if: always()
         run: |
@@ -70,14 +68,12 @@ jobs:
           echo ::endgroup::
         shell: bash
         working-directory: '.'
-
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@v3
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: ${{ steps.rcmdcheck.outputs.check-dir-path }}
-
       - name: Upload snapshots
         uses: actions/upload-artifact@v3
         with:

diff --git a/.github/workflows/render-README.yaml b/.github/workflows/render-README.yaml
@@ -20,9 +20,16 @@ jobs:
           use-public-rspm: true
       - uses: r-lib/actions/setup-r-dependencies@v2
       - uses: r-lib/actions/setup-pandoc@v2
-
       - name: install CRAN packages
         run: Rscript -e 'install.packages(c("rmarkdown","ggplot2", "dplyr", "purrr", "remotes", "devtools", "BiocManager", "Seurat"), force = TRUE)'
+      - name: Extra dependencies
+        id: extra-deps
+        run: |
+          install.packages("Matrix", type = "source", force = TRUE)
+          install.packages("irlba", type = "source", force = TRUE)
+          install.packages("TMB", type = "source", force = TRUE)
+          install.packages("glmmTMB", type = "source", force = TRUE)
+        shell: Rscript {0}
       - name: install BioConductor packages
         run: Rscript -e 'BiocManager::install(c("SingleCellExperiment", "scater", "scran", "scuttle", "bluster"), force = TRUE)'
       - name: install GitHub packages