Change github actions check file

Author: browaeysrobin

.github/workflows/check-bioc.yml

@@ -51,11 +51,12 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.1', bioc: '3.13', cont: "bioconductor/bioconductor_docker:RELEASE_3_13", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.1', bioc: '3.13'}
-          - { os: windows-latest, r: '4.1', bioc: '3.13'}
+          - { os: ubuntu-latest, r: '4.3', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.3', bioc: '3.17'}
+          - { os: windows-latest, r: '4.3', bioc: '3.17'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM_ROOT: https://packagemanager.posit.co.
       RSPM: ${{ matrix.config.rspm }}
       NOT_CRAN: true
       TZ: UTC
@@ -76,45 +77,54 @@ jobs:
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - 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
+      - name: Restore R package cache
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
+          
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
         run: |
+          apt-get update -y
+          apt-get upgrade -y
+          apt autoremove -y
+          apt-get install libmariadb-dev-compat -y
+          apt-get install libmariadb-dev -y
+          apt-get install libmysqlclient-dev -y
+          apt-get install default-libmysqlclient-dev -y
+          apt-get install libgdal-dev -y
           sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
           echo $sysreqs
           sudo -s eval "$sysreqs"
@@ -153,7 +163,7 @@ jobs:
 
       - name: Set BiocVersion
         run: |
-          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
+          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, update = FALSE)
         shell: Rscript {0}
 
       - name: Install dependencies pass 1
@@ -168,8 +178,10 @@ jobs:
           ## Pass #1 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
           BiocManager::install("limma", update = FALSE)
+          BiocManager::install("ComplexHeatmap", update = FALSE)
           BiocManager::install("sva", update = FALSE)
           BiocManager::install("scran", update = FALSE)
+          remotes::install_cran("circlize")
           remotes::install_cran("tidyverse")
           remotes::install_cran("covr") #### remove this later? this to currently fix the Ubuntu error
           remotes::install_cran("ggraph") 
@@ -222,6 +234,7 @@ jobs:
       - name: Run CMD check
         env:
           _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
         run: |
           rcmdcheck::rcmdcheck(
               args = c("--no-build-vignettes", "--no-manual", "--timings"),
@@ -279,5 +292,5 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-results
           path: check