fix system dependencies and ubuntu version

Author: lpantano

.github/workflows/run_visium_qc.yaml

@@ -1,4 +1,4 @@
-name: R Restore and Run
+name: Visium Quality Control
 
 on:
   push:
@@ -8,7 +8,7 @@ on:
 
 jobs:
   r-restore:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-noble
 
     env:
       RENV_PATHS_ROOT: ~/.local/share/renv  # persistent cache location
@@ -20,6 +20,12 @@ jobs:
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
 
+      - name: Install system dependencies for R packages
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev
+        shell: bash
+
       - name: Cache R packages (renv)
         uses: actions/cache@v4
         with:
@@ -28,6 +34,9 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-renv-
 
+      - name: Set repositories
+        run: Rscript ubuntu.R
+
       - name: Restore environment from renv.lock
         run: |
           install.packages("renv", repos = "https://cloud.r-project.org")

ubuntu.R

@@ -0,0 +1,11 @@
+# Configure BiocManager to use Posit Package Manager
+options(BioC_mirror = "https://packagemanager.posit.co/bioconductor/latest")
+
+# Configure BiocManager to load its configuration from Package Manager
+options(BIOCONDUCTOR_CONFIG_FILE = "https://packagemanager.posit.co/bioconductor/latest/config.yaml")
+
+# Set the Bioconductor version to prevent defaulting to a newer version
+Sys.setenv("R_BIOC_VERSION" = "3.22")
+
+# Configure a CRAN snapshot compatible with Bioconductor 3.22
+options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/noble/latest"))