chore(repositories): changed R package manager behavior

Author: phlg

base/scripts/onyxia-set-repositories.sh

@@ -26,20 +26,39 @@ if command -v uv &>/dev/null; then
 fi
 
 # R configuration
-
 if command -v R &>/dev/null; then
   if [[ -n "$R_REPOSITORY" ]] || [[ -n "$PACKAGE_MANAGER_URL" ]]; then
       echo "configuration r (add local repository)"
 
-      echo '# https://docs.rstudio.com/rspm/admin/serving-binaries/#binaries-r-configuration-linux' >> ${R_HOME}/etc/Rprofile.site
-      echo 'options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"])))' >> ${R_HOME}/etc/Rprofile.site
+      # /!\ Possible regression point for other users depending on this code.
+      # The rocker image used as base injects a repository based on the CRAN environment variable, see for instance
+      # https://github.com/rocker-org/rocker-versioned2/blob/677573589638617e04cad971ceafef84d5004f10/scripts/setup_R.sh#L34
+      # This behavior might be unwanted when using an internal repository (eg: Nexus) instead of the public Posit
+      # Package Manager instance. As such, when the PACKAGE_MANAGER_URL variable is set, we should overwrite
+      # the Rprofile.site instead of appending to it. But as there might be unforeseen use cases where this
+      # change could trigger problems, so I'm flagging this as such.
+      if [[ -n "$PACKAGE_MANAGER_URL" ]]; then
+        echo '# Rocker default configuration removed by /opt/onyxia-set-repositories.sh' > ${R_HOME}/etc/Rprofile.site
+
+        # The unwanted behavior is setting options("repos"), but we might want to keep the user agent change from Rocker,
+        # as this can potentially be used depending on how the local package manager is configured.
+        echo '# https://docs.rstudio.com/rspm/admin/serving-binaries/#binaries-r-configuration-linux' >> ${R_HOME}/etc/Rprofile.site
+        echo 'options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"])))' >> ${R_HOME}/etc/Rprofile.site
+      fi
+      
       echo '# Proxy repository for R' >> ${R_HOME}/etc/Rprofile.site
       echo 'local({' >> ${R_HOME}/etc/Rprofile.site
       echo '  r <- getOption("repos")' >> ${R_HOME}/etc/Rprofile.site
 
       if [[ -n "$PACKAGE_MANAGER_URL" ]]; then
-          UBUNTU_CODENAME=$(cat /etc/lsb-release | grep DISTRIB_CODENAME | cut -d= -f2)
-          echo "  r[\"PackageManager\"] <- \"${PACKAGE_MANAGER_URL}/${UBUNTU_CODENAME}/latest\"" >> ${R_HOME}/etc/Rprofile.site
+
+        UBUNTU_CODENAME=$(cat /etc/lsb-release | grep DISTRIB_CODENAME | cut -d= -f2)
+        # Moving from "/__linux__/" style URLs to "/bin/linux" style URLS for PACKAGE_MANAGER_URL,
+        # as this allows easier management for local package managers (at least Nexus, where it allows
+        # using a single repository as opposed to one per major.minor version of R)
+        # See also : https://docs.posit.co/rspm/admin/serving-binaries.html#using-linux-binary-packages
+        #echo "  r[\"PackageManager\"] <- \"${PACKAGE_MANAGER_URL}/${UBUNTU_CODENAME}/latest\"" >> ${R_HOME}/etc/Rprofile.site
+        echo "  r[\"PackageManager\"] <- sprintf(\"${PACKAGE_MANAGER_URL}/latest/bin/linux/${UBUNTU_CODENAME}-%s/%s\", R.version[\"arch\"], substr(getRversion(), 1, 3))" >> ${R_HOME}/etc/Rprofile.site
       fi
 
       if [[ -n "$R_REPOSITORY" ]]; then