From 374936c28fc60d283d6d483bd0a14b6256c13d7d Mon Sep 17 00:00:00 2001
From: Bryan Roessler <bryanroessler@gmail.com>
Date: Fri, 2 Aug 2024 19:22:18 -0400
Subject: [PATCH] Restructure R library loading

---
 workflow/qhtcp-workflow | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/workflow/qhtcp-workflow b/workflow/qhtcp-workflow
index 664a07b9..69a602df 100755
--- a/workflow/qhtcp-workflow
+++ b/workflow/qhtcp-workflow
@@ -439,14 +439,18 @@ install_dependencies() {
 
   # Install system-wide dependencies
   echo "Installing system dependencies"
+  echo "You may be prompted for your sudo password to install packages using your system package manager"
   case "$(uname -s)" in
     Linux*|CYGWIN*|MINGW*)
-      ask "Detected Linux platform, continue?" || return 1
-      echo "You may be prompted for your sudo password to install system packages"
       if hash dnf &>/dev/null; then
+        ask "Detected Linux RPM platform, continue?" || return 1
         sudo dnf install "${depends_rpm[@]}"
       elif hash apt &>/dev/null; then
+        ask "Detected Linux DEB platform, continue?" || return 1
         sudo apt install "${depends_deb[@]}"
+      else
+        echo "Sorry, your Linux platform is not supported for automatic dependency installation"
+        echo "You will need to resolve dependencies manually"
       fi
       ;;
     Darwin*)
@@ -478,10 +482,9 @@ install_dependencies() {
   }
   depends_r_to_string
   
-
   # Install R packages
   for d in "${depends_r[@]}"; do
-  debug "$RSCRIPT -e \"if (!require(\"$d\", quietly = TRUE)); install.packages(\"$d\", dep=TRUE, repos=\"https://cloud.r-project.org\")\""
+  debug "$RSCRIPT -e \"if (!require(\"$d\", quietly = TRUE)); {install.packages(\"$d\", dep=TRUE, repos=\"https://cloud.r-project.org\")}\""
     "$RSCRIPT" -e "if (!require(\"$d\", quietly = TRUE)); {install.packages(\"$d\", dep=TRUE, repos=\"https://cloud.r-project.org\")}"
   done