Merge pull request #300 from nmfs-opensci/unbound-vars

Unbound vars

Author: eeholmes

scripts/fix-home-permissions.sh

@@ -1,5 +1,6 @@
 #!/bin/bash
 # Required User: root
+set -euo pipefail
 
 echo "Running fix-home-permissions.sh"
 

scripts/install-r-packages.sh

@@ -18,6 +18,12 @@ fi
 # Main script execution as NB_USER
 echo "Running install-r-packages.sh as ${NB_USER}"
 
+# Get R_HOME from R itself if not already set
+if [[ -z "${R_HOME:-}" ]]; then
+    export R_HOME="$(R RHOME)"
+    echo "  R_HOME set to: ${R_HOME}"
+fi
+
 # Make sure we install to the site-library
 echo ".libPaths('${R_HOME}/site-library')" > /tmp/rprofile.site
 export R_PROFILE=/tmp/rprofile.site

scripts/run-postbuild.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+set -euo pipefail
 
 echo "Running run-postbuild.sh"
 

scripts/setup-desktop.sh

@@ -4,7 +4,7 @@
 # First we are altering the user directiory which seems rude, second orphan desktop files might be in ~/Desktop so who knows
 # what the user Desktop experience with be, here the Desktop dir is set to /usr/share/Desktop so is part of the image.
 # users that want to customize Desktop can change /etc/xdg/user-dirs.dirs though py-rocket resets that each time the server is restarted.
-set -e
+set -euo pipefail
 
 # Check if the script is run as root
 if [[ $(id -u) -ne 0 ]]; then

scripts/setup-start.sh

@@ -1,5 +1,6 @@
 #!/bin/bash
 # Required User: NB_USER
+set -euo pipefail
 
 # Check if a filename argument is provided
 if [ -z "$1" ]; then