Merge pull request SyneRBI#876 from KrisThielemans/update_VM_STIR_fix

VM update script updates

Author: KrisThielemans

VirtualBox/documentation/Basic-usage.md

@@ -86,9 +86,12 @@ We  provide a script to update an existing VM to a new version of course softwar
 
 If you have decided to upgrade your existing VM, type the following in a terminal
 
+     cd ~/devel
+     rm -rf install/lib install/include
+     rm -rf buildVM
      update_VM.sh -s
 
-The `-s` option will update your system dependencies via APT.
+The `-s` option will update your system dependencies via APT. If you are a developer and have made specific changes to your system, you might not want to execute the steps removing existing files.
 
 The script has some additional options for advanced usage only. For instance, if you
 are a developer and want to use the latest version of the software and want

VirtualBox/scripts/UPDATE.sh

@@ -82,6 +82,11 @@ if [ -d $SIRF_SRC_PATH/SyneRBI_VM ]; then
     echo '======================================================'
 fi
 
+# Remove old installed STIR version
+# See https://github.com/SyneRBI/SIRF-SuperBuild/issues/869
+rm -rf "$SIRF_INSTALL_PATH"/include/stir
+rm -f "$SIRF_INSTALL_PATH"/lib/STIR*.cmake
+
 # Checkout correct version of the SuperBuild
 SuperBuild_git_update "$SB_TAG"
 

VirtualBox/scripts/UPDATE_functions.sh

@@ -36,7 +36,11 @@ print_usage(){
   echo "   Otherwise the most recent release will be used."
   echo "Use the -j option to change the number of parallel builds from the default ${num_parallel}"
   echo "Use the -s option to update and install necessary system and Python components."
-  echo "  We recommend to do this once when upgrading between major versions."
+  echo "   We recommend to do this once when upgrading between major versions."
+  echo "We also recommend to remove all previously installed files before running this script:"
+  echo "   rm -rf ~/devel/install/lib ~/devel/install/include"
+  echo "If you experience problems, you could even remove previous build files:"
+  echo "   rm -rf ~/devel/buildVM/"
 }
 
 # process any options and set env variables