Variables (such as GSL_DIR) which are set at configure time are not checked immediately, but instead only lead to errors if they are incorrect at CST or even worse at thorn-build time. This leads to a lot of wasted time when trying out new options, especially if multiple libraries (HDF5, GSL, etc) need to be built.
One solution would be for thorns to provide a script which checked that its variables were set correctly. For example it could check that the directory existed and contained the required libraries. This script would be called at configure time.