You should not run tests or models in the GAMS system directory.
Instead of doing this, you should create a directory somewhere to run model or tests. Use the GAMSIDE to create a project directory at another location.
If you are using the command line interface enter:
mkdir \models\temp cd \models\temp gamslib trnsport ...
At best running in the GAMS sysdir will create a clutter of temp files there that you can't distinguish from the real system files. At worst, it could delete or alter some system files.