The warnings during the make process are normal, and as long as the executable was generated successfully you don't need to care about them.
The error probably shows up because you are using a fix nvt/npt/nph command incorrectly (just like the error message states). When you get errors like this after updating LAMMPS, always check the "Newest features and bug fixes" page to see what is updated in the previous versions:
Scroll down to 7 Apr 2010, and you will see that there have been changes to the fix nvt/npt/nph commands, and that "the syntax for the old commands is not allowed in the new commands".
So in the future, if you get errors by running scripts that worked before, please have a look at the above page first.
Hope this helps solving your problem.