I'm having the same problem on Ubuntu Linux 14.04 with QSys 13.1 and the FIFOED avalon uart failing to generate. The same project generates/compiles fine on a Windows Quartus II/QSys 13.1 installation on the same computer. Was there a resolution for this?
Error: fifoed_avalon_uart_0: Generation callback did not provide a top level file (expected `add_file $output_dir/soc_system_fifoed_avalon_uart_0.v|vhd|sv {SIMULATION SYNTHESIS}`)
Error: fifoed_avalon_uart_0: syntax error at /home/xxx/altera/13.1/quartus/sopc_builder/bin//europa/e_lpm_altsyncram.pm line 203, near ")"
(Might be a runaway multi-line () string starting on line 197)
syntax error at /home/xxx/altera/13.1/quartus/sopc_builder/bin//europa/e_lpm_altsyncram.pm line 207, near "}"
Global symbol "$this" requires explicit package name at /home/xxx/altera/13.1/quartus/sopc_builder/bin//europa/e_lpm_altsyncram.pm line 222.
syntax error at /home/xxx/altera/13.1/quartus/sopc_builder/bin//europa/e_lpm_altsyncram.pm line 248, near "}"
Compilation failed in require at /home/xxx/altera/13.1/quartus/sopc_builder/bin//europa/europa_all.pm line 203.
BEGIN failed--compilation aborted at /home/xxx/altera/13.1/quartus/sopc_builder/bin//europa/europa_all.pm line 203.
Compilation failed in require at mk_em_uart_sa.pl line 8.
BEGIN failed--compilation aborted at mk_em_uart_sa.pl line 8.
while executing
"exec perl -I . -I /home/xxx/altera/13.1/quartus/sopc_builder/bin/ -I /home/xxx/altera/13.1/quartus/sopc_builder/bin//europa/ -I /home/xxx/..."
("eval" body line 1)
invoked from within
"eval $exec_list"
(procedure "generate" line 70)
invoked from within
"generate"