Hello, Could you please explain the meaning of this warning:

Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.

to me that I got using the makeTxDbFromGFF function? Thank you.

See here for the GFF specification, in particular the part about column 8. By definition having anything in column 8 of a GFF for a stop codon is meaningless.