don't know anything about calibre
taking a stab in the dark
WARNING: Cell <cell name> is referenced but not defined. Empty cell used
you used a cell name that was not previously defined.
such as putting a variable in an equation when you did not specify anything about the variable earlier
WARNING: Cell <cell name> already exists, will overwrite
this seems like you defined the same variable name (cell name) twice
both or either may be the result of a misspelled cell name
Assuming you are using calibre for DRC, these errors happen when you generate broken GDS. Maybe the reason is a library is missing, maybe the reasons is two libraries have cells with the same name.