SQLite error 'attempt to write a readonly database' during insert?

This can happen when the owner of the SQLite file itself is not the same as the user running the script. Similar errors can occur if the entire directory path (meaning each directory along the way) can't be written to.

Who owns the SQLite file? You?

Who is the script running as? Apache or Nobody?

For me the issue was SELinux enforcement rather than permissions. The "read only database" error went away once I disabled enforcement, following the suggestion made by Steve V. in a comment on the accepted answer.

echo 0 >/selinux/enforce

Upon running this command, everything worked as intended (CentOS 6.3).

The specific issue I had encountered was during setup of Graphite. I had triple-checked that the apache user owned and could write to both my graphite.db and its parent directory. But until I "fixed" SELinux, all I got was a stack trace to the effect of: DatabaseError: attempt to write a readonly database

The problem, as it turns out, is that the PDO SQLite driver requires that if you are going to do a write operation (INSERT,UPDATE,DELETE,DROP, etc), then the folder the database resides in must have write permissions, as well as the actual database file.

I found this information in a comment at the very bottom of the PDO SQLite driver manual page.