There was a significant upgrade to the organization of the libraries going from v4 to v5. Unfortunately, the upgrade process doesn’t touch user settings (where the map(s) to the standard libraries are). Thus your install is pointing to the v4 library structure which was removed and replaced with the v5 library structure. Please see this FAQ entry for more details and to help you navigate the manual portion of the upgrade.
You may also want to review this FAQ entry about remapping projects started in v4 to being able to be used in v5. Note, this is a one-way process, keep a backup (a zip archive of the project file should be sufficient) of your v4 project just in case of problems upgrading (so you can return to step 1 if necessary).