Lo resolví...
La consulta debe tener este aspecto:
@Query(
value = "SELECT * FROM \n" +
"(institution INNER JOIN user ON institution.user_id = user.id) \n" +
"LEFT JOIN \n" +
"(SELECT * FROM \n" +
"building_institutions \n" +
"WHERE building_id = :userId)\n" +
" AS reserved_institutions \n" +
"ON reserved_institutions.institutions_user_id = kits_nwt.institution.user_id \n" +
" where reserved_institutions.institutions_user_id IS null \n"
+ "ORDER BY ?#{#pageable}"
,
countQuery = "SELECT count(*) FROM \n" +
"(institution INNER JOIN user ON institution.user_id = user.id) \n" +
"LEFT JOIN \n" +
"(SELECT * FROM \n" +
"building_institutions \n" +
"WHERE building_id =:userId)\n" +
" AS reserved_institutions \n" +
"ON reserved_institutions.institutions_user_id = kits_nwt.institution.user_id \n" +
"where reserved_institutions.institutions_user_id IS null \n" +
"ORDER BY ?#{#pageable}",
nativeQuery = true)
Page<Institution> findPotentialInstitutionsByBuildingId(@Param("userId") Long userId, Pageable pageable);
Estaba recibiendo el error en la línea 4 cerca de DONDE, cuando mi consulta se veía así:
@Query(
value = "SELECT username, password, description, location, title, user_id FROM (institution INNER JOIN user ON institution.user_id = user.id) LEFT JOIN\n" +
"(SELECT * FROM building_institutions WHERE building_institutions.building_id = 1) AS reserved_institutions\n" +
"ON reserved_institutions.institutions_user_id = kits_nwt.institution.user_id\n" +
"WHERE reserved_institutions.institutions_user_id IS null ORDER BY ?#{#pageable}",
nativeQuery = true)
Page<Institution> findPotentialInstitutionsByBuildingId(Long userId, Pageable pageable);
y eso fue porque no agregué countQuery
parámetro a @Query
anotación.
Muchas gracias a todos los que intentaron ayudar.
Espero que le ahorre a alguien más muchas horas de miseria.
¡Salud! :)