Can't connect to MySQL after upgrading OS and packages

I tried an upgrade via my OS’s packages system after a major OS version upgrade. (The OS upgrade prompted this, since there could be incompatible binaries left over which linked to the old version.) Now I can’t get RT working. I think I’m having some sort of database issue, but I’m not sure. Here is what makes me think that.

root@localhost [mysql]> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| mysql              |
| performance_schema |
| rt4                |
| test               |
+--------------------+
5 rows in set (0.00 sec)

root@localhost [mysql]> \r rt4
Connection id:    33
Current database: rt4

root@localhost [rt4]> show tables;
+-------------------------+
| Tables_in_rt4           |
+-------------------------+
| ACL                     |
| Articles                |
| Assets                  |
| Attachments             |
| Attributes              |
| CachedGroupMembers      |
| Catalogs                |
| Classes                 |
| CustomFieldValues       |
| CustomFields            |
| CustomRoles             |
| FM_ArticleCFValues      |
| FM_Articles             |
| FM_ClassCustomFields    |
| FM_Classes              |
| FM_CustomFieldValues    |
| FM_CustomFields         |
| FM_Transactions         |
| GroupMembers            |
| Groups                  |
| Links                   |
| ObjectClasses           |
| ObjectCustomFieldValues |
| ObjectCustomFields      |
| ObjectCustomRoles       |
| ObjectScrips            |
| ObjectTopics            |
| Principals              |
| Queues                  |
| ScripActions            |
| ScripConditions         |
| Scrips                  |
| Templates               |
| Tickets                 |
| Topics                  |
| Transactions            |
| Users                   |
| sessions                |
+-------------------------+
38 rows in set (0.00 sec)

root@localhost [rt4]> select * from Users;
ERROR 1146 (42S02): Table 'rt4.users' doesn't exist
root@localhost [rt4]> select * from users;
ERROR 1146 (42S02): Table 'rt4.users' doesn't exist
root@localhost [rt4]> select * from Tickets;
ERROR 1146 (42S02): Table 'rt4.tickets' doesn't exist
root@localhost [rt4]> 

Any ideas what I might be missing?

More data:

# apachectl configtest
Performing sanity check on apache24 configuration:
[9652] [Thu Dec 10 19:54:16 2020] [warning]: DBD::mysql::st execute failed: Table 'rt4.users' doesn't exist at /usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Handle.pm line 603. (/usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Handle.pm:603)
[9652] [Thu Dec 10 19:54:16 2020] [warning]: RT::Handle=HASH(0x803b06a68) couldn't execute the query 'SELECT  * FROM Users WHERE Name = ?' at /usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Handle.pm line 616.
    DBIx::SearchBuilder::Handle::SimpleQuery(RT::Handle=HASH(0x803b06a68), "SELECT  * FROM Users WHERE Name = ?", "RT_System") called at /usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Record.pm line 1234
    DBIx::SearchBuilder::Record::_LoadFromSQL(RT::CurrentUser=HASH(0x803940690), "SELECT  * FROM Users WHERE Name = ?", "RT_System") called at /usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Record.pm line 1153
    DBIx::SearchBuilder::Record::LoadByCols(RT::CurrentUser=HASH(0x803940690), "Name", "RT_System") called at /usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Record/Cachable.pm line 120
    DBIx::SearchBuilder::Record::Cachable::LoadByCols(RT::CurrentUser=HASH(0x803940690), "Name", "RT_System") called at /usr/local/lib/perl5/site_perl/RT/Record.pm line 376
    RT::Record::LoadByCols(RT::CurrentUser=HASH(0x803940690), "Name", "RT_System") called at /usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Record.pm line 1098
    DBIx::SearchBuilder::Record::LoadByCol(RT::CurrentUser=HASH(0x803940690), "Name", "RT_System") called at /usr/local/lib/perl5/site_perl/RT/User.pm line 588
    RT::User::Load(RT::CurrentUser=HASH(0x803940690), "RT_System") called at /usr/local/lib/perl5/site_perl/RT/Handle.pm line 248
    RT::Handle::CheckIntegrity("RT::Handle") called at /usr/local/sbin/rt-server line 95
    require /usr/local/sbin/rt-server called at (eval 7) line 3
    eval 'package Plack::Sandbox::_2fusr_2flocal_2fsbin_2frt_2dserver;
{
    my $app = do $_file;
    if ( !$app && ( my $error = $@ || $! )) { die $error; }
    $app;
}
' called at /usr/local/lib/perl5/site_perl/Plack/Util.pm line 120
    Plack::Util::_load_sandbox("/usr/local/sbin/rt-server") called at /usr/local/lib/perl5/site_perl/Plack/Util.pm line 136
    Plack::Util::load_psgi("/usr/local/sbin/rt-server") called at /usr/local/lib/perl5/site_perl/Plack/Handler/Apache2.pm line 42
    Plack::Handler::Apache2::load_app("Plack::Handler::Apache2", "/usr/local/sbin/rt-server") called at /usr/local/lib/perl5/site_perl/Plack/Handler/Apache2.pm line 24
    Plack::Handler::Apache2::preload("Plack::Handler::Apache2", "/usr/local/sbin/rt-server") called at /usr/local/etc/apache24/Includes/local.requesttracker.conf line 44
    eval 'package Apache2::ReadConfig::usr::local::etc::apache24::Includes::local_requesttracker_conf::line_43;
#line 43 /usr/local/etc/apache24/Includes/local.requesttracker.conf
use Plack::Handler::Apache2;
Plack::Handler::Apache2->preload("/usr/local/sbin/rt-server");
' called at /usr/local/sbin/rt-server line 0 (/usr/local/lib/perl5/5.32/Carp.pm:294)

RT couldn't connect to the database where tickets are stored.
If this is a new installation of RT, you should visit the URL below
to configure RT and initialize your database.

If this is an existing RT installation, this may indicate a database
connectivity problem.

The error RT got back when trying to connect to your database was:

Couldn't find RT_System user in the DB 'dbi:mysql:dbname=rt4;host=localhost'

[9652] [Thu Dec 10 19:54:22 2020] [warning]: DBD::mysql::st execute failed: Table 'rt4.users' doesn't exist at /usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Handle.pm line 603. (/usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Handle.pm:603)
[9652] [Thu Dec 10 19:54:22 2020] [warning]: RT::Handle=HASH(0x803b06a68) couldn't execute the query 'SELECT  * FROM Users WHERE Name = ?' at /usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Handle.pm line 616.
    DBIx::SearchBuilder::Handle::SimpleQuery(RT::Handle=HASH(0x803b06a68), "SELECT  * FROM Users WHERE Name = ?", "RT_System") called at /usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Record.pm line 1234
    DBIx::SearchBuilder::Record::_LoadFromSQL(RT::CurrentUser=HASH(0x80670ccf0), "SELECT  * FROM Users WHERE Name = ?", "RT_System") called at /usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Record.pm line 1153
    DBIx::SearchBuilder::Record::LoadByCols(RT::CurrentUser=HASH(0x80670ccf0), "Name", "RT_System") called at /usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Record/Cachable.pm line 120
    DBIx::SearchBuilder::Record::Cachable::LoadByCols(RT::CurrentUser=HASH(0x80670ccf0), "Name", "RT_System") called at /usr/local/lib/perl5/site_perl/RT/Record.pm line 376
    RT::Record::LoadByCols(RT::CurrentUser=HASH(0x80670ccf0), "Name", "RT_System") called at /usr/local/lib/perl5/site_perl/DBIx/SearchBuilder/Record.pm line 1098
    DBIx::SearchBuilder::Record::LoadByCol(RT::CurrentUser=HASH(0x80670ccf0), "Name", "RT_System") called at /usr/local/lib/perl5/site_perl/RT/User.pm line 588
    RT::User::Load(RT::CurrentUser=HASH(0x80670ccf0), "RT_System") called at /usr/local/lib/perl5/site_perl/RT/Handle.pm line 248
    RT::Handle::CheckIntegrity("RT::Handle") called at /usr/local/lib/perl5/site_perl/RT.pm line 786
    RT::InstallMode("RT", 1) called at /usr/local/sbin/rt-server line 124
    require /usr/local/sbin/rt-server called at (eval 7) line 3
    eval 'package Plack::Sandbox::_2fusr_2flocal_2fsbin_2frt_2dserver;
{
    my $app = do $_file;
    if ( !$app && ( my $error = $@ || $! )) { die $error; }
    $app;
}
' called at /usr/local/lib/perl5/site_perl/Plack/Util.pm line 120
    Plack::Util::_load_sandbox("/usr/local/sbin/rt-server") called at /usr/local/lib/perl5/site_perl/Plack/Util.pm line 136
    Plack::Util::load_psgi("/usr/local/sbin/rt-server") called at /usr/local/lib/perl5/site_perl/Plack/Handler/Apache2.pm line 42
    Plack::Handler::Apache2::load_app("Plack::Handler::Apache2", "/usr/local/sbin/rt-server") called at /usr/local/lib/perl5/site_perl/Plack/Handler/Apache2.pm line 24
    Plack::Handler::Apache2::preload("Plack::Handler::Apache2", "/usr/local/sbin/rt-server") called at /usr/local/etc/apache24/Includes/local.requesttracker.conf line 44
    eval 'package Apache2::ReadConfig::usr::local::etc::apache24::Includes::local_requesttracker_conf::line_43;
#line 43 /usr/local/etc/apache24/Includes/local.requesttracker.conf
use Plack::Handler::Apache2;
Plack::Handler::Apache2->preload("/usr/local/sbin/rt-server");
' called at /usr/local/sbin/rt-server line 0 (/usr/local/lib/perl5/5.32/Carp.pm:294)
[9652] [Thu Dec 10 19:54:23 2020] [warning]:    (in cleanup) Error while loading /usr/local/sbin/rt-server: Can't locate RTx/Calendar.pm in @INC (you may need to install the RTx::Calendar module) (@INC contains: /usr/local/share/rt44/lib /usr/local/lib/perl5/site_perl /usr/local/lib/perl5/site_perl/mach/5.32 /usr/local/lib/perl5/5.32/mach /usr/local/lib/perl5/5.32 /usr/local) at /usr/local/lib/perl5/site_perl/RT.pm line 775. (/usr/local/lib/perl5/site_perl/RT.pm:410)
AH00526: Syntax error on line 43 of /usr/local/etc/apache24/Includes/local.requesttracker.conf:
Can't locate RTx/Calendar.pm in @INC (you may need to install the RTx::Calendar module) (@INC contains: /usr/local/share/rt44/lib /usr/local/lib/perl5/site_perl /usr/local/lib/perl5/site_perl/mach/5.32 /usr/local/lib/perl5/5.32/mach /usr/local/lib/perl5/5.32 /usr/local) at /usr/local/lib/perl5/site_perl/RT.pm line 775.\n
root@its1:/usr/local/etc #

Which version of MySQL did you upgrade to?

I upgraded from MySQL server 5.6.43 to 5.7.32.

Maybe one of these options, seems you need to upgrade the databases in MySQL:

I figured out a work-around. I had to comment out two settings: innodb_data_file_path (to get the server started) and lower_case_table_names (to let it see tables with capital letters in them, like Users.)