So my logger has not worked for a long time.
So I decided to re-install just the logger package and didn't solve the problem.
So I decided to re-install the same version of zimbra ontop of an existing working install.
Well things didn't work very well.
Now nothing starts.

Given that the log files fill with all kinds of stuff that are not really errors, is there something in this log file that is an error that should not be ignored?

PS. I created snapshots of the vmware image and tried these installs.



Code:
COMMAND: zmlocalconfig -s | sed -e "s/ = \(.*\)/=\'\1\'/" > /opt/zimbra/.saveconfig/config.save
COMMAND: zmcontrol shutdown
Host mail.DOMAIN.com
	Stopping stats...Done
	Stopping mta...Done
	Stopping spell...Done
	Stopping snmp...Done
	Stopping antivirus...Done
	Stopping antispam...Done
	Stopping imapproxy...Done
	Stopping mailbox...Done
	Stopping logger...Done
	Stopping ldap...Done
Preparing packages for installation...
zimbra-core-4.5.11_GA_1751.RHEL5-20080128142638
mkdir: cannot create directory `/opt/zimbra/ssl': File exists
mkdir: cannot create directory `/opt/zimbra/.ssh': File exists
mkdir: cannot create directory `/opt/zimbra/zmstat': File exists
find: /opt/zimbra/lib/ext-common: No such file or directory
find: /opt/zimbra/lib/ext-common: No such file or directory
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: cannot access `/opt/zimbra/openldap/etc': No such file or directory
chown: cannot access `/opt/zimbra/openldap/var': No such file or directory
chmod: missing operand after `755'
Try `chmod --help' for more information.
chown: cannot access `/opt/zimbra/amavisd/sbin': No such file or directory
chown: cannot access `/opt/zimbra/tomcat/bin': No such file or directory
chmod: cannot access `/opt/zimbra/postfix/conf/postfix-script': No such file or directory
chmod: cannot access `/opt/zimbra/postfix/conf/post-install': No such file or directory
Loading classes to share ... done. 
Rewriting and unlinking classes ... done. 
Calculating hash values for String objects .. done. 
Calculating fingerprints ... done. 
Removing unshareable information ... done. 
Moving pre-ordered read-only objects to shared space at 0x94250000 ... done. 
Moving read-only objects to shared space at 0x9466c230 ... done. 
Moving common symbols to shared space at 0x9466dba8 ... done. 
Moving remaining symbols to shared space at 0x94735b88 ... done. 
Moving string char arrays to shared space at 0x947367f8 ... done. 
Moving additional symbols to shared space at 0x947cd068 ... done. 
Read-only space ends at 0x94833310, 6173456 bytes.
Moving pre-ordered read-write objects to shared space at 0x94a50000 ... done. 
Moving read-write objects to shared space at 0x950c7100 ... done. 
Moving String objects to shared space at 0x95104680 ... done. 
Read-write space ends at 0x95148570, 7308656 bytes.
Updating references to shared objects ... done. 

Preparing packages for installation...
zimbra-ldap-4.5.11_GA_1751.RHEL5-20080128142638
find: /opt/zimbra/lib/ext-common: No such file or directory
find: /opt/zimbra/lib/ext-common: No such file or directory
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: cannot access `/opt/zimbra/amavisd/sbin': No such file or directory
chown: cannot access `/opt/zimbra/tomcat/bin': No such file or directory
chmod: cannot access `/opt/zimbra/postfix/conf/postfix-script': No such file or directory
chmod: cannot access `/opt/zimbra/postfix/conf/post-install': No such file or directory
Preparing packages for installation...
zimbra-logger-4.5.11_GA_1751.RHEL5-20080128142638
find: /opt/zimbra/lib/ext-common: No such file or directory
find: /opt/zimbra/lib/ext-common: No such file or directory
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: cannot access `/opt/zimbra/amavisd/sbin': No such file or directory
chown: cannot access `/opt/zimbra/tomcat/bin': No such file or directory
chmod: cannot access `/opt/zimbra/postfix/conf/postfix-script': No such file or directory
chmod: cannot access `/opt/zimbra/postfix/conf/post-install': No such file or directory
Preparing packages for installation...
zimbra-mta-4.5.11_GA_1751.RHEL5-20080128142638
umount2: Invalid argument
umount: /opt/zimbra/amavisd/tmp: not mounted
find: /opt/zimbra/lib/ext-common: No such file or directory
find: /opt/zimbra/lib/ext-common: No such file or directory
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: cannot access `/opt/zimbra/tomcat/bin': No such file or directory
Preparing packages for installation...
zimbra-snmp-4.5.11_GA_1751.RHEL5-20080128142638
find: /opt/zimbra/lib/ext-common: No such file or directory
find: /opt/zimbra/lib/ext-common: No such file or directory
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: missing operand after `root:root'
Try `chown --help' for more information.
chown: cannot access `/opt/zimbra/tomcat/bin': No such file or directory
Preparing packages for installation...
zimbra-store-4.5.11_GA_1751.RHEL5-20080128142638
chmod: cannot access `/opt/zimbra/logs': No such file or directory
Preparing packages for installation...
zimbra-apache-4.5.11_GA_1751.RHEL5-20080128142638
find: /opt/zimbra/lib/ext-common: No such file or directory
find: /opt/zimbra/lib/ext-common: No such file or directory
Preparing packages for installation...
zimbra-spell-4.5.11_GA_1751.RHEL5-20080128142638
find: /opt/zimbra/lib/ext-common: No such file or directory
find: /opt/zimbra/lib/ext-common: No such file or directory
COMMAND: zmlocalconfig -f -e av_notify_user='admin@DOMAIN.com'
COMMAND: zmlocalconfig -f -e calendar_entourage_compatible_timezones='true'
COMMAND: zmlocalconfig -f -e calendar_outlook_compatible_allday_events='true'
COMMAND: zmlocalconfig -f -e data_source_trust_self_signed_certs='false'
COMMAND: zmlocalconfig -f -e debug_mailboxindex_use_new_locking='true'
COMMAND: zmlocalconfig -f -e ldap_cache_account_maxage='15'
COMMAND: zmlocalconfig -f -e ldap_cache_account_maxsize='5000'
COMMAND: zmlocalconfig -f -e ldap_cache_cos_maxage='15'
COMMAND: zmlocalconfig -f -e ldap_cache_cos_maxsize='100'
COMMAND: zmlocalconfig -f -e ldap_cache_domain_maxage='15'
COMMAND: zmlocalconfig -f -e ldap_cache_domain_maxsize='100'
COMMAND: zmlocalconfig -f -e ldap_cache_server_maxage='15'
COMMAND: zmlocalconfig -f -e ldap_cache_server_maxsize='100'
COMMAND: zmlocalconfig -f -e ldap_cache_timezone_maxsize='100'
COMMAND: zmlocalconfig -f -e ldap_cache_zimlet_maxage='15'
COMMAND: zmlocalconfig -f -e ldap_cache_zimlet_maxsize='100'
COMMAND: zmlocalconfig -f -e ldap_connect_pool_debug='false'
COMMAND: zmlocalconfig -f -e ldap_connect_pool_initsize='1'
COMMAND: zmlocalconfig -f -e ldap_connect_pool_master='false'
COMMAND: zmlocalconfig -f -e ldap_connect_pool_maxsize='50'
COMMAND: zmlocalconfig -f -e ldap_connect_pool_prefsize='0'
COMMAND: zmlocalconfig -f -e ldap_connect_pool_timeout='120000'
COMMAND: zmlocalconfig -f -e ldap_connect_timeout='30000'
COMMAND: zmlocalconfig -f -e ldap_host='mail.DOMAIN.com'
COMMAND: zmlocalconfig -f -e ldap_is_master='true'
COMMAND: zmlocalconfig -f -e ldap_log_level='32768'
COMMAND: zmlocalconfig -f -e ldap_master_url='ldap://mail.DOMAIN.com:389'
COMMAND: zmlocalconfig -f -e ldap_port='389'
COMMAND: zmlocalconfig -f -e ldap_root_password='PASS'
COMMAND: zmlocalconfig -f -e ldap_url='ldap://mail.DOMAIN.com:389'
COMMAND: zmlocalconfig -f -e localized_msgs_directory='${zimbra_home}/conf/msgs'
COMMAND: zmlocalconfig -f -e logger_mysql_bind_address='localhost'
COMMAND: zmlocalconfig -f -e logger_mysql_data_directory='${zimbra_home}/logger/db/data'
COMMAND: zmlocalconfig -f -e logger_mysql_directory='${zimbra_home}/logger/mysql'
COMMAND: zmlocalconfig -f -e logger_mysql_mycnf='${zimbra_home}/conf/my.logger.cnf'
COMMAND: zmlocalconfig -f -e logger_mysql_pidfile='${zimbra_home}/logger/db/mysql.pid'
COMMAND: zmlocalconfig -f -e logger_mysql_port='7307'
COMMAND: zmlocalconfig -f -e logger_mysql_socket='${zimbra_home}/logger/db/mysql.sock'
COMMAND: zmlocalconfig -f -e mysql_bind_address='localhost'
COMMAND: zmlocalconfig -f -e mysql_data_directory='${zimbra_db_directory}/data'
COMMAND: zmlocalconfig -f -e mysql_directory='${zimbra_home}/mysql'
COMMAND: zmlocalconfig -f -e mysql_innodb_log_buffer_size='8388608'
COMMAND: zmlocalconfig -f -e mysql_innodb_log_file_size='104857600'
COMMAND: zmlocalconfig -f -e mysql_logger_root_password='PASS'
COMMAND: zmlocalconfig -f -e mysql_memory_percent='30'
COMMAND: zmlocalconfig -f -e mysql_mycnf='${zimbra_home}/conf/my.cnf'
COMMAND: zmlocalconfig -f -e mysql_pidfile='${zimbra_db_directory}/mysql.pid'
COMMAND: zmlocalconfig -f -e mysql_port='7306'
COMMAND: zmlocalconfig -f -e mysql_read_buffer_size='1048576'
COMMAND: zmlocalconfig -f -e mysql_root_password='PASS'
COMMAND: zmlocalconfig -f -e mysql_socket='${zimbra_db_directory}/mysql.sock'
COMMAND: zmlocalconfig -f -e mysql_sort_buffer_size='1048576'
COMMAND: zmlocalconfig -f -e mysql_table_cache='500'
COMMAND: zmlocalconfig -f -e nio_imap_enable='false'
COMMAND: zmlocalconfig -f -e nio_imap_log_buffers='false'
COMMAND: zmlocalconfig -f -e nio_imap_write_queue_max_size='10240000'
COMMAND: zmlocalconfig -f -e nio_imap_write_queue_max_size_unauth='20480'
COMMAND: zmlocalconfig -f -e nio_write_buffer_compaction_percent='50'
COMMAND: zmlocalconfig -f -e postfix_alias_maps='hash:/etc/aliases'
COMMAND: zmlocalconfig -f -e postfix_broken_sasl_auth_clients='yes'
COMMAND: zmlocalconfig -f -e postfix_command_directory='/opt/zimbra/postfix-${postfix_version}/sbin'
COMMAND: zmlocalconfig -f -e postfix_daemon_directory='/opt/zimbra/postfix-${postfix_version}/libexec'
COMMAND: zmlocalconfig -f -e postfix_header_checks='pcre:/opt/zimbra/conf/postfix_header_checks'
COMMAND: zmlocalconfig -f -e postfix_mailq_path='/opt/zimbra/postfix-${postfix_version}/sbin/mailq'
COMMAND: zmlocalconfig -f -e postfix_manpage_directory='/opt/zimbra/postfix-${postfix_version}/man'
COMMAND: zmlocalconfig -f -e postfix_newaliases_path='/opt/zimbra/postfix-${postfix_version}/sbin/newaliases'
COMMAND: zmlocalconfig -f -e postfix_queue_directory='/opt/zimbra/postfix-${postfix_version}/spool'
COMMAND: zmlocalconfig -f -e postfix_sender_canonical_maps='ldap:/opt/zimbra/conf/ldap-scm.cf'
COMMAND: zmlocalconfig -f -e postfix_sendmail_path='/opt/zimbra/postfix-${postfix_version}/sbin/sendmail'
COMMAND: zmlocalconfig -f -e postfix_smtpd_client_restrictions='reject_unauth_pipelining'
COMMAND: zmlocalconfig -f -e postfix_smtpd_data_restrictions='reject_unauth_pipelining'
COMMAND: zmlocalconfig -f -e postfix_smtpd_helo_required='yes'
COMMAND: zmlocalconfig -f -e postfix_smtpd_tls_cert_file='${zimbra_home}/conf/smtpd.crt'
COMMAND: zmlocalconfig -f -e postfix_smtpd_tls_key_file='${zimbra_home}/conf/smtpd.key'
COMMAND: zmlocalconfig -f -e postfix_smtpd_tls_loglevel='1'
COMMAND: zmlocalconfig -f -e postfix_transport_maps='ldap:/opt/zimbra/conf/ldap-transport.cf'
COMMAND: zmlocalconfig -f -e postfix_version='2.2.9'
COMMAND: zmlocalconfig -f -e postfix_virtual_alias_domains='ldap:/opt/zimbra/conf/ldap-vad.cf'
COMMAND: zmlocalconfig -f -e postfix_virtual_alias_maps='ldap:/opt/zimbra/conf/ldap-vam.cf'
COMMAND: zmlocalconfig -f -e postfix_virtual_mailbox_domains='ldap:/opt/zimbra/conf/ldap-vmd.cf'
COMMAND: zmlocalconfig -f -e postfix_virtual_mailbox_maps='ldap:/opt/zimbra/conf/ldap-vmm.cf'
COMMAND: zmlocalconfig -f -e postfix_virtual_transport='error'
COMMAND: zmlocalconfig -f -e search_dbfirst_term_percentage_cutoff='0.8'
COMMAND: zmlocalconfig -f -e search_disable_database_hints='false'
COMMAND: zmlocalconfig -f -e smtp_destination='admin@DOMAIN.com'
COMMAND: zmlocalconfig -f -e smtp_notify='yes'
COMMAND: zmlocalconfig -f -e smtp_source='admin@DOMAIN.com'
COMMAND: zmlocalconfig -f -e snmp_notify='yes'
COMMAND: zmlocalconfig -f -e snmp_trap_host='mail.DOMAIN.com'
COMMAND: zmlocalconfig -f -e ssl_allow_untrusted_certs='TRUE'
COMMAND: zmlocalconfig -f -e stats_img_folder='${zimbra_home}/logger/db/work'
COMMAND: zmlocalconfig -f -e timezone_file='${zimbra_home}/conf/timezones.ics'
COMMAND: zmlocalconfig -f -e tomcat_directory='${zimbra_home}/tomcat'
COMMAND: zmlocalconfig -f -e tomcat_java_heap_memory_percent='40'
COMMAND: zmlocalconfig -f -e tomcat_java_home='${zimbra_java_home}'
COMMAND: zmlocalconfig -f -e tomcat_java_options='-client -XX:NewRatio=2 -Djava.awt.headless=true'
COMMAND: zmlocalconfig -f -e tomcat_keystore='${tomcat_directory}/conf/keystore'
COMMAND: zmlocalconfig -f -e tomcat_keystore_password='zimbra'
COMMAND: zmlocalconfig -f -e tomcat_pidfile='${zimbra_log_directory}/tomcat.pid'
COMMAND: zmlocalconfig -f -e tomcat_thread_stack_size='256k'
COMMAND: zmlocalconfig -f -e tomcat_truststore_password='changeit'
COMMAND: zmlocalconfig -f -e wiki_enabled='false'
COMMAND: zmlocalconfig -f -e wiki_user='wiki'
COMMAND: zmlocalconfig -f -e zimbra_admin_service_port='7071'
COMMAND: zmlocalconfig -f -e zimbra_attrs_directory='${zimbra_home}/conf/attrs'
COMMAND: zmlocalconfig -f -e zimbra_auth_always_send_refer='false'
COMMAND: zmlocalconfig -f -e zimbra_class_mboxmanager='com.zimbra.cs.mailbox.MailboxManager'
COMMAND: zmlocalconfig -f -e zimbra_class_provisioning='com.zimbra.cs.account.ldap.LdapProvisioning'
COMMAND: zmlocalconfig -f -e zimbra_db_directory='${zimbra_home}/db'
COMMAND: zmlocalconfig -f -e zimbra_extension_common_directory='${zimbra_home}/lib/ext-common'
COMMAND: zmlocalconfig -f -e zimbra_extension_directory='${zimbra_home}/lib/ext'
COMMAND: zmlocalconfig -f -e zimbra_gid='500'
COMMAND: zmlocalconfig -f -e zimbra_home='/opt/zimbra'
COMMAND: zmlocalconfig -f -e zimbra_index_directory='${zimbra_home}/index'
COMMAND: zmlocalconfig -f -e zimbra_index_idle_flush_time='600'
COMMAND: zmlocalconfig -f -e zimbra_index_lru_size='100'
COMMAND: zmlocalconfig -f -e zimbra_index_max_uncommitted_operations='200'
COMMAND: zmlocalconfig -f -e zimbra_java_home='/opt/zimbra/java'
COMMAND: zmlocalconfig -f -e zimbra_ldap_password='PASS'
COMMAND: zmlocalconfig -f -e zimbra_ldap_user='zimbra'
COMMAND: zmlocalconfig -f -e zimbra_ldap_userdn='uid=zimbra,cn=admins,cn=zimbra'
COMMAND: zmlocalconfig -f -e zimbra_log4j_properties='${zimbra_home}/conf/log4j.properties'
COMMAND: zmlocalconfig -f -e zimbra_log_directory='${zimbra_home}/log'
COMMAND: zmlocalconfig -f -e zimbra_logger_mysql_password='PASS'
COMMAND: zmlocalconfig -f -e zimbra_mailbox_active_cache='500'
COMMAND: zmlocalconfig -f -e zimbra_mailbox_groups='100'
COMMAND: zmlocalconfig -f -e zimbra_mailbox_inactive_cache='30'
COMMAND: zmlocalconfig -f -e zimbra_mailbox_purgeable='true'
COMMAND: zmlocalconfig -f -e zimbra_mtareport_max_recipients='50'
COMMAND: zmlocalconfig -f -e zimbra_mtareport_max_senders='50'
COMMAND: zmlocalconfig -f -e zimbra_mysql_connector_maxActive='10'
COMMAND: zmlocalconfig -f -e zimbra_mysql_password='PASS'
COMMAND: zmlocalconfig -f -e zimbra_mysql_user='zimbra'
COMMAND: zmlocalconfig -f -e zimbra_server_hostname='mail.DOMAIN.com'
COMMAND: zmlocalconfig -f -e zimbra_spam_report_queue_size='100'
COMMAND: zmlocalconfig -f -e zimbra_store_directory='${zimbra_home}/store'
COMMAND: zmlocalconfig -f -e zimbra_store_sweeper_max_age='480'
COMMAND: zmlocalconfig -f -e zimbra_throttle_op_concurrency='1000,1000,1000,1000,1000'
COMMAND: zmlocalconfig -f -e zimbra_tmp_directory='/tmp/zimbra'
COMMAND: zmlocalconfig -f -e zimbra_uid='500'
COMMAND: zmlocalconfig -f -e zimbra_user='zimbra'
COMMAND: zmlocalconfig -f -e zimbra_zmprov_default_soap_server='localhost'
COMMAND: zmlocalconfig -f -e zimbra_zmprov_default_to_ldap='false'
COMMAND: zmlocalconfig -f -e zimlet_directory='${tomcat_directory}/webapps/service/zimlet'
COMMAND: zmlocalconfig -f -e zmstat_interval='30'
COMMAND: zmlocalconfig -f -e zmstat_log_directory='${zimbra_home}/zmstat'