Error while updating Theming app from 11.02 to 12.0

[GrandSteak10]

Steps to reproduce

1. Update from 11.02 to 12.0 with web Updater
2. Go to base address for login after update is finished in the web updater
3. Accept final update on the login page

Expected behaviour

Update should finish and login page should appear

Actual behaviour

Error in updating "theming app" :
Doctrine\DBAL\Exception\SyntaxErrorException: An exception occurred while executing 'DELETE FROM oc_reader_bookmarks b WHERE b.file_id = ?' with params [219]: SQLSTATE[42000]: Syntax error or access violation: 1064 You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'b WHERE b.file_id = '219'' at line 1

Server configuration

Operating system:
Debian

Web server:
Apache 2.4.10

Database:
MYSQL 5.5.55

PHP version:
7.0

Nextcloud version: (see Nextcloud admin page)
Somewhere between 11.02 and 12.0

Updated from an older Nextcloud/ownCloud or fresh install:
From 11.02

Where did you install Nextcloud from:
Web

List of activated apps:
Enabled:

• activity: 2.5.2
• calendar: 1.5.2
• comments: 1.2.0
• contacts: 1.5.3
• dav: 1.3.0
• deck: 0.1.2
• federatedfilesharing: 1.2.0
• federation: 1.2.0
• files: 1.7.2
• files_pdfviewer: 1.1.1
• files_reader: 1.0.2
• files_sharing: 1.4.0
• files_texteditor: 2.4.1
• files_trashbin: 1.2.0
• files_versions: 1.5.0
• files_videoplayer: 1.1.0
• firstrunwizard: 2.1
• gallery: 17.0.0
• logreader: 2.0.0
• lookup_server_connector: 1.0.0
• nextcloud_announcements: 1.1
• notes: 2.2.0
• notifications: 2.0.0
• oauth2: true
• password_policy: 1.2.2
• provisioning_api: 1.2.0
• serverinfo: 1.2.0
• sharebymail: 1.2.0
• survey_client: 1.0.0
• systemtags: 1.2.0
• theming: 1.1.1
• twofactor_backupcodes: 1.1.1
• updatenotification: 1.2.0
• workflowengine: 1.2.0
  Disabled:
• activitylog
• admin_audit
• apporder
• audioplayer
• direct_menu
• encryption
• files_downloadactivity
• files_external
• tasks
• user_external
• user_ldap
• weather

Nextcloud configuration:
{
"system": {
"passwordsalt": "REMOVED SENSITIVE VALUE",
"secret": "REMOVED SENSITIVE VALUE",
"trusted_domains": [
"localhost",
"xxxxxxxxx"
],
"datadirectory": "/var/www/nextcloud/data",
"overwrite.cli.url": "http://localhost",
"dbtype": "mysql",
"version": "11.0.2.7",
"dbname": "nextcloud",
"dbhost": "localhost",
"dbport": "",
"dbtableprefix": "oc_",
"dbuser": "REMOVED SENSITIVE VALUE",
"dbpassword": "REMOVED SENSITIVE VALUE",
"logtimezone": "UTC",
"installed": true,
"instanceid": "ocpmmmazz784",
"ldapIgnoreNamingRules": false,
"ldapProviderFactory": "\OCA\User_LDAP\LDAPProviderFactory",
"maintenance": false,
"theme": "",
"loglevel": 2,
"updater.secret": "REMOVED SENSITIVE VALUE"
}
}

Are you using external storage, if yes which one: local/smb/sftp/...
No

Are you using encryption: yes/no
No

Are you using an external user-backend, if yes which one: LDAP/ActiveDirectory/Webdav/...
No

[mattsmallman]

+1.

Actual behaviours slightly different but appears to be related to thumbing app as well: (Can't find log file to export)

Preparing update
Set log level to debug
Turned on maintenance mode
Updating database schema
Updated database
OCP\Files\NotPermittedException:

[juliusknorr]

@GrandSteak10 @mattsmallman Can you check the data/nextcloud.log file for more detailed error messages?

Doctrine\DBAL\Exception\SyntaxErrorException: An exception occurred while executing 'DELETE FROM oc_reader_bookmarks b WHERE b.file_id = ?' with params [219]: SQLSTATE[42000]: Syntax error or access violation: 1064 You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'b WHERE b.file_id = '219'' at line 1

That looks more like there is an error with the files_reader app.

[GrandSteak10]

@juliushaertl

{"reqId":"pFdtumxnfVjiRStOo7yF","level":3,"time":"2017-05-24T05:39:55+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"no app in contex
t","method":"GET","url":"\/","message":"Exception: {\"Exception\":\"Symfony\\\\Component\\\\Routing\\\\Exception\\\\RouteNotFoundException\"
,\"Message\":\"Unable to generate a URL for the named route \\\"theming.Theming.getLogo\\\" as such route does not exist.\",\"Code\":0,\"Tra
ce\":\"#0 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Route\\\/Router.php(339): Symfony\\\\Component\\\\Routing\\\\Generator\\\\UrlGene
rator->generate('theming.Theming...', Array, 1)\\n#1 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/URLGenerator.php(70): OC\\\\Route\\\\R
outer->generate('theming.Theming...', Array)\\n#2 \\\/var\\\/www\\\/nextcloud\\\/apps\\\/theming\\\/lib\\\/ThemingDefaults.php(156): OC\\\\U
RLGenerator->linkToRoute('theming.Theming...')\\n#3 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/public\\\/Defaults.php(186): OCA\\\\Theming\\\\The
mingDefaults->getLogo(true)\\n#4 \\\/var\\\/www\\\/nextcloud\\\/core\\\/templates\\\/layout.guest.php(45): OCP\\\\Defaults->getLogo()\\n#5 \
\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Template\\\/Base.php(176): include('\\\/var\\\/www\\\/nextcl...')\\n#6 \\\/var\\\/www\\\/nex
tcloud\\\/lib\\\/private\\\/Template\\\/Base.php(151): OC\\\\Template\\\\Base->load('\\\/var\\\/www\\\/nextcl...', NULL)\\n#7 \\\/var\\\/www
\\\/nextcloud\\\/lib\\\/private\\\/legacy\\\/template.php(202): OC\\\\Template\\\\Base->fetchPage(NULL)\\n#8 \\\/var\\\/www\\\/nextcloud\\\/
lib\\\/private\\\/legacy\\\/template.php(224): OC_Template->fetchPage()\\n#9 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Template\\\/Ba
se.php(132): OC_Template->fetchPage()\\n#10 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/base.php(404): OC\\\\Template\\\\Base->printPage()\\n#11 \
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{"reqId":"QsdAqEbzGVfNLPp8FfiR","level":3,"time":"2017-05-24T05:39:55+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"no app in contex
t","method":"GET","url":"\/?v=25","message":"Exception: {\"Exception\":\"Symfony\\\\Component\\\\Routing\\\\Exception\\\\RouteNotFoundExcept
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\"Trace\":\"#0 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Route\\\/Router.php(339): Symfony\\\\Component\\\\Routing\\\\Generator\\\\Ur
lGenerator->generate('theming.Theming...', Array, 1)\\n#1 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/URLGenerator.php(70): OC\\\\Route
\\\\Router->generate('theming.Theming...', Array)\\n#2 \\\/var\\\/www\\\/nextcloud\\\/apps\\\/theming\\\/lib\\\/ThemingDefaults.php(156): OC
\\\\URLGenerator->linkToRoute('theming.Theming...')\\n#3 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/public\\\/Defaults.php(186): OCA\\\\Theming\\
\\ThemingDefaults->getLogo(true)\\n#4 \\\/var\\\/www\\\/nextcloud\\\/core\\\/templates\\\/layout.guest.php(45): OCP\\\\Defaults->getLogo()\\
n#5 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Template\\\/Base.php(176): include('\\\/var\\\/www\\\/nextcl...')\\n#6 \\\/var\\\/www\\
\/nextcloud\\\/lib\\\/private\\\/Template\\\/Base.php(151): OC\\\\Template\\\\Base->load('\\\/var\\\/www\\\/nextcl...', NULL)\\n#7 \\\/var\\
\/www\\\/nextcloud\\\/lib\\\/private\\\/legacy\\\/template.php(202): OC\\\\Template\\\\Base->fetchPage(NULL)\\n#8 \\\/var\\\/www\\\/nextclou
d\\\/lib\\\/private\\\/legacy\\\/template.php(224): OC_Template->fetchPage()\\n#9 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Template\
\\/Base.php(132): OC_Template->fetchPage()\\n#10 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/base.php(404): OC\\\\Template\\\\Base->printPage()\\n
#11 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/base.php(297): OC::printUpgradePage()\\n#12 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/base.php(958): O
C::checkUpgrade()\\n#13 \\\/var\\\/www\\\/nextcloud\\\/index.php(40): OC::handleRequest()\\n#14 {main}\",\"File\":\"\\\/var\\\/www\\\/nextcl
oud\\\/3rdparty\\\/symfony\\\/routing\\\/Generator\\\/UrlGenerator.php\",\"Line\":130}","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x
64; rv:53.0) Gecko\/20100101 Firefox\/53.0","version":"11.0.2.7"}
{"reqId":"fPojlYIPfv9oAjIZKxxW","level":3,"time":"2017-05-24T05:39:56+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"no app in contex
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ion\",\"Message\":\"Unable to generate a URL for the named route \\\"theming.Theming.getLogo\\\" as such route does not exist.\",\"Code\":0,
\"Trace\":\"#0 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Route\\\/Router.php(339): Symfony\\\\Component\\\\Routing\\\\Generator\\\\Ur
lGenerator->generate('theming.Theming...', Array, 1)\\n#1 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/URLGenerator.php(70): OC\\\\Route
\\\\Router->generate('theming.Theming...', Array)\\n#2 \\\/var\\\/www\\\/nextcloud\\\/apps\\\/theming\\\/lib\\\/ThemingDefaults.php(156): OC
\\\\URLGenerator->linkToRoute('theming.Theming...')\\n#3 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/public\\\/Defaults.php(186): OCA\\\\Theming\\
\\ThemingDefaults->getLogo(true)\\n#4 \\\/var\\\/www\\\/nextcloud\\\/core\\\/templates\\\/layout.guest.php(45): OCP\\\\Defaults->getLogo()\\
n#5 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Template\\\/Base.php(176): include('\\\/var\\\/www\\\/nextcl...')\\n#6 \\\/var\\\/www\\
\/nextcloud\\\/lib\\\/private\\\/Template\\\/Base.php(151): OC\\\\Template\\\\Base->load('\\\/var\\\/www\\\/nextcl...', NULL)\\n#7 \\\/var\\
\/www\\\/nextcloud\\\/lib\\\/private\\\/legacy\\\/template.php(202): OC\\\\Template\\\\Base->fetchPage(NULL)\\n#8 \\\/var\\\/www\\\/nextclou
d\\\/lib\\\/private\\\/legacy\\\/template.php(224): OC_Template->fetchPage()\\n#9 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Template\
\\/Base.php(132): OC_Template->fetchPage()\\n#10 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/base.php(404): OC\\\\Template\\\\Base->printPage()\\n
#11 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/base.php(297): OC::printUpgradePage()\\n#12 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/base.php(958): O
C::checkUpgrade()\\n#13 \\\/var\\\/www\\\/nextcloud\\\/index.php(40): OC::handleRequest()\\n#14 {main}\",\"File\":\"\\\/var\\\/www\\\/nextcl
oud\\\/3rdparty\\\/symfony\\\/routing\\\/Generator\\\/UrlGenerator.php\",\"Line\":130}","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x
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{"reqId":"OusS1HutLvhZAhNVZVV7","level":1,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"updater","method
":"GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvs
d9VANtDJY%3D","message":"\\OC\\Updater::maintenanceEnabled: Turned on maintenance mode","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x
64; rv:53.0) Gecko\/20100101 Firefox\/53.0","version":"11.0.2.7"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":0,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"core","method":"
GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvsd9V
ANtDJY%3D","message":"starting upgrade from 11.0.2.7 to 12.0.0.29","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64; rv:53.0) Gecko\/2
0100101 Firefox\/53.0","version":"11.0.2.7"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":3,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"PHP","method":"G
ET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvsd9VA
NtDJY%3D","message":"file_put_contents(\/var\/www\/nextcloud\/data\/.htaccess): failed to open stream: Permission denied at \/var\/www\/next
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":"11.0.2.7"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":1,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"updater","method
":"GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvs
d9VANtDJY%3D","message":"\\OC\\Repair::step: Repair step: Repair MySQL collation","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64; rv
:53.0) Gecko\/20100101 Firefox\/53.0","version":"11.0.2.7"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":1,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"updater","method
":"GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvs
d9VANtDJY%3D","message":"\\OC\\Repair::info: Repair info: All tables already have the correct collation -> nothing to do","userAgent":"Mozil
la\/5.0 (Windows NT 10.0; Win64; x64; rv:53.0) Gecko\/20100101 Firefox\/53.0","version":"11.0.2.7"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":1,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"updater","method
":"GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvs
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{"reqId":"OusS1HutLvhZAhNVZVV7","level":1,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"updater","method
":"GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvs
d9VANtDJY%3D","message":"\\OC\\Repair::step: Repair step: Copy data from accounts table when migrating from ownCloud","userAgent":"Mozilla\/
5.0 (Windows NT 10.0; Win64; x64; rv:53.0) Gecko\/20100101 Firefox\/53.0","version":"11.0.2.7"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":1,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"updater","method
":"GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvs
d9VANtDJY%3D","message":"\\OC\\Updater::dbUpgradeBefore: Updating database schema","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64; r
v:53.0) Gecko\/20100101 Firefox\/53.0","version":"11.0.2.7"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":1,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"updater","method
":"GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvs
d9VANtDJY%3D","message":"\\OC\\Updater::dbUpgrade: Updated database","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64; rv:53.0) Gecko\
/20100101 Firefox\/53.0","version":"11.0.2.7"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":1,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"updater","method
":"GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvs
d9VANtDJY%3D","message":"\\OC\\Updater::appUpgradeStarted: Updating <theming> ...","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64; r
v:53.0) Gecko\/20100101 Firefox\/53.0","version":"11.0.2.7"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":1,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"updater","method
":"GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvs
d9VANtDJY%3D","message":"\\OC\\Repair::step: Repair step: Move theming files to AppData storage","userAgent":"Mozilla\/5.0 (Windows NT 10.0;
 Win64; x64; rv:53.0) Gecko\/20100101 Firefox\/53.0","version":"11.0.2.7"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":3,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"core","method":"
GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvsd9V
ANtDJY%3D","message":"Exception: {\"Exception\":\"Doctrine\\\\DBAL\\\\Exception\\\\SyntaxErrorException\",\"Message\":\"An exception occurre
d while executing 'DELETE FROM `oc_reader_bookmarks` b WHERE b.file_id = ?' with params [219]:\\n\\nSQLSTATE[42000]: Syntax error or access 
violation: 1064 You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to
 use near 'b WHERE b.file_id = '219'' at line 1\",\"Code\":0,\"Trace\":\"#0 \\\/var\\\/www\\\/nextcloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/l
ib\\\/Doctrine\\\/DBAL\\\/DBALException.php(128): Doctrine\\\\DBAL\\\\Driver\\\\AbstractMySQLDriver->convertException('An exception oc...', 
Object(Doctrine\\\\DBAL\\\\Driver\\\\PDOException))\\n#1 \\\/var\\\/www\\\/nextcloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/D
BAL\\\/Connection.php(1015): Doctrine\\\\DBAL\\\\DBALException::driverExceptionDuringQuery(Object(Doctrine\\\\DBAL\\\\Driver\\\\PDOMySql\\\\
Driver), Object(Doctrine\\\\DBAL\\\\Driver\\\\PDOException), 'DELETE FROM `oc...', Array)\\n#2 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private
\\\/DB\\\/Connection.php(213): Doctrine\\\\DBAL\\\\Connection->executeUpdate('DELETE FROM `oc...', Array, Array)\\n#3 \\\/var\\\/www\\\/next
cloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Query\\\/QueryBuilder.php(208): OC\\\\DB\\\\Connection->executeUpdate('D
ELETE FROM `oc...', Array, Array)\\n#4 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/DB\\\/QueryBuilder\\\/QueryBuilder.php(213): Doctrin
e\\\\DBAL\\\\Query\\\\QueryBuilder->execute()\\n#5 \\\/var\\\/www\\\/nextcloud\\\/apps\\\/files_reader\\\/lib\\\/Hooks.php(36): OC\\\\DB\\\\
QueryBuilder\\\\QueryBuilder->execute()\\n#6 \\\/var\\\/www\\\/nextcloud\\\/apps\\\/files_reader\\\/lib\\\/Hooks.php(24): OCA\\\\Files_Reade
r\\\\Hooks::deleteFile(Object(OC\\\\DB\\\\Connection), 219)\\n#7 [internal function]: OCA\\\\Files_Reader\\\\Hooks::OCA\\\\Files_Reader\\\\{
closure}(Object(OC\\\\Files\\\\Node\\\\File))\\n#8 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Hooks\\\/EmitterTrait.php(99): call_user
_func_array(Object(Closure), Array)\\n#9 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Hooks\\\/PublicEmitter.php(33): OC\\\\Hooks\\\\Bas
icEmitter->emit('\\\\\\\\OC\\\\\\\\Files', 'preDelete', Array)\\n#10 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Files\\\/Node\\\/Root.
php(134): OC\\\\Hooks\\\\PublicEmitter->emit('\\\\\\\\OC\\\\\\\\Files', 'preDelete', Array)\\n#11 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/priv
ate\\\/Files\\\/Node\\\/Node.php(108): OC\\\\Files\\\\Node\\\\Root->emit('\\\\\\\\OC\\\\\\\\Files', 'preDelete', Array)\\n#12 \\\/var\\\/www
\\\/nextcloud\\\/lib\\\/private\\\/Files\\\/Node\\\/File.php(114): OC\\\\Files\\\\Node\\\\Node->sendHooks(Array)\\n#13 \\\/var\\\/www\\\/nex
tcloud\\\/apps\\\/theming\\\/lib\\\/Migration\\\/ThemingImages.php(63): OC\\\\Files\\\\Node\\\\File->delete()\\n#14 \\\/var\\\/www\\\/nextcl
oud\\\/lib\\\/private\\\/Repair.php(85): OCA\\\\Theming\\\\Migration\\\\ThemingImages->run(Object(OC\\\\Repair))\\n#15 \\\/var\\\/www\\\/nex
tcloud\\\/lib\\\/private\\\/legacy\\\/app.php(1114): OC\\\\Repair->run()\\n#16 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/legacy\\\/ap
p.php(1049): OC_App::executeRepairSteps('theming', Array)\\n#17 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Updater.php(381): OC_App::u
pdateApp('theming')\\n#18 \\\/var\\\/www\\\/nextcloud\\\/lib\\\/private\\\/Updater.php(264): OC\\\\Updater->doAppUpgrade()\\n#19 \\\/var\\\/
www\\\/nextcloud\\\/lib\\\/private\\\/Updater.php(130): OC\\\\Updater->doUpgrade('12.0.0.29', '11.0.2.7')\\n#20 \\\/var\\\/www\\\/nextcloud\
\\/core\\\/ajax\\\/update.php(206): OC\\\\Updater->upgrade()\\n#21 {main}\",\"File\":\"\\\/var\\\/www\\\/nextcloud\\\/3rdparty\\\/doctrine\\
\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Driver\\\/AbstractMySQLDriver.php\",\"Line\":90}","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x6
4; rv:53.0) Gecko\/20100101 Firefox\/53.0","version":"11.0.2.7"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":3,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"updater","method
":"GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvs
d9VANtDJY%3D","message":"\\OC\\Updater::failure: Doctrine\\DBAL\\Exception\\SyntaxErrorException: An exception occurred while executing 'DEL
ETE FROM `oc_reader_bookmarks` b WHERE b.file_id = ?' with params [219]:\n\nSQLSTATE[42000]: Syntax error or access violation: 1064 You have
 an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'b WHERE b.fil
e_id = '219'' at line 1","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64; rv:53.0) Gecko\/20100101 Firefox\/53.0","version":"11.0.2.7
"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":3,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"updater","method
":"GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvs
d9VANtDJY%3D","message":"\\OC\\Updater::updateEnd: Update failed","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64; rv:53.0) Gecko\/20
100101 Firefox\/53.0","version":"11.0.2.7"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":1,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"updater","method
":"GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvs
d9VANtDJY%3D","message":"\\OC\\Updater::maintenanceActive: Maintenance mode is kept active","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win6
4; x64; rv:53.0) Gecko\/20100101 Firefox\/53.0","version":"11.0.2.7"}
{"reqId":"OusS1HutLvhZAhNVZVV7","level":1,"time":"2017-05-24T05:39:57+00:00","remoteAddr":"xx.xx.xx.xx","user":"--","app":"updater","method
":"GET","url":"\/core\/ajax\/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvs
d9VANtDJY%3D","message":"\\OC\\Updater::resetLogLevel: Reset log level to Warning(2)","userAgent":"Mozilla\/5.0 (Windows NT 10.0; Win64; x64
; rv:53.0) Gecko\/20100101 Firefox\/53.0","version":"11.0.2.7"}

[GrandSteak10]

@juliushaertl
Could start again nextcloud by:

• through command line:
  • disable the theming app
  • re run the upgrade command (success)
  • exit the maintenance mode

logged as admin:
"some files have not passed the integrity check" -> relaunch -> failed
"list of invalid files":

=====================
The following list covers which files have failed the integrity check. Please read
the previous linked documentation to learn more about the errors and how to fix
them.

Results

• direct_menu
  • EXCEPTION
    • OC\IntegrityCheck\Exceptions\InvalidSignatureException
    • Certificate is not valid.

Raw output

Array
(
[direct_menu] => Array
(
[EXCEPTION] => Array
(
[class] => OC\IntegrityCheck\Exceptions\InvalidSignatureException
[message] => Certificate is not valid.
)

    )

)

[juliusknorr]

{
  "reqId": "OusS1HutLvhZAhNVZVV7",
  "level": 3,
  "time": "2017-05-24T05:39:57+00:00",
  "remoteAddr": "xx.xx.xx.xx",
  "user": "--",
  "app": "core",
  "method": "GET",
  "url": "/core/ajax/update.php?requesttoken=grDgWbNPwCo9smikzpDkTUItwWAJq5cyzIsyN009Wc8%3D%3AtNjWbd4YwXhIiwHNjdKyrRNX9BZr%2F%2B8Bvsd9VANtDJY%3D",
  "message": "Exception: {\"Exception\":\"Doctrine\\\\DBAL\\\\Exception\\\\SyntaxErrorException\",\"Message\":\"An exception occurred while executing 'DELETE FROM `oc_reader_bookmarks` b WHERE b.file_id = ?' with params [219]:\\n\\nSQLSTATE[42000]: Syntax error or access violation: 1064 You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'b WHERE b.file_id = '219'' at line 1\",\"Code\":0,\"Trace\":\"#0 \\/var\\/www\\/nextcloud\\/3rdparty\\/doctrine\\/dbal\\/lib\\/Doctrine\\/DBAL\\/DBALException.php(128): Doctrine\\\\DBAL\\\\Driver\\\\AbstractMySQLDriver->convertException('An exception oc...', Object(Doctrine\\\\DBAL\\\\Driver\\\\PDOException))\\n#1 \\/var\\/www\\/nextcloud\\/3rdparty\\/doctrine\\/dbal\\/lib\\/Doctrine\\/DBAL\\/Connection.php(1015): Doctrine\\\\DBAL\\\\DBALException::driverExceptionDuringQuery(Object(Doctrine\\\\DBAL\\\\Driver\\\\PDOMySql\\\\Driver), Object(Doctrine\\\\DBAL\\\\Driver\\\\PDOException), 'DELETE FROM `oc...', Array)\\n#2 \\/var\\/www\\/nextcloud\\/lib\\/private\\/DB\\/Connection.php(213): Doctrine\\\\DBAL\\\\Connection->executeUpdate('DELETE FROM `oc...', Array, Array)\\n#3 \\/var\\/www\\/nextcloud\\/3rdparty\\/doctrine\\/dbal\\/lib\\/Doctrine\\/DBAL\\/Query\\/QueryBuilder.php(208): OC\\\\DB\\\\Connection->executeUpdate('DELETE FROM `oc...', Array, Array)\\n#4 \\/var\\/www\\/nextcloud\\/lib\\/private\\/DB\\/QueryBuilder\\/QueryBuilder.php(213): Doctrine\\\\DBAL\\\\Query\\\\QueryBuilder->execute()\\n#5 \\/var\\/www\\/nextcloud\\/apps\\/files_reader\\/lib\\/Hooks.php(36): OC\\\\DB\\\\QueryBuilder\\\\QueryBuilder->execute()\\n#6 \\/var\\/www\\/nextcloud\\/apps\\/files_reader\\/lib\\/Hooks.php(24): OCA\\\\Files_Reader\\\\Hooks::deleteFile(Object(OC\\\\DB\\\\Connection), 219)\\n#7 [internal function]: OCA\\\\Files_Reader\\\\Hooks::OCA\\\\Files_Reader\\\\{closure}(Object(OC\\\\Files\\\\Node\\\\File))\\n#8 \\/var\\/www\\/nextcloud\\/lib\\/private\\/Hooks\\/EmitterTrait.php(99): call_user_func_array(Object(Closure), Array)\\n#9 \\/var\\/www\\/nextcloud\\/lib\\/private\\/Hooks\\/PublicEmitter.php(33): OC\\\\Hooks\\\\BasicEmitter->emit('\\\\\\\\OC\\\\\\\\Files', 'preDelete', Array)\\n#10 \\/var\\/www\\/nextcloud\\/lib\\/private\\/Files\\/Node\\/Root.php(134): OC\\\\Hooks\\\\PublicEmitter->emit('\\\\\\\\OC\\\\\\\\Files', 'preDelete', Array)\\n#11 \\/var\\/www\\/nextcloud\\/lib\\/private\\/Files\\/Node\\/Node.php(108): OC\\\\Files\\\\Node\\\\Root->emit('\\\\\\\\OC\\\\\\\\Files', 'preDelete', Array)\\n#12 \\/var\\/www\\/nextcloud\\/lib\\/private\\/Files\\/Node\\/File.php(114): OC\\\\Files\\\\Node\\\\Node->sendHooks(Array)\\n#13 \\/var\\/www\\/nextcloud\\/apps\\/theming\\/lib\\/Migration\\/ThemingImages.php(63): OC\\\\Files\\\\Node\\\\File->delete()\\n#14 \\/var\\/www\\/nextcloud\\/lib\\/private\\/Repair.php(85): OCA\\\\Theming\\\\Migration\\\\ThemingImages->run(Object(OC\\\\Repair))\\n#15 \\/var\\/www\\/nextcloud\\/lib\\/private\\/legacy\\/app.php(1114): OC\\\\Repair->run()\\n#16 \\/var\\/www\\/nextcloud\\/lib\\/private\\/legacy\\/app.php(1049): OC_App::executeRepairSteps('theming', Array)\\n#17 \\/var\\/www\\/nextcloud\\/lib\\/private\\/Updater.php(381): OC_App::updateApp('theming')\\n#18 \\/var\\/www\\/nextcloud\\/lib\\/private\\/Updater.php(264): OC\\\\Updater->doAppUpgrade()\\n#19 \\/var\\/www\\/nextcloud\\/lib\\/private\\/Updater.php(130): OC\\\\Updater->doUpgrade('12.0.0.29', '11.0.2.7')\\n#20 \\/var\\/www\\/nextcloud\\/core\\/ajax\\/update.php(206): OC\\\\Updater->upgrade()\\n#21 {main}\",\"File\":\"\\/var\\/www\\/nextcloud\\/3rdparty\\/doctrine\\/dbal\\/lib\\/Doctrine\\/DBAL\\/Driver\\/AbstractMySQLDriver.php\",\"Line\":90}",
  "userAgent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:53.0) Gecko/20100101 Firefox/53.0",
  "version": "11.0.2.7"
}

This is caused by files_reader, so you may want to open an issue there: https://github.com/Yetangitu/owncloud-apps/tree/master/files_reader

The other errors have already been reported here: #4987

[johnramsden]

I just ran into this problem on a fresh install of nextcloud 12. It broke my install and I was unable to start it at all.