Upgrade from 13.0.0 to 13.0.1 crashed - JSCombiner: deps file empty: merged-template-prepend.js.deps

Nextcloud version : eg, 13.0.1
Operating system and version : Debian 9.3 - Kernel 4.9.0-6-amd64)
Apache or nginx version : nginx/1.10.3
PHP version (eg, 7.1): PHP 7.0.27-0+deb9u1 / Zend OPcache v7.0.27-0+deb9u1

The issue you are facing:

I’ve recieved a notification v13.0.1 available, tried to upgrade over cli but gave me a notification my version up-to-date therefore tried to upgrade over web upgrade but failed stuck on maintanence screen, therefore i’ve deleted .step file and tried to upgrade again and it was successfull till i recieve an empty page writes following :

Internal Server Error

The server encountered an internal error and was unable to complete your request.
Please contact the server administrator if this error reappears multiple times, please include the technical details below in your report.
More details can be found in the server log.

i manually downloaded zip and copied config.php and apps to new fresh folder but result was same even after restarting nginx. Forgot to mention i’ve also rebooted server too.
I also tried a suggestion (5th comment by fauno) mentioned here https://github.com/nextcloud/server/issues/5696 but still no luck. Any suggestions ?

Is this the first time you’ve seen this error? (Y/N): Y

Steps to replicate it:

  1. upgrade via web interface
  2. delete .steps file under data/updater-XXX/ and occ set maintanence off
  3. upgrade via web interface again

The output of your Nextcloud log in Admin > Logging:

{"reqId":"aLdVQOVLVmE6O01BoAPO","level":1,"time":"2018-03-15T18:12:34+01:00","remoteAddr":"192.168.1.19","user":"mucahid","app":"no app in context","method":"GET","url":"\/apps\/files\/","message":"JSCombiner: deps file empty: merged-template-prepend.js.deps","userAgent":"Mozilla\/5.0 (X11; Linux x86_64) AppleWebKit\/537.36 (KHTML, like Gecko) Ubuntu Chromium\/64.0.3282.167 Chrome\/64.0.3282.167 Safari\/537.36","version":"13.0.1.1"}

{"reqId":"aLdVQOVLVmE6O01BoAPO","level":3,"time":"2018-03-15T18:12:49+01:00","remoteAddr":"192.168.1.19","user":"mucahid","app":"index","method":"GET","url":"\/apps\/files\/","message":"Exception: {\"Exception\":\"OCP\\\\Files\\\\NotFoundException\",\"Message\":\"\\\/mucahid\\\/files\\\/Shared\\\/music\",\"Code\":0,\"Trace\":\"#0 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Files\\\/Node\\\/Folder.php(133): OC\\\\Files\\\\Node\\\\Root->get('\\\/mucahid\\\/files\\\/...')\\n#1 \\\/var\\\/www\\\/html\\\/nextcloud\\\/apps\\\/music\\\/utility\\\/scanner.php(367): OC\\\\Files\\\\Node\\\\Folder->get('\\\/Shared\\\/music\\\/')\\n#2 \\\/var\\\/www\\\/html\\\/nextcloud\\\/apps\\\/music\\\/utility\\\/scanner.php(120): OCA\\\\Music\\\\Utility\\\\Scanner->getUserMusicFolder('mucahid', Object(OC\\\\Files\\\\Node\\\\Folder))\\n#3 \\\/var\\\/www\\\/html\\\/nextcloud\\\/apps\\\/music\\\/utility\\\/scanner.php(101): OCA\\\\Music\\\\Utility\\\\Scanner->pathIsUnderMusicFolder('\\\/appdata_ocuhf8...', 'mucahid', Object(OC\\\\Files\\\\Node\\\\Folder))\\n#4 \\\/var\\\/www\\\/html\\\/nextcloud\\\/apps\\\/music\\\/hooks\\\/filehooks.php(67): OCA\\\\Music\\\\Utility\\\\Scanner->update(Object(OC\\\\Files\\\\Node\\\\File), 'mucahid', Object(OC\\\\Files\\\\Node\\\\Folder))\\n#5 [internal function]: OCA\\\\Music\\\\Hooks\\\\FileHooks::updated(Object(OC\\\\Files\\\\Node\\\\File))\\n#6 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Hooks\\\/EmitterTrait.php(99): call_user_func_array(Array, Array)\\n#7 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Hooks\\\/PublicEmitter.php(36): OC\\\\Hooks\\\\BasicEmitter->emit('\\\\\\\\OC\\\\\\\\Files', 'postWrite', Array)\\n#8 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Files\\\/Node\\\/Root.php(136): OC\\\\Hooks\\\\PublicEmitter->emit('\\\\\\\\OC\\\\\\\\Files', 'postWrite', Array)\\n#9 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Files\\\/Node\\\/Node.php(108): OC\\\\Files\\\\Node\\\\Root->emit('\\\\\\\\OC\\\\\\\\Files', 'postWrite', Array)\\n#10 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Files\\\/Node\\\/File.php(66): OC\\\\Files\\\\Node\\\\Node->sendHooks(Array)\\n#11 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Files\\\/SimpleFS\\\/SimpleFile.php(104): OC\\\\Files\\\\Node\\\\File->putContent('(function($) {\\\\n...')\\n#12 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Template\\\/JSCombiner.php(194): OC\\\\Files\\\\SimpleFS\\\\SimpleFile->putContent('(function($) {\\\\n...')\\n#13 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Template\\\/JSCombiner.php(103): OC\\\\Template\\\\JSCombiner->cache('\\\/var\\\/www\\\/html\\\/n...', 'merged-template...', Object(OC\\\\Files\\\\SimpleFS\\\\SimpleFolder))\\n#14 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Template\\\/JSResourceLocator.php(113): OC\\\\Template\\\\JSCombiner->process('\\\/var\\\/www\\\/html\\\/n...', 'core\\\/js\\\/merged-...', 'core')\\n#15 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Template\\\/JSResourceLocator.php(69): OC\\\\Template\\\\JSResourceLocator->cacheAndAppendCombineJsonIfExist('\\\/var\\\/www\\\/html\\\/n...', 'core\\\/js\\\/merged-...')\\n#16 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Template\\\/ResourceLocator.php(78): OC\\\\Template\\\\JSResourceLocator->doFind('js\\\/merged-templ...')\\n#17 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/TemplateLayout.php(306): OC\\\\Template\\\\ResourceLocator->find(Array)\\n#18 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/TemplateLayout.php(146): OC\\\\TemplateLayout::findJavascriptFiles(Array)\\n#19 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/legacy\\\/template.php(207): OC\\\\TemplateLayout->__construct('user', 'files')\\n#20 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/public\\\/AppFramework\\\/Http\\\/TemplateResponse.php(157): OC_Template->fetchPage()\\n#21 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/AppFramework\\\/Http\\\/Dispatcher.php(114): OCP\\\\AppFramework\\\\Http\\\\TemplateResponse->render()\\n#22 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/AppFramework\\\/App.php(115): OC\\\\AppFramework\\\\Http\\\\Dispatcher->dispatch(Object(OCA\\\\Files\\\\Controller\\\\ViewController), 'index')\\n#23 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/AppFramework\\\/Routing\\\/RouteActionHandler.php(47): OC\\\\AppFramework\\\\App::main('ViewController', 'index', Object(OC\\\\AppFramework\\\\DependencyInjection\\\\DIContainer), Array)\\n#24 [internal function]: OC\\\\AppFramework\\\\Routing\\\\RouteActionHandler->__invoke(Array)\\n#25 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Route\\\/Router.php(297): call_user_func(Object(OC\\\\AppFramework\\\\Routing\\\\RouteActionHandler), Array)\\n#26 \\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/base.php(998): OC\\\\Route\\\\Router->match('\\\/apps\\\/files\\\/')\\n#27 \\\/var\\\/www\\\/html\\\/nextcloud\\\/index.php(37): OC::handleRequest()\\n#28 {main}\",\"File\":\"\\\/var\\\/www\\\/html\\\/nextcloud\\\/lib\\\/private\\\/Files\\\/Node\\\/Root.php\",\"Line\":202}","userAgent":"Mozilla\/5.0 (X11; Linux x86_64) AppleWebKit\/537.36 (KHTML, like Gecko) Ubuntu Chromium\/64.0.3282.167 Chrome\/64.0.3282.167 Safari\/537.36","version":"13.0.1.1"}

The output of your config.php file in /path/to/nextcloud (make sure you remove any identifiable information!):

<?php
$CONFIG = array (
  'instanceid' => 'XXXXXX',
  'passwordsalt' => 'XXXXXXX',
  'secret' => 'XXXXXXX',
  'trusted_domains' => 
  array (
    0 => 'mydomain.com',
    2 => 'mydomain.org',
  ),
  'datadirectory' => '/media/cloud',
  'overwrite.cli.url' => 'https://mydomain.com',
  'dbtype' => 'mysql',
  'version' => '13.0.1.1',
  'dbname' => 'nc_data',
  'dbhost' => 'localhost',
  'dbport' => '',
  'dbtableprefix' => 'oc_',
  'mysql.utf8mb4' => true,
  'dbuser' => 'dbadmin',
  'dbpassword' => 'dbpasword',
  'loglevel' => 1,
  'logtimezone' => 'Europe/Berlin',
  'logfile' => '/var/log/nextcloud.log',
  'log_rotate_size' => 104857600,
  'cron_log' => false,
  'installed' => true,
  'filesystem_check_changes' => 1,
  'quota_include_external_storage' => false,
  'knowledgebaseenabled' => false,
  'memcache.local' => '\\OC\\Memcache\\Redis',
  'redis' => 
  array (
    'host' => '/var/run/redis/redis.sock',
    'port' => 0,
    'timeout' => 0.0,
  ),
  'filelocking.enabled' => 'true',
  'memcache.locking' => '\\OC\\Memcache\\Redis',
  'maintenance' => false,
  'theme' => '',
  'enable_previews' => true,
  'mail_from_address' => 'postmaster',
  'mail_smtpmode' => 'php',
  'mail_smtpauthtype' => 'LOGIN',
  'mail_domain' => 'mydomain.org',
  'updater.secret' => 'XXXXXXXX',
);

The output of your Apache/nginx/system log in /var/log/____:

nothing to show as i'm logging under nextcloud.log which pasted above 

for those who are facing similar problem reason looks like 3rd party apps. I’ve disabled TOTP referring to first log and able to login however was unable to browse admin menu therefore disabled music app too.

sudo -u www-data php occ app:disable twofactor_tot
sudo -u www-data php occ app:disable music

Not sure if this is the same issue but I also upgraded from 13.0.0. to 13.0.1.
Now I cannot login anymore. I do get the login page when in Private browsing mode but after login it fails with an error message at the url: cloud.owndomain.org/apps/files/

> Internal Server Error
> The server encountered an internal error and was unable to complete your request.
> Please contact the server administrator if this error reappears multiple times, please include the technical details below in your report.
> More details can be found in the server log.

Note that the Desktop client and the Android app can normally connected.
In The Server log I can find:

{“reqId”:“WryGe0iE-6cEmyKOuLtxAAAAABw”,“level”:3,“time”:“2018-03-29T06:23:57+00:00”,“remoteAddr”:“176.74.156.189”,“user”:“admin”,“app”:“core”,“method”:“GET”,“url”:"/apps/files/",“message”:“Exception: {“Exception”:“OCP\\Files\\NotFoundException”,“Message”:”",“Code”:0,“Trace”:"#0 \/home\/joephein\/public_html\/lib\/private\/Files\/Node\/Node.php(217): OC\\Files\\Node\\Node->getFileInfo()\n#1 \/home\/joephein\/public_html\/lib\/private\/Files\/Node\/Node.php(117): OC\\Files\\Node\\Node->getPermissions()\n#2 \/home\/joephein\/public_html\/lib\/private\/Files\/Node\/File.php(62): OC\\Files\\Node\\Node->checkPermissions(2)\n#3 \/home\/joephein\/public_html\/lib\/private\/Files\/SimpleFS\/SimpleFile.php(104): OC\\Files\\Node\\File->putContent(’\/\\n * Copyright…’)\n#4 \/home\/joephein\/public_html\/lib\/private\/Template\/JSCombiner.php(194): OC\\Files\\SimpleFS\\SimpleFile->putContent(’\/\\n * Copyright…’)\n#5 \/home\/joephein\/public_html\/lib\/private\/Template\/JSCombiner.php(103): OC\\Template\\JSCombiner->cache(’\/home\/joephein\/…’, ‘merged.json’, Object(OC\\Files\\SimpleFS\\SimpleFolder))\n#6 \/home\/joephein\/public_html\/lib\/private\/Template\/JSResourceLocator.php(113): OC\\Template\\JSCombiner->process(’\/home\/joephein\/…’, ‘js\/merged.json’, ‘files_versions’)\n#7 \/home\/joephein\/public_html\/lib\/private\/Template\/JSResourceLocator.php(100): OC\\Template\\JSResourceLocator->cacheAndAppendCombineJsonIfExist(’\/home\/joephein\/…’, ‘js\/merged.json’, ‘files_versions’)\n#8 \/home\/joephein\/public_html\/lib\/private\/Template\/ResourceLocator.php(78): OC\\Template\\JSResourceLocator->doFind(‘files_versions\/…’)\n#9 \/home\/joephein\/public_html\/lib\/private\/TemplateLayout.php(306): OC\\Template\\ResourceLocator->find(Array)\n#10 \/home\/joephein\/public_html\/lib\/private\/TemplateLayout.php(146): OC\\TemplateLayout::findJavascriptFiles(Array)\n#11 \/home\/joephein\/public_html\/lib\/private\/legacy\/template.php(207): OC\\TemplateLayout->__construct(‘error’, ‘’)\n#12 \/home\/joephein\/public_html\/lib\/private\/Template\/Base.php(132): OC_Template->fetchPage()\n#13 \/home\/joephein\/public_html\/lib\/private\/legacy\/template.php(351): OC\\Template\\Base->printPage()\n#14 \/home\/joephein\/public_html\/index.php(65): OC_Template::printExceptionErrorPage(Object(OCP\\Files\\NotFoundException))\n#15 {main}",“File”:"\/home\/joephein\/public_html\/lib\/private\/Files\/Node\/Node.php",“Line”:97}",“userAgent”:“Mozilla/5.0 (Windows NT 10.0; WOW64; Trident/7.0; Touch; rv:11.0) like Gecko”,“version”:“13.0.1.1”}

I do not have occ access since I am using ownCube hosting.`

The issue in the log looks similar like what is mentioned here: User cannot connect to NC OCP\Files\NotFoundException but that solution is not applicable for me. I am on Nextcloud since the beginning and those users and their folder exist already for a long time with a lot of data in their folders.