BrokenUpdaterRepair SQL issue #331

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PVince81 opened this Issue Apr 26, 2016 · 11 comments

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@PVince81
Contributor

Steps

  1. Setup owncloud-9.0.0.tar.bz2
  2. Go to admin page
  3. Set channel to "daily"
  4. Open updater
  5. Start update

Expected result

Updater runs fine

Actual result

Hangs on "Updating core", CPU is at 100%, log contains these:

SQLSTATE[08S01]: Communication link failure: 1153 Got a packet bigger than 'max_allowed_packet' bytes\",\"Code\":0,\"Trace\":\"#0 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/DBALException.php(116): Doctrine\\\\DBAL\\\\Driver\\\\AbstractMySQLDriver->convertException('An exception oc...', Object(Doctrine\\\\DBAL\\\\Driver\\\\PDOException))\\n#1 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(996): Doctrine\\\\DBAL\\\\DBALException::driverExceptionDuringQuery(Object(Doctrine\\\\DBAL\\\\Driver\\\\PDOMySql\\\\Driver), Object(Doctrine\\\\DBAL\\\\Driver\\\\PDOException), 'INSERT INTO `oc...', Array)\\n#2 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/db\\\/connection.php(205): Doctrine\\\\DBAL\\\\Connection->executeUpdate('INSERT INTO `oc...', Array, Array)\\n#3 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/db\\\/adapter.php(93): OC\\\\DB\\\\Connection->executeUpdate('INSERT INTO `*P...', Array)\\n#4 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/db\\\/connection.php(243): OC\\\\DB\\\\Adapter->insertIfNotExist('*PREFIX*appconf...', Array, Array)\\n#5 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/appconfig.php(158): OC\\\\DB\\\\Connection->insertIfNotExist('*PREFIX*appconf...', Array, Array)\\n#6 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/allconfig.php(160): OC\\\\AppConfig->setValue('core', 'oc.integrityche...', '{\\\"core\\\":{\\\"EXTRA...')\\n#7 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/integritycheck\\\/checker.php(431): OC\\\\AllConfig->setAppValue('core', 'oc.integrityche...', '{\\\"core\\\":{\\\"EXTRA...')\\n#8 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/integritycheck\\\/checker.php(544): OC\\\\IntegrityCheck\\\\Checker->storeResults('core', Array)\\n#9 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/integritycheck\\\/checker.php(555): OC\\\\IntegrityCheck\\\\Checker->verifyCoreSignature()\\n#10 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/repair\\\/brokenupdaterrepair.php(96): OC\\\\IntegrityCheck\\\\Checker->runInstanceVerification()\\n#11 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/repair\\\/brokenupdaterrepair.php(102): OC\\\\Repair\\\\BrokenUpdaterRepair->recheckIntegrity()\\n#12 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/repair.php(87): OC\\\\Repair\\\\BrokenUpdaterRepair->run()\\n#13 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/updater.php(346): OC\\\\Repair->run()\\n#14 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/updater.php(215): OC\\\\Updater->doUpgrade('9.0.1.3', '9.0.0.19')\\n#15 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/core\\\/command\\\/upgrade.php(246): OC\\\\Updater->upgrade()\\n#16 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/3rdparty\\\/symfony\\\/console\\\/Command\\\/Command.php(259): OC\\\\Core\\\\Command\\\\Upgrade->execute(Object(Symfony\\\\Component\\\\Console\\\\Input\\\\ArgvInput), Object(Symfony\\\\Component\\\\Console\\\\Output\\\\ConsoleOutput))\\n#17 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/core\\\/command\\\/base.php(158): Symfony\\\\Component\\\\Console\\\\Command\\\\Command->run(Object(Symfony\\\\Component\\\\Console\\\\Input\\\\ArgvInput), Object(Symfony\\\\Component\\\\Console\\\\Output\\\\ConsoleOutput))\\n#18 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/3rdparty\\\/symfony\\\/console\\\/Application.php(840): OC\\\\Core\\\\Command\\\\Base->run(Object(Symfony\\\\Component\\\\Console\\\\Input\\\\ArgvInput), Object(Symfony\\\\Component\\\\Console\\\\Output\\\\ConsoleOutput))\\n#19 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/3rdparty\\\/symfony\\\/console\\\/Application.php(192): Symfony\\\\Component\\\\Console\\\\Application->doRunCommand(Object(OC\\\\Core\\\\Command\\\\Upgrade), Object(Symfony\\\\Component\\\\Console\\\\Input\\\\ArgvInput), Object(Symfony\\\\Component\\\\Console\\\\Output\\\\ConsoleOutput))\\n#20 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/3rdparty\\\/symfony\\\/console\\\/Application.php(123): Symfony\\\\Component\\\\Console\\\\Application->doRun(Object(Symfony\\\\Component\\\\Console\\\\Input\\\\ArgvInput), Object(Symfony\\\\Component\\\\Console\\\\Output\\\\ConsoleOutput))\\n#21 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/lib\\\/private\\\/console\\\/application.php(145): Symfony\\\\Component\\\\Console\\\\Application->run(NULL, NULL)\\n#22 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/console.php(88): OC\\\\Console\\\\Application->run()\\n#23 \\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/occ(11): require_once('\\\/srv\\\/www\\\/htdocs...')\\n#24 {main}\",\"File\":\"\\\/srv\\\/www\\\/htdocs\\\/owncloudtest\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Driver\\\/AbstractMySQLDriver.php\",\"Line\":115}","level":3,"time":"2016-04-26T09:36:13+00:00","method":"--","url":"--","user":"--"}

apparently related to BrokenUpdaterRepair.

Will attach the full log soon.

@PVince81
Contributor
% ls -l

-rw-r--r-- 1 wwwrun www  3737 Apr 26 11:36 .htaccess
-rw-r--r-- 1 wwwrun www   163 Apr 26 05:00 .user.ini
drwxr-xr-x 1 wwwrun www   592 Apr 26 11:33 3rdparty
-rw-r--r-- 1 wwwrun www  8065 Apr 26 05:00 AUTHORS
-rw-r--r-- 1 wwwrun www 34520 Apr 26 05:00 COPYING-AGPL
drwxrwxr-x 1 wwwrun www   578 Apr 26 11:33 __apps
drwxr-xr-x 1 wwwrun www    34 Apr 26 11:36 _oc_upgrade
drwxr-xr-x 1 wwwrun www     0 Apr 26 11:36 apps
drwxrwxr-x 1 wwwrun www    72 Apr 26 11:36 config
-rw-r--r-- 1 wwwrun www  3691 Apr 26 05:00 console.php
drwxr-xr-x 1 wwwrun www   312 Apr 26 05:04 core
-rw-r--r-- 1 wwwrun www  5919 Apr 26 05:00 cron.php
drwxrwx--- 1 wwwrun www   138 Apr 26 11:35 data
-rw-r--r-- 1 wwwrun www 32727 Apr 26 05:00 db_structure.xml
-rw-r--r-- 1 wwwrun www   179 Apr 26 05:00 index.html
-rw-r--r-- 1 wwwrun www  2026 Apr 26 05:00 index.php
drwxr-xr-x 1 wwwrun www    58 Apr 26 05:00 l10n
drwxr-xr-x 1 wwwrun www    78 Apr 26 05:00 lib
-rwxr-xr-x 1 wwwrun www   283 Apr 26 05:00 occ
drwxr-xr-x 1 wwwrun www    70 Apr 26 05:00 ocs
drwxr-xr-x 1 wwwrun www    42 Apr 26 05:00 ocs-provider
-rw-r--r-- 1 wwwrun www  2969 Apr 26 05:00 public.php
-rw-r--r-- 1 wwwrun www  4599 Apr 26 05:00 remote.php
drwxr-xr-x 1 wwwrun www    60 Apr 26 05:00 resources
-rw-r--r-- 1 wwwrun www    26 Apr 26 05:00 robots.txt
drwxr-xr-x 1 wwwrun www   288 Apr 26 05:00 settings
-rw-r--r-- 1 wwwrun www  1819 Apr 26 05:00 status.php
drwxr-xr-x 1 wwwrun www    26 Apr 26 11:33 themes
drwxr-xr-x 1 wwwrun www   330 Apr 26 11:35 updater
-rw-r--r-- 1 wwwrun www   232 Apr 26 05:03 version.php
@PVince81 PVince81 added this to the 9.0.2-current-maintenance milestone Apr 26, 2016
@LukasReschke
Member

@VicDeo Why is __apps not deleted in @PVince81's case as it is for us? 😕

@PVince81
Contributor

@LukasReschke it's still stuck on "Updating core", maybe it hasn't updated the apps yet.

Note that the update is hanging on this screen:
updater-confusion

and CPU is stuck at 100%, maybe an infinite loop.

@LukasReschke LukasReschke added a commit to owncloud/core that referenced this issue Apr 26, 2016
@LukasReschke LukasReschke Also exclude __apps
Workaround for owncloud/updater#331 for 9.0.2
2b25165
@LukasReschke LukasReschke referenced this issue in owncloud/core Apr 26, 2016
Closed

Also exclude __apps #24273

@PVince81
Contributor

Forgot to mention the permissions: I only did chmod g+w owncloudtest on the main folder, not on all subfolders. Does it matter ?

@PVince81 PVince81 referenced this issue Apr 26, 2016
Closed

More spinners #330

0 of 2 tasks complete
@LukasReschke
Member

It's not related to the repair step itself but more to the fact that in your case somehow __apps is still there. I'd propose:

9.0.2:

9.1.0:

  • Move cache from integrity check to file
@PVince81
Contributor

Can we move "store __apps in data folder" to 9.0.3 ? Running out of time and there are other updater issues that need adressing

@LukasReschke
Member

Can we move "store __apps in data folder" to 9.0.3 ? Running out of time and there are other updater issues that need adressing

Fair enough. But we should do this within the 9.0.x cycle :)

@PVince81
Contributor

@LukasReschke understood, I'll move the ticket to 9.0.3 then.

@PVince81
Contributor

My exact steps now, just in case:

  1. Run these
/srv/www/htdocs # rm -Rf owncloudtest/
/srv/www/htdocs # cp -R ~vincent/temp/owncloud-9.0.0 owncloudtest
/srv/www/htdocs # chown -R wwwrun:www owncloudtest
/srv/www/htdocs # cd owncloudtest
/srv/www/htdocs/owncloudtest # mkdir -p data; chown -R wwwrun:www config data; chgrp www apps; chmod g+w apps config data
  1. Run setup in web UI with DB "owncloudtest"
  2. Go to "Updater" section in admin page
  3. Switch dropdown to "daily"
  4. Reload page
  5. Click "Open updater"
  6. Click "Start"
  7. Wait

Additionally, I redid the update with the php5-pcntl module enabled to avoid the warnings, but the same symptoms appears. So the absence of this module isn't related to my issue.

@PVince81 PVince81 added a commit to owncloud/core that referenced this issue Apr 26, 2016
@LukasReschke @PVince81 LukasReschke + PVince81 Also exclude __apps
Workaround for owncloud/updater#331 for 9.0.2
590ed3e
@PVince81 PVince81 referenced this issue in owncloud/core Apr 26, 2016
Merged

[stable9] Also exclude __apps #24292

@PVince81
Contributor

Fixed through owncloud/core#24292

@PVince81 PVince81 closed this Apr 26, 2016
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