Migration failed from 9.2.7 to 9.3.1

Summary

I tried to migrate my gitlab-instance from 9.2.7 to 9.3.1 (was unable to update to 9.3.0 due to missing 32 bit-support of bootsnap, see #34084 (closed)) using a mysql-database. bundle install --without postgres development test --deployment went flawless, but bundle exec rake db:migrate RAILS_ENV=production ended up with an error.

Steps to reproduce

Update from 9.2.7 to 9.3.1

What is the current bug behavior?

Database migration stopped

What is the expected correct behavior?

Database migration shouldn't stop

Relevant logs and/or screenshots

== 20170511082759 RenameWebHooksBuildEventsToJobEvents: migrating =============
-- transaction_open?()
   -> 0.0001s
-- columns(:web_hooks)
   -> 0.0071s
-- add_column(:web_hooks, :job_events, :boolean, {:limit=>1, :precision=>nil, :scale=>nil})

StandardError: An error has occurred, all later migrations canceled:

Mysql2::Error: Duplicate column name 'job_events': ALTER TABLE `web_hooks` ADD `job_events` tinyint(1)/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/peek-mysql2-1.1.0/lib/peek/views/mysql2.rb:14:in `query'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/peek-mysql2-1.1.0/lib/peek/views/mysql2.rb:14:in `query_with_timing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:309:in `block in execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_adapter.rb:484:in `block in log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/notifications/instrumenter.rb:20:in `instrument'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_adapter.rb:478:in `log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:309:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/mysql2_adapter.rb:225:in `execute'
/home/git/gitlab/config/initializers/connection_fix.rb:20:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract/schema_statements.rb:407:in `add_column'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:665:in `block in method_missing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:634:in `block in say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:634:in `say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:654:in `method_missing'
/home/git/gitlab/lib/gitlab/database/migration_helpers.rb:317:in `rename_column_concurrently'
/home/git/gitlab/db/migrate/20170511082759_rename_web_hooks_build_events_to_job_events.rb:12:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:611:in `exec_migration'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:592:in `block (2 levels) in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:591:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract/connection_pool.rb:292:in `with_connection'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:590:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:768:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:998:in `block in execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:1046:in `ddl_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:997:in `execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:959:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:955:in `each'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:955:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:823:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:801:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/tasks/database_tasks.rb:137:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/railties/databases.rake:44:in `block (2 levels) in <top (required)>'
/usr/bin/bundle:22:in `load'
/usr/bin/bundle:22:in `<main>'
ActiveRecord::StatementInvalid: Mysql2::Error: Duplicate column name 'job_events': ALTER TABLE `web_hooks` ADD `job_events` tinyint(1)
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/peek-mysql2-1.1.0/lib/peek/views/mysql2.rb:14:in `query'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/peek-mysql2-1.1.0/lib/peek/views/mysql2.rb:14:in `query_with_timing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:309:in `block in execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_adapter.rb:484:in `block in log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/notifications/instrumenter.rb:20:in `instrument'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_adapter.rb:478:in `log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:309:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/mysql2_adapter.rb:225:in `execute'
/home/git/gitlab/config/initializers/connection_fix.rb:20:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract/schema_statements.rb:407:in `add_column'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:665:in `block in method_missing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:634:in `block in say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:634:in `say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:654:in `method_missing'
/home/git/gitlab/lib/gitlab/database/migration_helpers.rb:317:in `rename_column_concurrently'
/home/git/gitlab/db/migrate/20170511082759_rename_web_hooks_build_events_to_job_events.rb:12:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:611:in `exec_migration'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:592:in `block (2 levels) in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:591:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract/connection_pool.rb:292:in `with_connection'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:590:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:768:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:998:in `block in execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:1046:in `ddl_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:997:in `execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:959:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:955:in `each'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:955:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:823:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:801:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/tasks/database_tasks.rb:137:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/railties/databases.rake:44:in `block (2 levels) in <top (required)>'
/usr/bin/bundle:22:in `load'
/usr/bin/bundle:22:in `<main>'
Mysql2::Error: Duplicate column name 'job_events'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/peek-mysql2-1.1.0/lib/peek/views/mysql2.rb:14:in `query'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/peek-mysql2-1.1.0/lib/peek/views/mysql2.rb:14:in `query_with_timing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:309:in `block in execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_adapter.rb:484:in `block in log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/notifications/instrumenter.rb:20:in `instrument'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_adapter.rb:478:in `log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:309:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/mysql2_adapter.rb:225:in `execute'
/home/git/gitlab/config/initializers/connection_fix.rb:20:in `execute'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract/schema_statements.rb:407:in `add_column'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:665:in `block in method_missing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:634:in `block in say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:634:in `say_with_time'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:654:in `method_missing'
/home/git/gitlab/lib/gitlab/database/migration_helpers.rb:317:in `rename_column_concurrently'
/home/git/gitlab/db/migrate/20170511082759_rename_web_hooks_build_events_to_job_events.rb:12:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:611:in `exec_migration'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:592:in `block (2 levels) in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:591:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract/connection_pool.rb:292:in `with_connection'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:590:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:768:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:998:in `block in execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:1046:in `ddl_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:997:in `execute_migration_in_transaction'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:959:in `block in migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:955:in `each'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:955:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:823:in `up'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/migration.rb:801:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/tasks/database_tasks.rb:137:in `migrate'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/railties/databases.rake:44:in `block (2 levels) in <top (required)>'
/usr/bin/bundle:22:in `load'
/usr/bin/bundle:22:in `<main>'
Tasks: TOP => db:migrate
(See full trace by running task with --trace)

Output of checks

Results of GitLab environment info

Expand for output related to GitLab environment info 
System information
System:
Current User:   git
Using RVM:      no
Ruby Version:   2.3.4p301
Gem Version:    2.5.2
Bundler Version:1.15.1
Rake Version:   10.5.0
Redis Version:  3.2.9
Git Version:    2.13.2
Sidekiq Version:5.0.0
Go Version:     go1.8.3 linux/arm


GitLab information
Version:        9.3.1
Revision:       b2dd17b2f2
Directory:      /home/git/gitlab
DB Adapter:     mysql2
URL:            https://gitlab.sytes.net
HTTP Clone URL: https://gitlab.sytes.net/some-group/some-project.git
SSH Clone URL:  ssh://git@gitlab.sytes.net:2222/some-group/some-project.git
Using LDAP:     no
Using Omniauth: no


GitLab Shell
Version:        5.0.5
Repository storage paths:
  • default: /home/git/repositories Hooks: /home/git/gitlab-shell/hooks Git: /usr/bin/git

Results of GitLab application Check

Expand for output related to the GitLab application check 
Checking GitLab Shell ...


GitLab Shell version >= 5.0.5 ? ... OK (5.0.5)
Repo base directory exists?
default... yes
Repo storage directories are symlinks?
default... no
Repo paths owned by git:root, or git:git?
default... yes
Repo paths access is drwxrws---?
default... yes
hooks directories in repos are links: ...
3/1 ... rake aborted!
ActiveRecord::StatementInvalid: Mysql2::Error: Table 'gitlabhq_production.features' doesn't exist: SHOW FULL FIELDS FROM features
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/peek-mysql2-1.1.0/lib/peek/views/mysql2.rb:14:in query' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/peek-mysql2-1.1.0/lib/peek/views/mysql2.rb:14:in query_with_timing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:309:in block in execute' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_adapter.rb:484:in block in log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/notifications/instrumenter.rb:20:in instrument' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_adapter.rb:478:in log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:309:in execute' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/mysql2_adapter.rb:225:in execute'
/home/git/gitlab/config/initializers/connection_fix.rb:20:in execute' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:316:in execute_and_free'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:463:in columns' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/schema_cache.rb:43:in columns'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/attributes.rb:93:in columns' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/attributes.rb:98:in columns_hash'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/inheritance.rb:73:in descends_from_active_record?' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/inheritance.rb:79:in finder_needs_type_condition?'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/core.rb:256:in relation' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/scoping/named.rb:33:in default_scoped'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/scoping/named.rb:28:in all' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/flipper-active_record-0.10.2/lib/flipper/adapters/active_record.rb:43:in features'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/flipper-0.10.2/lib/flipper/adapters/memoizable.rb:36:in features' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/flipper-0.10.2/lib/flipper/dsl.rb:244:in features'
/home/git/gitlab/lib/feature.rb:16:in all' /home/git/gitlab/lib/feature.rb:27:in persisted?'
/home/git/gitlab/lib/gitlab/gitaly_client.rb:61:in feature_enabled?' /home/git/gitlab/lib/gitlab/gitaly_client.rb:72:in migrate'
/home/git/gitlab/lib/gitlab/git/repository.rb:1247:in gitaly_migrate' /home/git/gitlab/lib/gitlab/git/repository.rb:127:in branch_count'
/home/git/gitlab/app/models/repository.rb:508:in branch_count' /home/git/gitlab/app/models/repository.rb:51:in block (2 levels) in cache_method'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/cache.rb:299:in block in fetch' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/cache.rb:585:in block in save_block_result_to_cache'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/cache.rb:547:in block in instrument' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/notifications.rb:166:in instrument'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/cache.rb:547:in instrument' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/cache.rb:584:in save_block_result_to_cache'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/cache.rb:299:in fetch' /home/git/gitlab/lib/repository_cache.rb:20:in fetch'
/home/git/gitlab/app/models/repository.rb:1070:in cache_method_output' /home/git/gitlab/app/models/repository.rb:51:in block in cache_method'
/home/git/gitlab/app/models/repository.rb:83:in has_visible_content?' /home/git/gitlab/app/models/repository.rb:961:in empty_repo?'
/home/git/gitlab/app/models/project.rb:184:in empty_repo?' /home/git/gitlab/lib/tasks/gitlab/check.rake:190:in block in check_repos_hooks_directory_is_link'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/relation/batches.rb:51:in block (2 levels) in find_each' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/relation/batches.rb:51:in each'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/relation/batches.rb:51:in block in find_each' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/relation/batches.rb:124:in find_in_batches'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/relation/batches.rb:50:in find_each' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/querying.rb:9:in find_each'
/home/git/gitlab/lib/tasks/gitlab/check.rake:186:in check_repos_hooks_directory_is_link' /home/git/gitlab/lib/tasks/gitlab/check.rake:56:in block (3 levels) in <top (required)>'
/usr/bin/bundle:22:in load' /usr/bin/bundle:22:in '
Mysql2::Error: Table 'gitlabhq_production.features' doesn't exist
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/peek-mysql2-1.1.0/lib/peek/views/mysql2.rb:14:in query' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/peek-mysql2-1.1.0/lib/peek/views/mysql2.rb:14:in query_with_timing'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:309:in block in execute' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_adapter.rb:484:in block in log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/notifications/instrumenter.rb:20:in instrument' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_adapter.rb:478:in log'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:309:in execute' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/mysql2_adapter.rb:225:in execute'
/home/git/gitlab/config/initializers/connection_fix.rb:20:in execute' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:316:in execute_and_free'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:463:in columns' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/connection_adapters/schema_cache.rb:43:in columns'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/attributes.rb:93:in columns' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/attributes.rb:98:in columns_hash'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/inheritance.rb:73:in descends_from_active_record?' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/inheritance.rb:79:in finder_needs_type_condition?'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/core.rb:256:in relation' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/scoping/named.rb:33:in default_scoped'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/scoping/named.rb:28:in all' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/flipper-active_record-0.10.2/lib/flipper/adapters/active_record.rb:43:in features'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/flipper-0.10.2/lib/flipper/adapters/memoizable.rb:36:in features' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/flipper-0.10.2/lib/flipper/dsl.rb:244:in features'
/home/git/gitlab/lib/feature.rb:16:in all' /home/git/gitlab/lib/feature.rb:27:in persisted?'
/home/git/gitlab/lib/gitlab/gitaly_client.rb:61:in feature_enabled?' /home/git/gitlab/lib/gitlab/gitaly_client.rb:72:in migrate'
/home/git/gitlab/lib/gitlab/git/repository.rb:1247:in gitaly_migrate' /home/git/gitlab/lib/gitlab/git/repository.rb:127:in branch_count'
/home/git/gitlab/app/models/repository.rb:508:in branch_count' /home/git/gitlab/app/models/repository.rb:51:in block (2 levels) in cache_method'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/cache.rb:299:in block in fetch' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/cache.rb:585:in block in save_block_result_to_cache'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/cache.rb:547:in block in instrument' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/notifications.rb:166:in instrument'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/cache.rb:547:in instrument' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/cache.rb:584:in save_block_result_to_cache'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activesupport-4.2.8/lib/active_support/cache.rb:299:in fetch' /home/git/gitlab/lib/repository_cache.rb:20:in fetch'
/home/git/gitlab/app/models/repository.rb:1070:in cache_method_output' /home/git/gitlab/app/models/repository.rb:51:in block in cache_method'
/home/git/gitlab/app/models/repository.rb:83:in has_visible_content?' /home/git/gitlab/app/models/repository.rb:961:in empty_repo?'
/home/git/gitlab/app/models/project.rb:184:in empty_repo?' /home/git/gitlab/lib/tasks/gitlab/check.rake:190:in block in check_repos_hooks_directory_is_link'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/relation/batches.rb:51:in block (2 levels) in find_each' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/relation/batches.rb:51:in each'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/relation/batches.rb:51:in block in find_each' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/relation/batches.rb:124:in find_in_batches'
/home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/relation/batches.rb:50:in find_each' /home/git/gitlab/vendor/bundle/ruby/2.3.0/gems/activerecord-4.2.8/lib/active_record/querying.rb:9:in find_each'
/home/git/gitlab/lib/tasks/gitlab/check.rake:186:in check_repos_hooks_directory_is_link' /home/git/gitlab/lib/tasks/gitlab/check.rake:56:in block (3 levels) in <top (required)>'
/usr/bin/bundle:22:in load' /usr/bin/bundle:22:in '
Tasks: TOP => gitlab:check => gitlab:gitlab_shell:check
(See full trace by running task with --trace)

Possible fixes

I don't know :( ...