[Bioperl-l] Redmine server down

Fri Aug 16 14:29:07 UTC 2013

Thanks - forwarded on to the root-l list for our volunteer
SysAdmin team to take a look at. The RedMine instance
had been playing up recently, perhaps more of the same?

If anyone knows enough about this to help, a volunteer
to look after the RedMine server would be appreciated.

Meanwhile BioRuby has already moved to GitHub issues,
and Biopython has started transitioning as well.

Regards,

Peter

On Fri, Aug 16, 2013 at 3:14 PM, Francisco J. Ossandón
<fossandonc at hotmail.com> wrote:
> Hello all,
>
> Not sure if there is an specific email to report about Redmine, but the
> webpage has not been responding for some days, and now it gives me the
> following message down below.
>
>
>
> Cheers,
>
>
>
> Francisco J. Ossandon
>
>
>
>
> Ruby on Rails application could not be started
>
>
> There appears to be a database problem.
>
> *       Your config/database.yml may not be written correctly. Please check
> it and fix any errors.
> *       Your database schema may be out of date or nonexistant. Please run
> rake db:migrate to ensure that the database schema is up-to-date.
> *       The database server may not be running. Please check whether it's
> running, and start it if it isn't.
>
> Error message:
>
> Can't connect to local MySQL server through socket
> '/var/lib/mysql/mysql.sock' (2) (Mysql::Error)
>
> Exception class:
>
> Mysql::Error
>
> Application root:
>
> /home/webapps/redmine-1.1.1
>
> Backtrace:
>
>
> #
>
> File
>
> Line
>
> Location
>
>
> 0
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/mysql_adapter.rb
>
> 589
>
> in `real_connect'
>
>
> 1
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/mysql_adapter.rb
>
> 589
>
> in `connect'
>
>
> 2
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/mysql_adapter.rb
>
> 203
>
> in `initialize'
>
>
> 3
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/mysql_adapter.rb
>
> 75
>
> in `new'
>
>
> 4
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/mysql_adapter.rb
>
> 75
>
> in `mysql_connection'
>
>
> 5
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/abstract/connection_pool.rb
>
> 223
>
> in `send'
>
>
> 6
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/abstract/connection_pool.rb
>
> 223
>
> in `new_connection'
>
>
> 7
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/abstract/connection_pool.rb
>
> 245
>
> in `checkout_new_connection'
>
>
> 8
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/abstract/connection_pool.rb
>
> 188
>
> in `checkout'
>
>
> 9
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/abstract/connection_pool.rb
>
> 184
>
> in `loop'
>
>
> 10
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/abstract/connection_pool.rb
>
> 184
>
> in `checkout'
>
>
> 11
>
> /usr/lib/ruby/1.8/monitor.rb
>
> 242
>
> in `synchronize'
>
>
> 12
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/abstract/connection_pool.rb
>
> 183
>
> in `checkout'
>
>
> 13
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/abstract/connection_pool.rb
>
> 98
>
> in `connection'
>
>
> 14
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/abstract/connection_pool.rb
>
> 326
>
> in `retrieve_connection'
>
>
> 15
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/abstract/connection_specification.rb
>
> 123
>
> in `retrieve_connection'
>
>
> 16
>
> /home/webapps/redmine-1.1.1/vendor/rails/activerecord/lib/active_record/conn
> ection_adapters/abstract/connection_specification.rb
>
> 115
>
> in `connection'
>
>
> 17
>
> /home/webapps/redmine-1.1.1/vendor/plugins/awesome_nested_set/lib/awesome_ne
> sted_set.rb
>
> 217
>
> in `quoted_left_column_name'
>
>
> 18
>
> /home/webapps/redmine-1.1.1/vendor/plugins/awesome_nested_set/lib/awesome_ne
> sted_set.rb
>
> 93
>
> in `acts_as_nested_set'
>
>
> 19
>
> /home/webapps/redmine-1.1.1/app/models/issue.rb
>
> 37
>
>
>
> 20
>
> /usr/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb
>
> 31
>
> in `gem_original_require'
>
>
> 21
>
> /usr/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb
>
> 31
>
> in `require'
>
>
> 22
>
> /home/webapps/redmine-1.1.1/vendor/rails/activesupport/lib/active_support/de
> pendencies.rb
>
> 158
>
> in `require'
>
>
> 23
>
> /home/webapps/redmine-1.1.1/vendor/rails/activesupport/lib/active_support/de
> pendencies.rb
>
> 265
>
> in `require_or_load_without_engine_additions'
>
>
> 24
>
> /home/webapps/redmine-1.1.1/vendor/plugins/engines/lib/engines/rails_extensi
> ons/dependencies.rb
>
> 132
>
> in `require_or_load'
>
>
> 25
>
> /home/webapps/redmine-1.1.1/vendor/rails/activesupport/lib/active_support/de
> pendencies.rb
>
> 224
>
> in `depend_on'
>
>
> 26
>
> /home/webapps/redmine-1.1.1/vendor/rails/activesupport/lib/active_support/de
> pendencies.rb
>
> 136
>
> in `require_dependency'
>
>
> 27
>
> /home/webapps/redmine-1.1.1/vendor/plugins/redmine_newissuealerts/init.rb
>
> 6
>
> in `evaluate_init_rb'
>
>
> 28
>
> /home/webapps/redmine-1.1.1/vendor/rails/activesupport/lib/active_support/ca
> llbacks.rb
>
> 182
>
> in `call'
>
>
> 29
>
> /home/webapps/redmine-1.1.1/vendor/rails/activesupport/lib/active_support/ca
> llbacks.rb
>
> 182
>
> in `evaluate_method'
>
>
> 30
>
> /home/webapps/redmine-1.1.1/vendor/rails/activesupport/lib/active_support/ca
> llbacks.rb
>
> 166
>
> in `call'
>
>
> 31
>
> /home/webapps/redmine-1.1.1/vendor/rails/activesupport/lib/active_support/ca
> llbacks.rb
>
> 90
>
> in `run'
>
>
> 32
>
> /home/webapps/redmine-1.1.1/vendor/rails/activesupport/lib/active_support/ca
> llbacks.rb
>
> 90
>
> in `each'
>
>
> 33
>
> /home/webapps/redmine-1.1.1/vendor/rails/activesupport/lib/active_support/ca
> llbacks.rb
>
> 90
>
> in `send'
>
>
> 34
>
> /home/webapps/redmine-1.1.1/vendor/rails/activesupport/lib/active_support/ca
> llbacks.rb
>
> 90
>
> in `run'
>
>
> 35
>
> /home/webapps/redmine-1.1.1/vendor/rails/activesupport/lib/active_support/ca
> llbacks.rb
>
> 276
>
> in `run_callbacks'
>
>
> 36
>
> /home/webapps/redmine-1.1.1/vendor/rails/actionpack/lib/action_controller/di
> spatcher.rb
>
> 51
>
> in `send'
>
>
> 37
>
> /home/webapps/redmine-1.1.1/vendor/rails/actionpack/lib/action_controller/di
> spatcher.rb
>
> 51
>
> in `run_prepare_callbacks'
>
>
> 38
>
> /home/webapps/redmine-1.1.1/vendor/rails/railties/lib/initializer.rb
>
> 631
>
> in `prepare_dispatcher'
>
>
> 39
>
> /home/webapps/redmine-1.1.1/vendor/rails/railties/lib/initializer.rb
>
> 185
>
> in `process'
>
>
> 40
>
> /home/webapps/redmine-1.1.1/vendor/rails/railties/lib/initializer.rb
>
> 113
>
> in `send'
>
>
> 41
>
> /home/webapps/redmine-1.1.1/vendor/rails/railties/lib/initializer.rb
>
> 113
>
> in `run'
>
>
> 42
>
> /home/webapps/redmine-1.1.1/config/environment.rb
>
> 23
>
>
>
> 43
>
> /usr/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb
>
> 31
>
> in `gem_original_require'
>
>
> 44
>
> /usr/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb
>
> 31
>
> in `require'
>
>
> 45
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/classic_ra
> ils/application_spawner.rb
>
> 222
>
> in `preload_application'
>
>
> 46
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/classic_ra
> ils/application_spawner.rb
>
> 181
>
> in `initialize_server'
>
>
> 47
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/utils.rb
>
> 572
>
> in `report_app_init_status'
>
>
> 48
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/classic_ra
> ils/application_spawner.rb
>
> 174
>
> in `initialize_server'
>
>
> 49
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/abstract_s
> erver.rb
>
> 204
>
> in `start_synchronously'
>
>
> 50
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/abstract_s
> erver.rb
>
> 180
>
> in `start'
>
>
> 51
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/classic_ra
> ils/application_spawner.rb
>
> 149
>
> in `start'
>
>
> 52
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/spawn_mana
> ger.rb
>
> 219
>
> in `spawn_rails_application'
>
>
> 53
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/abstract_s
> erver_collection.rb
>
> 132
>
> in `lookup_or_add'
>
>
> 54
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/spawn_mana
> ger.rb
>
> 214
>
> in `spawn_rails_application'
>
>
> 55
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/abstract_s
> erver_collection.rb
>
> 82
>
> in `synchronize'
>
>
> 56
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/abstract_s
> erver_collection.rb
>
> 79
>
> in `synchronize'
>
>
> 57
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/spawn_mana
> ger.rb
>
> 213
>
> in `spawn_rails_application'
>
>
> 58
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/spawn_mana
> ger.rb
>
> 132
>
> in `spawn_application'
>
>
> 59
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/spawn_mana
> ger.rb
>
> 275
>
> in `handle_spawn_application'
>
>
> 60
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/abstract_s
> erver.rb
>
> 357
>
> in `__send__'
>
>
> 61
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/abstract_s
> erver.rb
>
> 357
>
> in `server_main_loop'
>
>
> 62
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/lib/phusion_passenger/abstract_s
> erver.rb
>
> 206
>
> in `start_synchronously'
>
>
> 63
>
> /usr/lib/ruby/gems/1.8/gems/passenger-3.0.4/helper-scripts/passenger-spawn-s
> erver
>
> 99
>
>
>
> Powered by  <http://www.modrails.com/> Phusion Passenger, mod_rails /
> mod_rack for Apache.
>
>
>
>