[Bioperl-l] Redmine server down
Fields, Christopher J
cjfields at illinois.edu
Fri Aug 16 17:52:35 UTC 2013
I'm beginning to think the same re: transitioning to GitHub Issues, but there isn't real advantage to expending time on this unless everyone currently using redmine is on board with a move.
BTW, I can look into the redmine problems (I helped with Chris D. in setting it up), but I may need the .pem for it.
chris
On Aug 16, 2013, at 9:29 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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 * Your database schema may be out of date or nonexistant.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.
>>
>>
>>
>>
>
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