{"PID":16970,"command":"[gem list --details bundler]","dir":"services/api","level":"info","msg":"executing","time":"2020-11-05T17:30:08.060896638-03:00"}
[openssl] ..................................................[services/api: bundle] Don't run Bundler as root. Bundler can ask for sudo if it is needed, and installing your bundle as root will break this application for all non-root users on this machine.
[-D] The files belonging to this database system will be owned by user "postgres".
[-D] This user must also own the server process.
[-D]
[-D] The database cluster will be initialized with locale "en_US.UTF-8".
[-D] The default text search configuration will be set to "english".
[-D]
[-D] Data page checksums are disabled.
[-D]
[-D] fixing permissions on existing directory /tmp/arvados-server-boot-420120283/pgdata ... ok
[-D] creating subdirectories ... ok
[-D] selecting default max_connections ... 100
[-D] selecting default shared_buffers ... 128MB
[-D] selecting default timezone ... [services/api: bundle] Using rake 13.0.1
[services/api: bundle] Using concurrent-ruby 1.1.6
[services/api: bundle] Using i18n 0.9.5
[services/api: bundle] Using minitest 5.10.3
[services/api: bundle] Using thread_safe 0.3.6
[services/api: bundle] Using tzinfo 1.2.7
[services/api: bundle] Using activesupport 5.2.4.3
[services/api: bundle] Using builder 3.2.4
[services/api: bundle] Using erubi 1.9.0
[services/api: bundle] Using mini_portile2 2.4.0
[services/api: bundle] Using nokogiri 1.10.10
[services/api: bundle] Using rails-dom-testing 2.0.3
[services/api: bundle] Using crass 1.0.6
[services/api: bundle] Using loofah 2.6.0
[services/api: bundle] Using rails-html-sanitizer 1.3.0
[services/api: bundle] Using actionview 5.2.4.3
[services/api: bundle] Using rack 2.2.3
[services/api: bundle] Using rack-test 1.1.0
[services/api: bundle] Using actionpack 5.2.4.3
[services/api: bundle] Using nio4r 2.5.2
[services/api: bundle] Using websocket-extensions 0.1.5
[services/api: bundle] Using websocket-driver 0.7.3
[services/api: bundle] Using actioncable 5.2.4.3
[services/api: bundle] Using globalid 0.4.2
[services/api: bundle] Using activejob 5.2.4.3
[services/api: bundle] Using mini_mime 1.0.2
[services/api: bundle] Using mail 2.7.1
[services/api: bundle] Using actionmailer 5.2.4.3
[services/api: bundle] Using activemodel 5.2.4.3
[services/api: bundle] Using arel 9.0.0
[services/api: bundle] Using activerecord 5.2.4.3
[services/api: bundle] Using mimemagic 0.3.5
[services/api: bundle] Using marcel 0.3.3
[services/api: bundle] Using activestorage 5.2.4.3
[services/api: bundle] Using acts_as_api 1.0.1
[services/api: bundle] Using public_suffix 4.0.3
[services/api: bundle] Using addressable 2.7.0
[services/api: bundle] Using andand 1.3.3
[services/api: bundle] Using extlib 0.9.16
[services/api: bundle] Using multi_json 1.14.1
[services/api: bundle] Using autoparse 0.3.3
[services/api: bundle] Using multipart-post 2.1.1
[services/api: bundle] Using faraday 0.15.4
[services/api: bundle] Using jwt 1.5.6
[services/api: bundle] Using memoist 0.16.2
[services/api: bundle] Using os 1.0.1
[services/api: bundle] Using signet 0.11.0
[services/api: bundle] Using googleauth 0.9.0
[services/api: bundle] Using launchy 2.4.3
[services/api: bundle] Using retriable 1.4.1
[services/api: bundle] Using arvados-google-api-client 0.8.7.4
[services/api: bundle] Using json 2.3.0
[services/api: bundle] Using arvados 1.5.0.pre20200114202620 from https://github.com/arvados/arvados.git (at /media/psf/arvados/services/api/vendor/cache/arvados-81725af5d5d2@81725af)
[services/api: bundle] Using msgpack 1.3.3
[services/api: bundle] Using bootsnap 1.4.7
[services/api: bundle] Using bundler 1.17.3
[services/api: bundle] Using byebug 11.0.1
[services/api: bundle] Using highline 2.0.1
[services/api: bundle] Using net-ssh 5.2.0
[services/api: bundle] Using net-scp 2.0.0
[services/api: bundle] Using net-sftp 2.1.2
[services/api: bundle] Using net-ssh-gateway 2.0.0
[services/api: bundle] Using capistrano 2.15.9
[services/api: bundle] Using execjs 2.7.0
[services/api: bundle] Using factory_bot 5.0.2
[services/api: bundle] Using method_source 1.0.0
[services/api: bundle] Using thor 1.0.1
[services/api: bundle] Using railties 5.2.4.3
[services/api: bundle] Using factory_bot_rails 5.0.1
[services/api: bundle] Using ffi 1.9.25
[services/api: bundle] Using hashie 3.6.0
[services/api: bundle] Using httpclient 2.8.3
[services/api: bundle] Using jquery-rails 4.3.3
[services/api: bundle] Using libv8 3.16.14.19 (x86_64-linux)
[services/api: bundle] Using rb-fsevent 0.10.3
[services/api: bundle] Using rb-inotify 0.9.10
[services/api: bundle] Using listen 3.2.1
[services/api: bundle] Using request_store 1.4.1
[services/api: bundle] Using lograge 0.10.0
[services/api: bundle] Using logstash-event 1.2.02
[services/api: bundle] Using metaclass 0.0.4
[services/api: bundle] Using mocha 1.8.0
[services/api: bundle] Using multi_xml 0.6.0
[services/api: bundle] Using oauth2 1.4.1
[services/api: bundle] Using oj 3.9.2
[services/api: bundle] Using omniauth 1.4.3
[services/api: bundle] Using omniauth-oauth2 1.5.0
[services/api: bundle] Using optimist 3.0.0
[services/api: bundle] Using passenger 6.0.2
[services/api: bundle] Using pg 1.1.4
[services/api: bundle] Using power_assert 1.1.4
[services/api: bundle] Using sprockets 3.7.2
[services/api: bundle] Using sprockets-rails 3.2.1
[services/api: bundle] Using rails 5.2.4.3
[services/api: bundle] Using rails-controller-testing 1.0.4
[services/api: bundle] Using rails-observers 0.1.5
[services/api: bundle] Using rails-perftest 0.0.7
[services/api: bundle] Using ref 2.0.0
[services/api: bundle] Using responders 2.4.1
[services/api: bundle] Using ruby-prof 0.15.9
[services/api: bundle] Using rvm-capistrano 1.5.6
[services/api: bundle] Using safe_yaml 1.0.5
[services/api: bundle] Using sass-listen 4.0.0
[services/api: bundle] Using sass 3.5.5
[services/api: bundle] Using tilt 2.0.8
[services/api: bundle] Using sass-rails 5.0.7
[services/api: bundle] Using simplecov-html 0.7.1
[services/api: bundle] Using simplecov 0.7.1
[services/api: bundle] Using simplecov-rcov 0.2.3
[services/api: bundle] Using sshkey 2.0.0
[services/api: bundle] Using test-unit 3.3.1
[services/api: bundle] Using themes_for_rails 0.5.1 from https://github.com/arvados/themes_for_rails (at /media/psf/arvados/services/api/vendor/cache/themes_for_rails-ddf6e592b3b6@ddf6e59)
[keep-web] {"level":"info","msg":"Listening at 127.0.0.1:32871","time":"2020-11-05T17:30:13.679582238-03:00"}
ok
[-D] syncing data to disk ... {"PID":16970,"command":"[/tmp/arvados-server-boot-420120283/bin/keepstore -version]","dir":"/tmp/arvados-server-boot-420120283","level":"info","msg":"executing","time":"2020-11-05T17:30:14.282407250-03:00"}
[-D] WARNING: enabling "trust" authentication for local connections
[-D] You can change this by editing pg_hba.conf or using the option -A, or
[-D] --auth-local and --auth-host, the next time you run initdb.
[-D] ok
[-D]
[-D] Success. You can now start the database server using:
{"PID":16970,"command":"[gem list --details bundler]","dir":"apps/workbench","level":"info","msg":"executing","time":"2020-11-05T17:30:17.253897623-03:00"}
[apps/workbench: bundle] Don't run Bundler as root. Bundler can ask for sudo if it is needed, and installing your bundle as root will break this application for all non-root users on this machine.
[services/api: passenger] [ W 2020-11-05 17:30:18.1602 17418/T1 age/Wat/WatchdogMain.cpp:1079 ]: WARNING: potential privilege escalation vulnerability detected. Phusion Passenger is running as root, and part(s) of the Passenger instance directory (/tmp/arvados-server-boot-420120283) can be changed by non-root user(s):
[services/api: passenger]
[services/api: passenger] - /tmp/arvados-server-boot-420120283 is not secure: it can be modified by user nobody
[services/api: passenger]
[services/api: passenger] Please either fix up the permissions for the insecure paths, or use a different location for the instance dir that can only be modified by root.
[apps/workbench: bundle] Using concurrent-ruby 1.1.6
[apps/workbench: bundle] Using i18n 0.9.5
[apps/workbench: bundle] Using minitest 5.10.3
[apps/workbench: bundle] Using thread_safe 0.3.6
[apps/workbench: bundle] Using tzinfo 1.2.7
[apps/workbench: bundle] Using activesupport 5.2.4.3
[apps/workbench: bundle] Using builder 3.2.4
[apps/workbench: bundle] Using erubi 1.9.0
[apps/workbench: bundle] Using mini_portile2 2.4.0
[apps/workbench: bundle] Using nokogiri 1.10.10
[apps/workbench: bundle] Using rails-dom-testing 2.0.3
[apps/workbench: bundle] Using crass 1.0.6
[apps/workbench: bundle] Using loofah 2.6.0
[apps/workbench: bundle] Using rails-html-sanitizer 1.3.0
[apps/workbench: bundle] Using actionview 5.2.4.3
[apps/workbench: bundle] Using rack 2.2.3
[apps/workbench: bundle] Using rack-test 1.1.0
[apps/workbench: bundle] Using actionpack 5.2.4.3
[apps/workbench: bundle] Using nio4r 2.5.2
[apps/workbench: bundle] Using websocket-extensions 0.1.5
[apps/workbench: bundle] Using websocket-driver 0.7.3
[apps/workbench: bundle] Using actioncable 5.2.4.3
[apps/workbench: bundle] Using globalid 0.4.2
[apps/workbench: bundle] Using activejob 5.2.4.3
[apps/workbench: bundle] Using mini_mime 1.0.2
[apps/workbench: bundle] Using mail 2.7.1
[apps/workbench: bundle] Using actionmailer 5.2.4.3
[apps/workbench: bundle] Using activemodel 5.2.4.3
[apps/workbench: bundle] Using arel 9.0.0
[apps/workbench: bundle] Using activerecord 5.2.4.3
[apps/workbench: bundle] Using activerecord-nulldb-adapter 0.3.9 from https://github.com/arvados/nulldb (at /media/psf/arvados/apps/workbench/vendor/cache/nulldb-d8e0073b665a@d8e0073)
[apps/workbench: bundle] Using mimemagic 0.3.5
[apps/workbench: bundle] Using marcel 0.3.3
[apps/workbench: bundle] Using activestorage 5.2.4.3
[apps/workbench: bundle] Using public_suffix 4.0.5
[apps/workbench: bundle] Using addressable 2.7.0
[apps/workbench: bundle] Using andand 1.3.3
[apps/workbench: bundle] Using angularjs-rails 1.3.15
[apps/workbench: bundle] Using extlib 0.9.16
[apps/workbench: bundle] Using multi_json 1.15.0
[apps/workbench: bundle] Using autoparse 0.3.3
[apps/workbench: bundle] Using multipart-post 2.1.1
[apps/workbench: bundle] Using faraday 0.15.4
[apps/workbench: bundle] Using jwt 1.5.6
[apps/workbench: bundle] Using memoist 0.16.2
[apps/workbench: bundle] Using os 1.1.1
[apps/workbench: bundle] Using signet 0.11.0
[apps/workbench: bundle] Using googleauth 0.9.0
[apps/workbench: bundle] Using launchy 2.4.3
[apps/workbench: bundle] Using retriable 1.4.1
[apps/workbench: bundle] Using arvados-google-api-client 0.8.7.4
[apps/workbench: bundle] Using json 2.3.0
[apps/workbench: bundle] Using arvados 1.5.0.pre20200114202620 from https://github.com/arvados/arvados.git (at /media/psf/arvados/apps/workbench/vendor/cache/arvados-c210114aa8c7@c210114)
[apps/workbench: bundle] Using execjs 2.7.0
[apps/workbench: bundle] Using autoprefixer-rails 9.5.1.1
[apps/workbench: bundle] Using msgpack 1.3.3
[apps/workbench: bundle] Using bootsnap 1.4.7
[apps/workbench: bundle] Using ffi 1.10.0
[apps/workbench: bundle] Using sassc 2.0.1
[apps/workbench: bundle] Using bootstrap-sass 3.4.1
[apps/workbench: bundle] Using method_source 1.0.0
[apps/workbench: bundle] Using thor 1.0.1
[apps/workbench: bundle] Using railties 5.2.4.3
[apps/workbench: bundle] Using bootstrap-tab-history-rails 0.1.0
[apps/workbench: bundle] Using bootstrap-x-editable-rails 1.5.1.1
[apps/workbench: bundle] Using bundler 1.17.3
[apps/workbench: bundle] Using byebug 11.0.1
[apps/workbench: bundle] Using highline 2.0.2
[apps/workbench: bundle] Using net-ssh 5.2.0
[apps/workbench: bundle] Using net-scp 2.0.0
[apps/workbench: bundle] Using net-sftp 2.1.2
[apps/workbench: bundle] Using net-ssh-gateway 2.0.0
[apps/workbench: bundle] Using capistrano 2.15.9
[apps/workbench: bundle] Using mime-types-data 3.2019.0331
[apps/workbench: bundle] Using mime-types 3.2.2
[apps/workbench: bundle] Using xpath 2.1.0
[apps/workbench: bundle] Using capybara 2.5.0
[apps/workbench: bundle] Using childprocess 0.9.0
[apps/workbench: bundle] Using cliver 0.3.2
[apps/workbench: bundle] Using coffee-script-source 1.12.2
[apps/workbench: bundle] Using coffee-script 2.4.1
[apps/workbench: bundle] Using coffee-rails 4.2.2
[apps/workbench: bundle] Using commonjs 0.2.7
[apps/workbench: bundle] Using deep_merge 1.2.1
[apps/workbench: bundle] Using docile 1.3.1
[apps/workbench: bundle] Using flamegraph 0.9.5
[apps/workbench: bundle] Using headless 1.0.2
[apps/workbench: bundle] Using httpclient 2.8.3
[apps/workbench: bundle] Using jquery-rails 4.3.3
[apps/workbench: bundle] Using less 2.6.0
[apps/workbench: bundle] Using sprockets 3.7.2
[apps/workbench: bundle] Using less-rails 4.0.0
[apps/workbench: bundle] Using libv8 3.16.14.19 (x86_64-linux)
[apps/workbench: bundle] Using request_store 1.4.1
[apps/workbench: bundle] Using lograge 0.10.0
[apps/workbench: bundle] Using logstash-event 1.2.02
[apps/workbench: bundle] Using metaclass 0.0.4
[apps/workbench: bundle] Using mocha 1.8.0
[apps/workbench: bundle] Using morrisjs-rails 0.5.1.2
[apps/workbench: bundle] Using sprockets-rails 3.2.1
[apps/workbench: bundle] Using rails 5.2.4.3
[apps/workbench: bundle] Using npm-rails 0.2.1
[apps/workbench: bundle] Using oj 3.7.12
[apps/workbench: bundle] Using passenger 6.0.2
[apps/workbench: bundle] Using piwik_analytics 1.0.2
[apps/workbench: bundle] Using poltergeist 1.5.1
[apps/workbench: bundle] Using rack-mini-profiler 1.0.2
[apps/workbench: bundle] Using rails-controller-testing 1.0.4
[apps/workbench: bundle] Using rails-perftest 0.0.7
[apps/workbench: bundle] Using raphael-rails 2.1.2
[apps/workbench: bundle] Using rb-fsevent 0.10.3
[apps/workbench: bundle] Using rb-inotify 0.10.0
[apps/workbench: bundle] Using ref 2.0.0
[apps/workbench: bundle] Using responders 2.4.1
[apps/workbench: bundle] Using ruby-debug-passenger 0.2.0
[apps/workbench: bundle] Using ruby-prof 0.17.0
[apps/workbench: bundle] Using rubyzip 1.3.0
[apps/workbench: bundle] Using rvm-capistrano 1.5.6
[apps/workbench: bundle] Using safe_yaml 1.0.5
[apps/workbench: bundle] Using sass-listen 4.0.0
[apps/workbench: bundle] Using sass 3.7.4
[apps/workbench: bundle] Using tilt 2.0.9
[apps/workbench: bundle] Using sassc-rails 2.1.0
[apps/workbench: bundle] Using selenium-webdriver 3.141.0
[apps/workbench: bundle] Using simplecov-html 0.10.2
[apps/workbench: bundle] Using simplecov 0.16.1
[apps/workbench: bundle] Using simplecov-rcov 0.2.3
[apps/workbench: bundle] Using sshkey 2.0.0
[apps/workbench: bundle] Using themes_for_rails 0.5.1 from https://github.com/arvados/themes_for_rails (at /media/psf/arvados/apps/workbench/vendor/cache/themes_for_rails-ddf6e592b3b6@ddf6e59)
[apps/workbench: bundle] Using therubyracer 0.12.3
[apps/workbench: bundle] Using uglifier 2.7.2
[apps/workbench: bundle] Updating files in vendor/cache
[services/api: passenger] [ N 2020-11-05 17:30:21.4001 17421/T8 age/Cor/SecurityUpdateChecker.h:519 ]: Security update check: no update found (next check in 24 hours)
[services/api: rake] [1m[35m (0.1ms)[0m [1m[35mSET TIME ZONE 'UTC'[0m
[services/api: rake] set_config
[services/api: rake] ------------
[services/api: rake]
[services/api: rake] (1 row)
[services/api: rake]
[services/api: passenger] App 17449 output: [1m[35m (0.6ms)[0m [1m[34mSELECT clock_timestamp() AT TIME ZONE 'UTC'[0m
[services/api: passenger] [ I 2020-11-05 17:30:23.3943 17421/Tf age/Cor/Spa/SmartSpawner.h:463 ]: Preloader for /media/psf/arvados/services/api started on PID 17449, listening on unix:/tmp/arvados-server-boot-420120283/passenger.Ltkue6W/apps.s/preloader.1h6yr0l
[services/api: passenger] App 17550 output: [1m[35m (0.1ms)[0m [1m[35mSET TIME ZONE 'UTC'[0m
[services/api: passenger] App 17550 output: [1m[36mUser Load (1.2ms)[0m [1m[34mSELECT "users".* FROM "users" WHERE (redirect_to_user_uuid is null) AND "users"."uuid" = $1 LIMIT $2[0m [["uuid", "zzzzz-tpzed-000000000000000"], ["LIMIT", 1]]
[services/api: passenger] App 17550 output: [1m[36mUser Load (0.6ms)[0m [1m[34mSELECT "users".* FROM "users" WHERE (redirect_to_user_uuid is null) AND "users"."uuid" = $1 ORDER BY "users"."id" ASC LIMIT $2[0m [["uuid", "zzzzz-tpzed-000000000000000"], ["LIMIT", 1]]
[services/api: passenger] App 17550 output: [1m[35m (1.2ms)[0m [1m[34mSELECT clock_timestamp() AT TIME ZONE 'UTC'[0m
[services/api: passenger] App 17550 output: [1m[35m (1.0ms)[0m [1m[34mSELECT COUNT(*) FROM "users" WHERE (redirect_to_user_uuid is null) AND "users"."uuid" = $1 AND (email = 'root') AND "users"."is_admin" = $2[0m [["uuid", "zzzzz-tpzed-000000000000000"], ["is_admin", true]]
[services/api: passenger] App 17550 output: [1m[35m (0.8ms)[0m [1m[34mSELECT COUNT(*) FROM "users" WHERE (redirect_to_user_uuid is null) AND "users"."uuid" = $1 AND (uuid not like '%-000000000000000') AND "users"."is_admin" = $2[0m [["uuid", "zzzzz-tpzed-000000000000000"], ["is_admin", true]]
[services/api: passenger] App 17550 output: select user_uuid, target_uuid, val as perm_level, traverse_owned from temp_perms_11405793009089601573 where val>0
[services/api: passenger] App 17550 output: on conflict (user_uuid, target_uuid) do update set perm_level=EXCLUDED.perm_level, traverse_owned=EXCLUDED.traverse_owned;
[services/api: rake] [1m[35m (0.6ms)[0m [1m[35mSET TIME ZONE 'UTC'[0m
[services/api: rake] [1m[35m (0.8ms)[0m [1m[34mSELECT "schema_migrations"."version" FROM "schema_migrations" ORDER BY "schema_migrations"."version" ASC[0m
[services/api: rake] [1m[35m (0.5ms)[0m [1m[34mSELECT clock_timestamp() AT TIME ZONE 'UTC'[0m
[services/api: rake] [1m[36mUser Load (1.0ms)[0m [1m[34mSELECT "users".* FROM "users" WHERE (redirect_to_user_uuid is null) AND "users"."uuid" = $1 ORDER BY "users"."id" ASC LIMIT $2[0m [["uuid", "zzzzz-tpzed-000000000000000"], ["LIMIT", 1]]
[services/api: rake] [1m[35m (0.6ms)[0m [1m[34mSELECT clock_timestamp() AT TIME ZONE 'UTC'[0m
[services/api: rake] [1m[35m (0.7ms)[0m [1m[34mSELECT COUNT(*) FROM "users" WHERE (redirect_to_user_uuid is null) AND "users"."uuid" = $1 AND (email = 'root') AND "users"."is_admin" = $2[0m [["uuid", "zzzzz-tpzed-000000000000000"], ["is_admin", true]]
[services/api: rake] [1m[35m (0.7ms)[0m [1m[34mSELECT COUNT(*) FROM "users" WHERE (redirect_to_user_uuid is null) AND "users"."uuid" = $1 AND (uuid not like '%-000000000000000') AND "users"."is_admin" = $2[0m [["uuid", "zzzzz-tpzed-000000000000000"], ["is_admin", true]]
[services/api: passenger] Stopping web server...nginx: [alert] could not open error log file: open() "/tmp/arvados-server-boot-420120283/passenger-standalone.10ef56t/logs/error.log" failed (2: No such file or directory)
[services/api: passenger] 2020/11/05 17:30:23 [emerg] 17591#0: open() "/tmp/arvados-server-boot-420120283/passenger-standalone.10ef56t/nginx.conf" failed (2: No such file or directory)
[services/api: passenger] PhusionPassenger::DaemonController::StopError: Daemon 'Nginx' failed to start.
[services/api: passenger] /root/.gem/ruby/2.5.0/gems/passenger-6.0.2/src/ruby_supportlib/phusion_passenger/vendor/daemon_controller.rb:448:in `rescue in kill_daemon'