Test and build the transmart Galaxy plugin

Build: #22 was successful

Job: Galaxy-Job-Main was successful

Stages & jobs

  1. Default Stage

Build log

The build generated 82 lines of output. Download or view full build log

11-Jan-2017 10:38:04 Build Release - Version 16.2 - 13-galaxy-blend4j-plugin - Galaxy-Job-Main #22 (DEPLOY-GLAXY-JOB1-22) started building on agent Default Agent
11-Jan-2017 10:38:04
11-Jan-2017 10:38:04 Build working directory is /opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1
11-Jan-2017 10:38:04 Executing build Release - Version 16.2 - 13-galaxy-blend4j-plugin - Galaxy-Job-Main #22 (DEPLOY-GLAXY-JOB1-22)
11-Jan-2017 10:38:04 Starting task 'Checkout Galaxy-release Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
11-Jan-2017 10:38:04 Updating source code to revision: f1effae8c78ff1a4c287393dc7ca454892166530
11-Jan-2017 10:38:05 Fetching 'refs/heads/release-16.2' from 'https://github.com/tranSMART-Foundation/blend4j-plugin.git'.
11-Jan-2017 10:38:05 Checking out revision f1effae8c78ff1a4c287393dc7ca454892166530.
11-Jan-2017 10:38:06 Already on 'release-16.2'
11-Jan-2017 10:38:06 Updated source code to revision: f1effae8c78ff1a4c287393dc7ca454892166530
11-Jan-2017 10:38:06 Finished task 'Checkout Galaxy-release Repository' with result: Success
11-Jan-2017 10:38:06 Running pre-build action: VCS Version Collector
11-Jan-2017 10:38:06 Skipping execution of task 'Grails test-app' as it is disabled
11-Jan-2017 10:38:06 Starting task 'Publish to repo.transmartfoundation.org' of type 'com.atlassian.bamboo.plugins.bamboo-grails-plugin:grailsBuilderTaskType'
11-Jan-2017 10:38:06
Beginning to execute external process for build 'Release - Version 16.2 - 13-galaxy-blend4j-plugin - Galaxy-Job-Main #22 (DEPLOY-GLAXY-JOB1-22)'
... running command line:
/opt/app/grails-wrapper/bin/grails upgrade -force -non-interactive
... in: /opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1
... using extra environment variables:
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bamboo_capability_system_builder_command_bash=/bin/bash
bamboo_repository_revision_number=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_repository_19333145_previous_revision_number=f1effae8c78ff1a4c287393dc7ca454892166530
GRAILS_HOME=/opt/app/grails-wrapper
bamboo_resultsUrl=https://ci.transmartfoundation.org/browse/DEPLOY-GLAXY-JOB1-22
bamboo_repository_19333145_branch_name=release-16.2
bamboo_planRepository_1_name=Galaxy-release
bamboo_build_working_directory=/opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1
bamboo_buildKey=DEPLOY-GLAXY-JOB1
bamboo_repository_19333145_git_repositoryUrl=https://github.com/tranSMART-Foundation/blend4j-plugin.git
bamboo_shortPlanName=13-galaxy-blend4j-plugin
bamboo_planRepository_name=Galaxy-release
bamboo_buildNumber=22
bamboo_shortJobName=Galaxy-Job-Main
bamboo_buildResultsUrl=https://ci.transmartfoundation.org/browse/DEPLOY-GLAXY-JOB1-22
bamboo_planRepository_repositoryUrl=https://github.com/tranSMART-Foundation/blend4j-plugin.git
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bamboo_planName=Release - Version 16.2 - 13-galaxy-blend4j-plugin
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bamboo_capability_system_hg_executable_ssh=system.hg.executable.ssh -o BatchMode=yes'
bamboo_planRepository_revision=f1effae8c78ff1a4c287393dc7ca454892166530
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bamboo_buildResultKey=DEPLOY-GLAXY-JOB1-22
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bamboo_repository_branch_name=release-16.2
bamboo_buildPlanName=Release - Version 16.2 - 13-galaxy-blend4j-plugin - Galaxy-Job-Main
bamboo_capability_system_jdk_JDK_1_7_0_25=/usr/lib/jvm/java-7-openjdk-amd64
bamboo_planRepository_1_revision=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_capability_system_hg_executable=system.hg.executable
bamboo_repository_name=Galaxy-release
JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64
bamboo_dependenciesDisabled=false
bamboo_capability_system_builder_mvn3_mvn=/usr/share/maven/
bamboo_planRepository_branch=release-16.2
bamboo_capability_system_builder_command_echo=/
bamboo_agentWorkingDirectory=/opt/bamboo/bamboo-home/xml-data/build-dir
bamboo_capability_system_git_executable=/usr/bin/git
bamboo_planRepository_1_previousRevision=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_repository_git_username=ricepeterm
bamboo_capability_system_builder_command_rm=/bin/rm
bamboo_planRepository_1_type=gh
bamboo_planRepository_branchName=release-16.2
bamboo_capability_system_builder_grailsBuilder_grails_wrapper=/opt/app/grails-wrapper
bamboo_repository_19333145_name=Galaxy-release
bamboo_repository_19333145_revision_number=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_planRepository_type=gh
bamboo_planRepository_1_username=ricepeterm
bamboo_ManualBuildTriggerReason_userName=peterrice
bamboo_repository_git_repositoryUrl=https://github.com/tranSMART-Foundation/blend4j-plugin.git
bamboo_capability_system_builder_ant_Ant=/usr/share/ant
bamboo_working_directory=/opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1
bamboo_planKey=DEPLOY-GLAXY
bamboo_planRepository_1_repositoryUrl=https://github.com/tranSMART-Foundation/blend4j-plugin.git
bamboo_planRepository_username=ricepeterm
bamboo_repository_19333145_git_username=ricepeterm
bamboo_capability_system_jdk_JDK_1_7=/usr/lib/jvm/java-7-openjdk-amd64
bamboo_repository_19333145_git_branch=release-16.2
bamboo_planRepository_1_branchName=release-16.2
PATH=/usr/lib/jvm/java-7-openjdk-amd64/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/puppetlabs/bin
11-Jan-2017 10:38:06 Ignoring grails upgrade
11-Jan-2017 10:38:06
Beginning to execute external process for build 'Release - Version 16.2 - 13-galaxy-blend4j-plugin - Galaxy-Job-Main #22 (DEPLOY-GLAXY-JOB1-22)'
... running command line:
/opt/app/grails-wrapper/bin/grails compile -non-interactive
... in: /opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=release-16.2
bamboo_capability_system_builder_command_bash=/bin/bash
bamboo_repository_revision_number=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_repository_19333145_previous_revision_number=f1effae8c78ff1a4c287393dc7ca454892166530
GRAILS_HOME=/opt/app/grails-wrapper
bamboo_resultsUrl=https://ci.transmartfoundation.org/browse/DEPLOY-GLAXY-JOB1-22
bamboo_repository_19333145_branch_name=release-16.2
bamboo_planRepository_1_name=Galaxy-release
bamboo_build_working_directory=/opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1
bamboo_buildKey=DEPLOY-GLAXY-JOB1
bamboo_repository_19333145_git_repositoryUrl=https://github.com/tranSMART-Foundation/blend4j-plugin.git
bamboo_shortPlanName=13-galaxy-blend4j-plugin
bamboo_planRepository_name=Galaxy-release
bamboo_buildNumber=22
bamboo_shortJobName=Galaxy-Job-Main
bamboo_buildResultsUrl=https://ci.transmartfoundation.org/browse/DEPLOY-GLAXY-JOB1-22
bamboo_planRepository_repositoryUrl=https://github.com/tranSMART-Foundation/blend4j-plugin.git
bamboo_agentId=229377
bamboo_planName=Release - Version 16.2 - 13-galaxy-blend4j-plugin
bamboo_shortPlanKey=GLAXY
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_JDK_1_7_0_21=/usr/lib/jvm/java-7-openjdk-amd64
bamboo_capability_system_hg_executable_ssh=system.hg.executable.ssh -o BatchMode=yes'
bamboo_planRepository_revision=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_repository_previous_revision_number=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_buildTimeStamp=2017-01-11T10:38:04.937+01:00
bamboo_planRepository_previousRevision=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_buildResultKey=DEPLOY-GLAXY-JOB1-22
bamboo_repository_git_branch=release-16.2
bamboo_repository_branch_name=release-16.2
bamboo_buildPlanName=Release - Version 16.2 - 13-galaxy-blend4j-plugin - Galaxy-Job-Main
bamboo_capability_system_jdk_JDK_1_7_0_25=/usr/lib/jvm/java-7-openjdk-amd64
bamboo_planRepository_1_revision=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_capability_system_hg_executable=system.hg.executable
bamboo_repository_name=Galaxy-release
JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64
bamboo_dependenciesDisabled=false
bamboo_capability_system_builder_mvn3_mvn=/usr/share/maven/
bamboo_planRepository_branch=release-16.2
bamboo_capability_system_builder_command_echo=/
bamboo_agentWorkingDirectory=/opt/bamboo/bamboo-home/xml-data/build-dir
bamboo_capability_system_git_executable=/usr/bin/git
bamboo_planRepository_1_previousRevision=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_repository_git_username=ricepeterm
bamboo_capability_system_builder_command_rm=/bin/rm
bamboo_planRepository_1_type=gh
bamboo_planRepository_branchName=release-16.2
bamboo_capability_system_builder_grailsBuilder_grails_wrapper=/opt/app/grails-wrapper
bamboo_repository_19333145_name=Galaxy-release
bamboo_repository_19333145_revision_number=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_planRepository_type=gh
bamboo_planRepository_1_username=ricepeterm
bamboo_ManualBuildTriggerReason_userName=peterrice
bamboo_repository_git_repositoryUrl=https://github.com/tranSMART-Foundation/blend4j-plugin.git
bamboo_capability_system_builder_ant_Ant=/usr/share/ant
bamboo_working_directory=/opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1
bamboo_planKey=DEPLOY-GLAXY
bamboo_planRepository_1_repositoryUrl=https://github.com/tranSMART-Foundation/blend4j-plugin.git
bamboo_planRepository_username=ricepeterm
bamboo_repository_19333145_git_username=ricepeterm
bamboo_capability_system_jdk_JDK_1_7=/usr/lib/jvm/java-7-openjdk-amd64
bamboo_repository_19333145_git_branch=release-16.2
bamboo_planRepository_1_branchName=release-16.2
PATH=/usr/lib/jvm/java-7-openjdk-amd64/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/puppetlabs/bin
11-Jan-2017 10:38:06 | Loading Grails 2.3.7
11-Jan-2017 10:38:07 | Configuring classpath
11-Jan-2017 10:38:08 | Downloading: org/grails/plugins/tomcat/7.0.50/tomcat-7.0.50.pom
11-Jan-2017 10:38:09 | Downloading: org/grails/plugins/tomcat/7.0.50/tomcat-7.0.50.zip
11-Jan-2017 10:38:10 | Downloading: org/grails/plugins/transmart-legacy-db/16.2/transmart-legacy-db-16.2.pom
11-Jan-2017 10:38:10 | Downloading: org/grails/plugins/hibernate/3.6.10.7/hibernate-3.6.10.7.zip
11-Jan-2017 10:38:11 | Downloading: org/grails/plugins/transmart-legacy-db/16.2/transmart-legacy-db-16.2.zip
11-Jan-2017 10:38:12 | Downloading: org/grails/plugins/transmart-legacy-db/16.2/transmart-legacy-db-16.2.zip.
11-Jan-2017 10:38:12 | Environment set to development
11-Jan-2017 10:38:12 | Environment set to development.
11-Jan-2017 10:38:12 | Environment set to development..
11-Jan-2017 10:38:12 | Environment set to development...
11-Jan-2017 10:38:12 | Environment set to development....
11-Jan-2017 10:38:13 | Environment set to development.....
11-Jan-2017 10:38:14
Beginning to execute external process for build 'Release - Version 16.2 - 13-galaxy-blend4j-plugin - Galaxy-Job-Main #22 (DEPLOY-GLAXY-JOB1-22)'
... running command line:
/opt/app/grails-wrapper/bin/grails publish-plugin --repository=repo.transmartfoundation.org-releases --allow-overwrite -non-interactive
... in: /opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=release-16.2
bamboo_capability_system_builder_command_bash=/bin/bash
bamboo_repository_revision_number=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_repository_19333145_previous_revision_number=f1effae8c78ff1a4c287393dc7ca454892166530
GRAILS_HOME=/opt/app/grails-wrapper
bamboo_resultsUrl=https://ci.transmartfoundation.org/browse/DEPLOY-GLAXY-JOB1-22
bamboo_repository_19333145_branch_name=release-16.2
bamboo_planRepository_1_name=Galaxy-release
bamboo_build_working_directory=/opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1
bamboo_buildKey=DEPLOY-GLAXY-JOB1
bamboo_repository_19333145_git_repositoryUrl=https://github.com/tranSMART-Foundation/blend4j-plugin.git
bamboo_shortPlanName=13-galaxy-blend4j-plugin
bamboo_planRepository_name=Galaxy-release
bamboo_buildNumber=22
bamboo_shortJobName=Galaxy-Job-Main
bamboo_buildResultsUrl=https://ci.transmartfoundation.org/browse/DEPLOY-GLAXY-JOB1-22
bamboo_planRepository_repositoryUrl=https://github.com/tranSMART-Foundation/blend4j-plugin.git
bamboo_agentId=229377
bamboo_planName=Release - Version 16.2 - 13-galaxy-blend4j-plugin
bamboo_shortPlanKey=GLAXY
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_JDK_1_7_0_21=/usr/lib/jvm/java-7-openjdk-amd64
bamboo_capability_system_hg_executable_ssh=system.hg.executable.ssh -o BatchMode=yes'
bamboo_planRepository_revision=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_repository_previous_revision_number=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_buildTimeStamp=2017-01-11T10:38:04.937+01:00
bamboo_planRepository_previousRevision=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_buildResultKey=DEPLOY-GLAXY-JOB1-22
bamboo_repository_git_branch=release-16.2
bamboo_repository_branch_name=release-16.2
bamboo_buildPlanName=Release - Version 16.2 - 13-galaxy-blend4j-plugin - Galaxy-Job-Main
bamboo_capability_system_jdk_JDK_1_7_0_25=/usr/lib/jvm/java-7-openjdk-amd64
bamboo_planRepository_1_revision=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_capability_system_hg_executable=system.hg.executable
bamboo_repository_name=Galaxy-release
JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64
bamboo_dependenciesDisabled=false
bamboo_capability_system_builder_mvn3_mvn=/usr/share/maven/
bamboo_planRepository_branch=release-16.2
bamboo_capability_system_builder_command_echo=/
bamboo_agentWorkingDirectory=/opt/bamboo/bamboo-home/xml-data/build-dir
bamboo_capability_system_git_executable=/usr/bin/git
bamboo_planRepository_1_previousRevision=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_repository_git_username=ricepeterm
bamboo_capability_system_builder_command_rm=/bin/rm
bamboo_planRepository_1_type=gh
bamboo_planRepository_branchName=release-16.2
bamboo_capability_system_builder_grailsBuilder_grails_wrapper=/opt/app/grails-wrapper
bamboo_repository_19333145_name=Galaxy-release
bamboo_repository_19333145_revision_number=f1effae8c78ff1a4c287393dc7ca454892166530
bamboo_planRepository_type=gh
bamboo_planRepository_1_username=ricepeterm
bamboo_ManualBuildTriggerReason_userName=peterrice
bamboo_repository_git_repositoryUrl=https://github.com/tranSMART-Foundation/blend4j-plugin.git
bamboo_capability_system_builder_ant_Ant=/usr/share/ant
bamboo_working_directory=/opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1
bamboo_planKey=DEPLOY-GLAXY
bamboo_planRepository_1_repositoryUrl=https://github.com/tranSMART-Foundation/blend4j-plugin.git
bamboo_planRepository_username=ricepeterm
bamboo_repository_19333145_git_username=ricepeterm
bamboo_capability_system_jdk_JDK_1_7=/usr/lib/jvm/java-7-openjdk-amd64
bamboo_repository_19333145_git_branch=release-16.2
bamboo_planRepository_1_branchName=release-16.2
PATH=/usr/lib/jvm/java-7-openjdk-amd64/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/puppetlabs/bin
11-Jan-2017 10:38:14 | Loading Grails 2.3.7
11-Jan-2017 10:38:15 | Configuring classpath
11-Jan-2017 10:38:18 | Configuring classpath.
11-Jan-2017 10:38:18 | Environment set to development
11-Jan-2017 10:38:18 | Environment set to development.
11-Jan-2017 10:38:18 | Environment set to development..
11-Jan-2017 10:38:18 | Environment set to development...
11-Jan-2017 10:38:18 | Environment set to development....
11-Jan-2017 10:38:19 | Environment set to development.....
11-Jan-2017 10:38:19 | Packaging Grails application
11-Jan-2017 10:38:19 | Packaging Grails application.
11-Jan-2017 10:38:19 | Packaging Grails application..
11-Jan-2017 10:38:19 | Packaging Grails application...
11-Jan-2017 10:38:19 | Packaging Grails application....
11-Jan-2017 10:38:19 | Packaging Grails application.....
11-Jan-2017 10:38:21 | Plugin packaged grails-blend4j-plugin-16.2.zip
11-Jan-2017 10:38:21 | Plugin packaged grails-blend4j-plugin-16.2.zip
11-Jan-2017 10:38:21 | Generating POM file...
11-Jan-2017 10:38:21 | Generating POM file....
11-Jan-2017 10:38:21 | Generating POM file.....
11-Jan-2017 10:38:22 | POM generated: /opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1/target/pom.xml
11-Jan-2017 10:38:22 WARN: No SCM provider installed.
11-Jan-2017 10:38:22 Publishing to Maven repository 'repo.transmartfoundation.org-releases'
11-Jan-2017 10:38:22 Using configured username and password from grails.project.repos.repo.transmartfoundation.org-releases
11-Jan-2017 10:38:22 WARNING: unknown protocol 'https' for repository 'repo.transmartfoundation.org-releases'
11-Jan-2017 10:38:22 This version of the plugin has already been published, it will be overwritten.
11-Jan-2017 10:38:22 | POM generated: /opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1/target/pom.xml.
11-Jan-2017 10:38:22 | POM generated: /opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1/target/pom.xml..
11-Jan-2017 10:38:22 | POM generated: /opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1/target/pom.xml...
11-Jan-2017 10:38:23 | POM generated: /opt/bamboo/bamboo-home/xml-data/build-dir/DEPLOY-GLAXY-JOB1/target/pom.xml....
11-Jan-2017 10:38:23 No default portal defined for repository 'repo.transmartfoundation.org-releases' - skipping portal notification
11-Jan-2017 10:38:23 Finished task 'Publish to repo.transmartfoundation.org' with result: Success
11-Jan-2017 10:38:23 Running post build plugin 'npm Cache Cleanup'
11-Jan-2017 10:38:23 Running post build plugin 'NCover Results Collector'
11-Jan-2017 10:38:23 Running post build plugin 'Clover Results Collector'
11-Jan-2017 10:38:23 Running post build plugin 'Docker Container Cleanup'
11-Jan-2017 10:38:23 Running post build plugin 'Artifact Copier'
11-Jan-2017 10:38:23 Finalising the build...
11-Jan-2017 10:38:23 Stopping timer.
11-Jan-2017 10:38:23 Build DEPLOY-GLAXY-JOB1-22 completed.
11-Jan-2017 10:38:23 Running on server: post build plugin 'NCover Results Collector'
11-Jan-2017 10:38:23 Running on server: post build plugin 'Clover Delta Calculator'
11-Jan-2017 10:38:23 Running on server: post build plugin 'Maven Dependencies Postprocessor'
11-Jan-2017 10:38:23 Running on server: post build plugin 'Build Hanging Detection Configuration'
11-Jan-2017 10:38:23 All post build plugins have finished
11-Jan-2017 10:38:23 Generating build results summary...
11-Jan-2017 10:38:23 Saving build results to disk...
11-Jan-2017 10:38:23 Logging substituted variables...
11-Jan-2017 10:38:23 Indexing build results...
11-Jan-2017 10:38:23 Finished building DEPLOY-GLAXY-JOB1-22.