Build #63

Build and run tests under Java 11

Build: #63 was successful

Job: Clover and Tests was successful

Stages & jobs

  1. Default Stage

Build log

The build generated 195 lines of output. Download or view full build log

30-Jun-2023 17:28:19 Build Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests #63 (JB-GDB329-JOB1-63) started building on agent Default Agent
30-Jun-2023 17:28:19
30-Jun-2023 17:28:19 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1
30-Jun-2023 17:28:19 Executing build Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests #63 (JB-GDB329-JOB1-63)
30-Jun-2023 17:28:19 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
30-Jun-2023 17:28:19 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1
30-Jun-2023 17:28:19 Updating source code to revision: bd990168d0b3c7772c961b56144c3dee94a09054
30-Jun-2023 17:28:19 Fetching 'refs/heads/releases/Release_2_11_2_Branch' from 'http://source.jalview.org/git/jalview.git'.
30-Jun-2023 17:28:19 Checking out revision bd990168d0b3c7772c961b56144c3dee94a09054.
30-Jun-2023 17:28:19 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164
30-Jun-2023 17:28:19    28bae9d..bd99016  releases/Release_2_11_2_Branch -> origin/releases/Release_2_11_2_Branch
30-Jun-2023 17:28:19 Already on 'releases/Release_2_11_2_Branch'
30-Jun-2023 17:28:19 Your branch is behind 'origin/releases/Release_2_11_2_Branch' by 1 commit, and can be fast-forwarded.
30-Jun-2023 17:28:19   (use "git pull" to update your local branch)
30-Jun-2023 17:28:19 HEAD is now at bd99016 JAL-4117 JAL-1551 source licensing
30-Jun-2023 17:28:19 Updated source code to revision: bd990168d0b3c7772c961b56144c3dee94a09054
30-Jun-2023 17:28:19 Finished task 'Checkout Default Repository' with result: Success
30-Jun-2023 17:28:19 Running pre-build action: VCS Version Collector
30-Jun-2023 17:28:19 Running pre-build action: Artifactory Release Staging
30-Jun-2023 17:28:19 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
30-Jun-2023 17:28:19 Bamboo Artifactory Plugin version: 2.6.2
30-Jun-2023 17:28:19
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests #63 (JB-GDB329-JOB1-63)'
... running command line:
/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test
... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=releases/Release_2_11_2_Branch
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=releases/Release_2_11_2_Branch
bamboo_repository_revision_number=bd990168d0b3c7772c961b56144c3dee94a09054
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB329-JOB1-63
JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048
bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1
bamboo_planRepository_1_name=Jalview Git
bamboo_buildKey=JB-GDB329-JOB1
bamboo_shortPlanName=releases-Release_2_11_2_Branch
bamboo_repository_27918600_previous_revision_number=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f
bamboo_planRepository_name=Jalview Git
bamboo_repository_27918600_name=Jalview Git
LOGNAME=bamboo
bamboo_buildNumber=63
PWD=/
bamboo_repository_27918600_git_username=
bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse
bamboo_shortJobName=Clover and Tests
bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB329-JOB1-63
bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git
SHELL=/bin/bash
bamboo_agentId=196609
bamboo_planName=Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch
bamboo_shortPlanKey=GDB329
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=bd990168d0b3c7772c961b56144c3dee94a09054
bamboo_buildTimeStamp=2023-06-30T17:28:19.294+01:00
bamboo_repository_previous_revision_number=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f
bamboo_repository_27918600_revision_number=bd990168d0b3c7772c961b56144c3dee94a09054
bamboo_planRepository_previousRevision=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f
bamboo_repository_git_branch=releases/Release_2_11_2_Branch
bamboo_buildResultKey=JB-GDB329-JOB1-63
bamboo_repository_branch_name=releases/Release_2_11_2_Branch
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_repository_27918600_git_branch=releases/Release_2_11_2_Branch
bamboo_planRepository_1_revision=bd990168d0b3c7772c961b56144c3dee94a09054
SHLVL=1
bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant
bamboo_repository_name=Jalview Git
bamboo_repository_27918600_git_repositoryUrl=http://source.jalview.org/git/jalview.git
JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/
LANG=en_GB.UTF-8
bamboo_buildFailed=false
bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk
bamboo_planRepository_branch=releases/Release_2_11_2_Branch
bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609
bamboo_repository_27918600_branch_name=releases/Release_2_11_2_Branch
bamboo_capability_system_git_executable=/bin/git
bamboo_repository_git_username=
bamboo_planRepository_1_previousRevision=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f
bamboo_planRepository_branchDisplayName=releases/Release_2_11_2_Branch
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=releases/Release_2_11_2_Branch
_=/usr/bin/java
bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11
bamboo_capability_system_builderivy_Ivy=/usr
bamboo_plan_storageTag=plan-27623951
bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle
bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache
bamboo_planRepository_1_username=
bamboo_planRepository_type=gitv2
USER=bamboo
bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache
bamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_capability_system_builder_ant_Ant=/usr/share/ant
bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven
bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp
bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1
bamboo_planKey=JB-GDB329
bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_planRepository_username=
HOME=/home/bamboo
bamboo_planRepository_1_branchName=releases/Release_2_11_2_Branch
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
30-Jun-2023 17:28:19 4894
30-Jun-2023 17:28:20
30-Jun-2023 17:28:20 > Configure project :
30-Jun-2023 17:28:20 Using properties from file './utils/channels/default/channel_gradle.properties'
30-Jun-2023 17:28:20 JALVIEW_VERSION is set to '2.11.2.7'
30-Jun-2023 17:28:20 HEADLESS BUILD
30-Jun-2023 17:28:20 J2S ENABLED
30-Jun-2023 17:28:20 Using a LOCAL profile.
30-Jun-2023 17:28:20 eclipseDir exists
30-Jun-2023 17:28:21
30-Jun-2023 17:28:21 > Task :clean
30-Jun-2023 17:28:21 > Task :cleanClover
30-Jun-2023 17:28:21 > Task :cleanTest UP-TO-DATE
30-Jun-2023 17:28:23
30-Jun-2023 17:28:23 > Task :cloverInstrJava
30-Jun-2023 17:28:23 Clover: About to instrument 1041 files
30-Jun-2023 17:28:23 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
30-Jun-2023 17:28:23 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/clover/clover.db'.
30-Jun-2023 17:28:23 Processing files at 1.9 source level.
30-Jun-2023 17:28:32 Clover all over. Instrumented 1041 files (103 packages).
30-Jun-2023 17:28:34
30-Jun-2023 17:28:34 > Task :cloverInstrTests
30-Jun-2023 17:28:34 Clover: About to instrument test files
30-Jun-2023 17:28:34 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
30-Jun-2023 17:28:34 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/clover/clover.db'.
30-Jun-2023 17:28:34 Processing files at 1.9 source level.
30-Jun-2023 17:28:36 Clover all over. Instrumented 269 files (50 packages).
30-Jun-2023 17:28:36 1495 test methods detected.
30-Jun-2023 17:28:36
30-Jun-2023 17:28:36 > Task :cloverInstr
30-Jun-2023 17:28:38
30-Jun-2023 17:28:38 > Task :compileCloverJava
30-Jun-2023 17:28:38 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
30-Jun-2023 17:28:38   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrJava' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:28:38   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrTests' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:28:38   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/clover/clover-instr'. Reason: Task ':compileCloverJava' uses this output of task ':cloverInstrJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:28:38 Setting target compatibility to 11
30-Jun-2023 17:28:51 Note: Some input files use or override a deprecated API.
30-Jun-2023 17:28:51 Note: Recompile with -Xlint:deprecation for details.
30-Jun-2023 17:28:51 Note: Some input files use unchecked or unsafe operations.
30-Jun-2023 17:28:51 Note: Recompile with -Xlint:unchecked for details.
30-Jun-2023 17:28:54
30-Jun-2023 17:28:54 > Task :processCloverResources NO-SOURCE
30-Jun-2023 17:28:54 > Task :cloverClasses
30-Jun-2023 17:28:55 > Task :copyHelp
30-Jun-2023 17:28:56 > Task :buildIndices
30-Jun-2023 17:28:56 > Task :copyResources
30-Jun-2023 17:28:56 > Task :copyChannelResources
30-Jun-2023 17:28:56
30-Jun-2023 17:28:56 > Task :createBuildProperties
30-Jun-2023 17:28:56 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
30-Jun-2023 17:28:56   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:28:56
30-Jun-2023 17:28:56 > Task :buildResources
30-Jun-2023 17:28:56 > Task :copyDocs
30-Jun-2023 17:28:56
30-Jun-2023 17:28:56 > Task :convertMdFiles
30-Jun-2023 17:28:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
30-Jun-2023 17:28:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build/doc/releaseprocess.html
30-Jun-2023 17:28:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
30-Jun-2023 17:28:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build/doc/building.html
30-Jun-2023 17:28:57
30-Jun-2023 17:28:57 > Task :releasesTemplates
30-Jun-2023 17:28:57 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
30-Jun-2023 17:28:57   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:28:57   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:28:57
30-Jun-2023 17:28:57 > Task :prepare
30-Jun-2023 17:28:59
30-Jun-2023 17:28:59 > Task :compileTestJava
30-Jun-2023 17:28:59 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
30-Jun-2023 17:28:59   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/clover/clover-classes'. Reason: Task ':compileTestJava' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:28:59   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/clover/clover-test-instr'. Reason: Task ':compileTestJava' uses this output of task ':cloverInstrTests' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:28:59 Setting target compatibility to 11
30-Jun-2023 17:29:03 Note: Some input files use or override a deprecated API.
30-Jun-2023 17:29:03 Note: Recompile with -Xlint:deprecation for details.
30-Jun-2023 17:29:03 Note: Some input files use unchecked or unsafe operations.
30-Jun-2023 17:29:03 Note: Recompile with -Xlint:unchecked for details.
30-Jun-2023 17:29:04
30-Jun-2023 17:29:04 > Task :processTestResources
30-Jun-2023 17:29:04 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
30-Jun-2023 17:29:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:29:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:29:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:29:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:29:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:29:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:29:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:29:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
30-Jun-2023 17:29:04
30-Jun-2023 17:29:04 > Task :testClasses
30-Jun-2023 17:29:06
30-Jun-2023 17:29:06 > Task :test
30-Jun-2023 17:29:06 Running tests WITH clover
30-Jun-2023 17:29:29 WARNING: An illegal reflective access operation has occurred
30-Jun-2023 17:29:29 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
30-Jun-2023 17:29:29 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
30-Jun-2023 17:29:29 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
30-Jun-2023 17:29:29 WARNING: All illegal access operations will be denied in a future release
30-Jun-2023 17:31:42
30-Jun-2023 17:31:42 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
30-Jun-2023 17:31:42
30-Jun-2023 17:31:42 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
30-Jun-2023 17:31:42
30-Jun-2023 17:31:42 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
30-Jun-2023 17:31:42
30-Jun-2023 17:31:42 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
30-Jun-2023 17:31:42 Please consult deprecation warnings for more details.
30-Jun-2023 17:31:42
30-Jun-2023 17:31:42 BUILD SUCCESSFUL in 3m 23s
30-Jun-2023 17:31:42 17 actionable tasks: 16 executed, 1 up-to-date
30-Jun-2023 17:31:43 Finished task 'Run tests with openclover under gradle' with result: Success
30-Jun-2023 17:31:43 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
30-Jun-2023 17:31:43 Bamboo Artifactory Plugin version: 2.6.2
30-Jun-2023 17:31:43
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests #63 (JB-GDB329-JOB1-63)'
... running command line:
/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport
... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=releases/Release_2_11_2_Branch
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=releases/Release_2_11_2_Branch
bamboo_repository_revision_number=bd990168d0b3c7772c961b56144c3dee94a09054
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB329-JOB1-63
JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048
bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1
bamboo_planRepository_1_name=Jalview Git
bamboo_buildKey=JB-GDB329-JOB1
bamboo_shortPlanName=releases-Release_2_11_2_Branch
bamboo_repository_27918600_previous_revision_number=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f
bamboo_planRepository_name=Jalview Git
bamboo_repository_27918600_name=Jalview Git
LOGNAME=bamboo
bamboo_buildNumber=63
PWD=/
bamboo_repository_27918600_git_username=
bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse
bamboo_shortJobName=Clover and Tests
bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB329-JOB1-63
bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git
SHELL=/bin/bash
bamboo_agentId=196609
bamboo_planName=Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch
bamboo_shortPlanKey=GDB329
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=bd990168d0b3c7772c961b56144c3dee94a09054
bamboo_buildTimeStamp=2023-06-30T17:28:19.294+01:00
bamboo_repository_previous_revision_number=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f
bamboo_repository_27918600_revision_number=bd990168d0b3c7772c961b56144c3dee94a09054
bamboo_planRepository_previousRevision=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f
bamboo_repository_git_branch=releases/Release_2_11_2_Branch
bamboo_buildResultKey=JB-GDB329-JOB1-63
bamboo_repository_branch_name=releases/Release_2_11_2_Branch
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_repository_27918600_git_branch=releases/Release_2_11_2_Branch
bamboo_planRepository_1_revision=bd990168d0b3c7772c961b56144c3dee94a09054
SHLVL=1
bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant
bamboo_repository_name=Jalview Git
bamboo_repository_27918600_git_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test
JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/
LANG=en_GB.UTF-8
bamboo_buildFailed=false
bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk
bamboo_planRepository_branch=releases/Release_2_11_2_Branch
bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609
bamboo_repository_27918600_branch_name=releases/Release_2_11_2_Branch
bamboo_jobFailed=false
bamboo_capability_system_git_executable=/bin/git
bamboo_repository_git_username=
bamboo_planRepository_1_previousRevision=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f
bamboo_planRepository_branchDisplayName=releases/Release_2_11_2_Branch
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=releases/Release_2_11_2_Branch
_=/usr/bin/java
bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11
bamboo_capability_system_builderivy_Ivy=/usr
bamboo_plan_storageTag=plan-27623951
bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle
bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache
bamboo_planRepository_1_username=
bamboo_planRepository_type=gitv2
USER=bamboo
bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache
bamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_capability_system_builder_ant_Ant=/usr/share/ant
bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven
bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp
bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1
bamboo_planKey=JB-GDB329
bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_planRepository_username=
HOME=/home/bamboo
bamboo_planRepository_1_branchName=releases/Release_2_11_2_Branch
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
30-Jun-2023 17:31:43 4894
30-Jun-2023 17:31:49
30-Jun-2023 17:31:49 > Configure project :
30-Jun-2023 17:31:49 Using properties from file './utils/channels/default/channel_gradle.properties'
30-Jun-2023 17:31:49 JALVIEW_VERSION is set to '2.11.2.7'
30-Jun-2023 17:31:49 HEADLESS BUILD
30-Jun-2023 17:31:49 J2S ENABLED
30-Jun-2023 17:31:49 Using a LOCAL profile.
30-Jun-2023 17:31:50 eclipseDir exists
30-Jun-2023 17:31:52
30-Jun-2023 17:31:52 > Task :cloverHtmlReport
30-Jun-2023 17:31:52 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
30-Jun-2023 17:31:53 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/reports/clover'
30-Jun-2023 17:32:22 Done. Processed 107 packages in 28864ms (269ms per package).
30-Jun-2023 17:32:26
30-Jun-2023 17:32:26 > Task :cloverXmlReport
30-Jun-2023 17:32:26 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
30-Jun-2023 17:32:27 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/reports/clover/clover.xml'
30-Jun-2023 17:32:27
30-Jun-2023 17:32:27 > Task :cloverReport
30-Jun-2023 17:32:27
30-Jun-2023 17:32:27 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
30-Jun-2023 17:32:27
30-Jun-2023 17:32:27 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
30-Jun-2023 17:32:27
30-Jun-2023 17:32:27 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
30-Jun-2023 17:32:27
30-Jun-2023 17:32:27 BUILD SUCCESSFUL in 44s
30-Jun-2023 17:32:27 2 actionable tasks: 2 executed
30-Jun-2023 17:32:27 Finished task 'Clover Report' with result: Success
30-Jun-2023 17:32:27 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
30-Jun-2023 17:32:27 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1...
30-Jun-2023 17:32:27 Finished task 'TestNG Parser' with result: Success
30-Jun-2023 17:32:27 Running post build plugin 'NCover Results Collector'
30-Jun-2023 17:32:27 Running post build plugin 'Artifact Copier'
30-Jun-2023 17:32:27 Publishing an artifact: Clover Report (System)
30-Jun-2023 17:32:29 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.680 s
30-Jun-2023 17:32:29 Publishing an artifact: TestNG report
30-Jun-2023 17:32:29 Finished publishing of artifact Job artifact: [TestNG report], pattern: [**/*] anchored at: [build/reports/tests/test] in 92.97 ms
30-Jun-2023 17:32:29 Running post build plugin 'Artifactory Release Management Staging'
30-Jun-2023 17:32:29 Running post build plugin 'Artifactory Build Info Copier'
30-Jun-2023 17:32:29 Running post build plugin 'Artifactory Gradle Properties Info Copier'
30-Jun-2023 17:32:29 Running post build plugin 'npm Cache Cleanup'
30-Jun-2023 17:32:29 Running post build plugin 'Clover Results Collector'
30-Jun-2023 17:32:29 Running post build plugin 'Docker Container Cleanup'
30-Jun-2023 17:32:29 Finalising the build...
30-Jun-2023 17:32:29 Stopping timer.
30-Jun-2023 17:32:29 Build JB-GDB329-JOB1-63 completed.
30-Jun-2023 17:32:29 Running on server: post build plugin 'NCover Results Collector'
30-Jun-2023 17:32:29 Running on server: post build plugin 'Build Hanging Detection Configuration'
30-Jun-2023 17:32:29 Running on server: post build plugin 'Clover Delta Calculator'
30-Jun-2023 17:32:29 Running on server: post build plugin 'Maven Dependencies Postprocessor'
30-Jun-2023 17:32:29 All post build plugins have finished
30-Jun-2023 17:32:29 Generating build results summary...
30-Jun-2023 17:32:29 Saving build results to disk...
30-Jun-2023 17:32:29 Logging substituted variables...
30-Jun-2023 17:32:29 Indexing build results...
30-Jun-2023 17:32:29 Finished building JB-GDB329-JOB1-63.