Build #64

Build and run tests under Java 11

Build: #64 was successful

Job: Clover and Tests was successful

Stages & jobs

  1. Default Stage

Build log

The build generated 215 lines of output. Download or view full build log

22-Jul-2023 11:05:24 Build Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests #64 (JB-GDB329-JOB1-64) started building on agent Default Agent
22-Jul-2023 11:05:24
22-Jul-2023 11:05:25 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1
22-Jul-2023 11:05:25 Executing build Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests #64 (JB-GDB329-JOB1-64)
22-Jul-2023 11:05:25 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
22-Jul-2023 11:05:25 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1
22-Jul-2023 11:05:25 Updating source code to revision: c2bb08e5dc01cc9de193f19b625c3f1abd0488c5
22-Jul-2023 11:05:25 Fetching 'refs/heads/releases/Release_2_11_2_Branch' from 'http://source.jalview.org/git/jalview.git'.
22-Jul-2023 11:05:25 Checking out revision c2bb08e5dc01cc9de193f19b625c3f1abd0488c5.
22-Jul-2023 11:05:28 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164
22-Jul-2023 11:05:28    bd99016..c2bb08e  releases/Release_2_11_2_Branch -> origin/releases/Release_2_11_2_Branch
22-Jul-2023 11:05:28 * [new branch]      bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server -> origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server
22-Jul-2023 11:05:28 * [new branch]      bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail_on_eclipse_error -> origin/bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail_on_eclipse_error
22-Jul-2023 11:05:28 * [new branch]      bug/JAL-4513_JvCacheableInputBoxTest_flaky_on_build_server -> origin/bug/JAL-4513_JvCacheableInputBoxTest_flaky_on_build_server
22-Jul-2023 11:05:28    74c36ac..94efd5c  develop    -> origin/develop
22-Jul-2023 11:05:28    49ab19e..8e3a12f  development/Release_2_12_Branch -> origin/development/Release_2_12_Branch
22-Jul-2023 11:05:28 * [new branch]      feature/JAL-244_Automatically_adjust_left_margin_to_avoid_cropping_annotation_labels -> origin/feature/JAL-244_Automatically_adjust_left_margin_to_avoid_cropping_annotation_labels
22-Jul-2023 11:05:28 * [new branch]      feature/JAL-4227_Rfam2020_sslines -> origin/feature/JAL-4227_Rfam2020_sslines
22-Jul-2023 11:05:28 * [new branch]      features/JAL-4219_extended_fasta_rna_ss -> origin/features/JAL-4219_extended_fasta_rna_ss
22-Jul-2023 11:05:28 * [new branch]      features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps -> origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps
22-Jul-2023 11:05:28    64c66c2..8b18316  improvement/JAL-3830_remove_dock_icon_in_headless_mode -> origin/improvement/JAL-3830_remove_dock_icon_in_headless_mode
22-Jul-2023 11:05:28    9476b45..c79c2ba  improvement/JAL-4212_remove_macos_test_java_icons -> origin/improvement/JAL-4212_remove_macos_test_java_icons
22-Jul-2023 11:05:28 * [new branch]      mmw/JAL-4199-task-execution-update -> origin/mmw/JAL-4199-task-execution-update
22-Jul-2023 11:05:28    6fb82c6..7badfcf  mmw/Release_2_12_ws_merge -> origin/mmw/Release_2_12_ws_merge
22-Jul-2023 11:05:28 * [new branch]      patch/JAL-3855_fixup_pae -> origin/patch/JAL-3855_fixup_pae
22-Jul-2023 11:05:28 * [new branch]      patch/JAL-4110_stdout_for_tests -> origin/patch/JAL-4110_stdout_for_tests
22-Jul-2023 11:05:28    b78a8a8..4b031bc  patch/JAL-4195_cli_eps_export_npe -> origin/patch/JAL-4195_cli_eps_export_npe
22-Jul-2023 11:05:28 * [new branch]      patch/JAL-4222_quit_with_gui_export_cli_args -> origin/patch/JAL-4222_quit_with_gui_export_cli_args
22-Jul-2023 11:05:28 * [new branch]      patch/JAL-4232-disable-unavailable-services -> origin/patch/JAL-4232-disable-unavailable-services
22-Jul-2023 11:05:28    82ccd12..95e3809  releases/Release_2_11_3_Branch -> origin/releases/Release_2_11_3_Branch
22-Jul-2023 11:05:28 * [new tag]         Release_2_11_2_7 -> Release_2_11_2_7
22-Jul-2023 11:05:29 Already on 'releases/Release_2_11_2_Branch'
22-Jul-2023 11:05:29 Your branch is behind 'origin/releases/Release_2_11_2_Branch' by 1 commit, and can be fast-forwarded.
22-Jul-2023 11:05:29   (use "git pull" to update your local branch)
22-Jul-2023 11:05:29 HEAD is now at c2bb08e JAL-4243 Jalview 2.11.2.7’s biotool record as JSON complete with update instructions as a README
22-Jul-2023 11:05:29 Updated source code to revision: c2bb08e5dc01cc9de193f19b625c3f1abd0488c5
22-Jul-2023 11:05:29 Finished task 'Checkout Default Repository' with result: Success
22-Jul-2023 11:05:29 Running pre-build action: VCS Version Collector
22-Jul-2023 11:05:29 Running pre-build action: Artifactory Release Staging
22-Jul-2023 11:05:29 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
22-Jul-2023 11:05:29 Bamboo Artifactory Plugin version: 2.6.2
22-Jul-2023 11:05:29
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests #64 (JB-GDB329-JOB1-64)'
... 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
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22-Jul-2023 11:05:29 28050
22-Jul-2023 11:05:32
22-Jul-2023 11:05:32 > Configure project :
22-Jul-2023 11:05:32 Using properties from file './utils/channels/default/channel_gradle.properties'
22-Jul-2023 11:05:32 JALVIEW_VERSION is set to '2.11.2.7'
22-Jul-2023 11:05:32 HEADLESS BUILD
22-Jul-2023 11:05:32 J2S ENABLED
22-Jul-2023 11:05:32 Using a LOCAL profile.
22-Jul-2023 11:05:32 eclipseDir exists
22-Jul-2023 11:05:34
22-Jul-2023 11:05:34 > Task :clean
22-Jul-2023 11:05:34 > Task :cleanClover
22-Jul-2023 11:05:34 > Task :cleanTest UP-TO-DATE
22-Jul-2023 11:05:36
22-Jul-2023 11:05:36 > Task :cloverInstrJava
22-Jul-2023 11:05:36 Clover: About to instrument 1041 files
22-Jul-2023 11:05:37 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
22-Jul-2023 11:05:38 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/clover/clover.db'.
22-Jul-2023 11:05:38 Processing files at 1.9 source level.
22-Jul-2023 11:05:54 Clover all over. Instrumented 1041 files (103 packages).
22-Jul-2023 11:05:56
22-Jul-2023 11:05:56 > Task :cloverInstrTests
22-Jul-2023 11:05:56 Clover: About to instrument test files
22-Jul-2023 11:05:56 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
22-Jul-2023 11:05:56 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/clover/clover.db'.
22-Jul-2023 11:05:56 Processing files at 1.9 source level.
22-Jul-2023 11:06:00 Clover all over. Instrumented 269 files (50 packages).
22-Jul-2023 11:06:00 1495 test methods detected.
22-Jul-2023 11:06:00
22-Jul-2023 11:06:00 > Task :cloverInstr
22-Jul-2023 11:06:02
22-Jul-2023 11:06:02 > Task :compileCloverJava
22-Jul-2023 11:06:02 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
22-Jul-2023 11:06:02   - 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.
22-Jul-2023 11:06:02   - 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.
22-Jul-2023 11:06:02   - 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.
22-Jul-2023 11:06:02 Setting target compatibility to 11
22-Jul-2023 11:06:16 Note: Some input files use or override a deprecated API.
22-Jul-2023 11:06:16 Note: Recompile with -Xlint:deprecation for details.
22-Jul-2023 11:06:16 Note: Some input files use unchecked or unsafe operations.
22-Jul-2023 11:06:16 Note: Recompile with -Xlint:unchecked for details.
22-Jul-2023 11:06:20
22-Jul-2023 11:06:20 > Task :processCloverResources NO-SOURCE
22-Jul-2023 11:06:20 > Task :cloverClasses
22-Jul-2023 11:06:21 > Task :copyHelp
22-Jul-2023 11:06:22 > Task :buildIndices
22-Jul-2023 11:06:22 > Task :copyResources
22-Jul-2023 11:06:22 > Task :copyChannelResources
22-Jul-2023 11:06:22
22-Jul-2023 11:06:22 > Task :createBuildProperties
22-Jul-2023 11:06:22 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
22-Jul-2023 11:06:22   - 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.
22-Jul-2023 11:06:22
22-Jul-2023 11:06:22 > Task :buildResources
22-Jul-2023 11:06:22 > Task :copyDocs
22-Jul-2023 11:06:23
22-Jul-2023 11:06:23 > Task :convertMdFiles
22-Jul-2023 11:06:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
22-Jul-2023 11:06:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build/doc/releaseprocess.html
22-Jul-2023 11:06:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
22-Jul-2023 11:06:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build/doc/building.html
22-Jul-2023 11:06:23
22-Jul-2023 11:06:23 > Task :releasesTemplates
22-Jul-2023 11:06:23 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
22-Jul-2023 11:06:23   - 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.
22-Jul-2023 11:06:23   - 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.
22-Jul-2023 11:06:23
22-Jul-2023 11:06:23 > Task :prepare
22-Jul-2023 11:06:25
22-Jul-2023 11:06:25 > Task :compileTestJava
22-Jul-2023 11:06:25 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
22-Jul-2023 11:06:25   - 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.
22-Jul-2023 11:06:25   - 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.
22-Jul-2023 11:06:25 Setting target compatibility to 11
22-Jul-2023 11:06:29 Note: Some input files use or override a deprecated API.
22-Jul-2023 11:06:29 Note: Recompile with -Xlint:deprecation for details.
22-Jul-2023 11:06:29 Note: Some input files use unchecked or unsafe operations.
22-Jul-2023 11:06:29 Note: Recompile with -Xlint:unchecked for details.
22-Jul-2023 11:06:30
22-Jul-2023 11:06:30 > Task :processTestResources
22-Jul-2023 11:06:30 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
22-Jul-2023 11:06:30   - 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.
22-Jul-2023 11:06:30   - 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.
22-Jul-2023 11:06:30   - 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.
22-Jul-2023 11:06:30   - 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.
22-Jul-2023 11:06:30   - 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.
22-Jul-2023 11:06:30   - 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.
22-Jul-2023 11:06:30   - 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.
22-Jul-2023 11:06:30   - 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.
22-Jul-2023 11:06:30
22-Jul-2023 11:06:30 > Task :testClasses
22-Jul-2023 11:06:32
22-Jul-2023 11:06:32 > Task :test
22-Jul-2023 11:06:32 Running tests WITH clover
22-Jul-2023 11:06:56 WARNING: An illegal reflective access operation has occurred
22-Jul-2023 11:06:56 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
22-Jul-2023 11:06:56 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
22-Jul-2023 11:06:56 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
22-Jul-2023 11:06:56 WARNING: All illegal access operations will be denied in a future release
22-Jul-2023 11:09:06
22-Jul-2023 11:09:06 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
22-Jul-2023 11:09:06
22-Jul-2023 11:09:06 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
22-Jul-2023 11:09:06
22-Jul-2023 11:09:06 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
22-Jul-2023 11:09:06
22-Jul-2023 11:09:06 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
22-Jul-2023 11:09:06 Please consult deprecation warnings for more details.
22-Jul-2023 11:09:06
22-Jul-2023 11:09:06 BUILD SUCCESSFUL in 3m 37s
22-Jul-2023 11:09:06 17 actionable tasks: 16 executed, 1 up-to-date
22-Jul-2023 11:09:07 Finished task 'Run tests with openclover under gradle' with result: Success
22-Jul-2023 11:09:07 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
22-Jul-2023 11:09:07 Bamboo Artifactory Plugin version: 2.6.2
22-Jul-2023 11:09:07
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests #64 (JB-GDB329-JOB1-64)'
... 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=c2bb08e5dc01cc9de193f19b625c3f1abd0488c5
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB329-JOB1-64
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=bd990168d0b3c7772c961b56144c3dee94a09054
bamboo_planRepository_name=Jalview Git
bamboo_repository_27918600_name=Jalview Git
LOGNAME=bamboo
bamboo_buildNumber=64
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-JOB1-64
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=c2bb08e5dc01cc9de193f19b625c3f1abd0488c5
bamboo_buildTimeStamp=2023-07-22T10:56:29.848+01:00
bamboo_repository_previous_revision_number=bd990168d0b3c7772c961b56144c3dee94a09054
bamboo_repository_27918600_revision_number=c2bb08e5dc01cc9de193f19b625c3f1abd0488c5
bamboo_planRepository_previousRevision=bd990168d0b3c7772c961b56144c3dee94a09054
bamboo_repository_git_branch=releases/Release_2_11_2_Branch
bamboo_buildResultKey=JB-GDB329-JOB1-64
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=c2bb08e5dc01cc9de193f19b625c3f1abd0488c5
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=bd990168d0b3c7772c961b56144c3dee94a09054
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
22-Jul-2023 11:09:07 28050
22-Jul-2023 11:09:11
22-Jul-2023 11:09:11 > Configure project :
22-Jul-2023 11:09:11 Using properties from file './utils/channels/default/channel_gradle.properties'
22-Jul-2023 11:09:12 JALVIEW_VERSION is set to '2.11.2.7'
22-Jul-2023 11:09:12 HEADLESS BUILD
22-Jul-2023 11:09:12 J2S ENABLED
22-Jul-2023 11:09:12 Using a LOCAL profile.
22-Jul-2023 11:09:13 eclipseDir exists
22-Jul-2023 11:09:15
22-Jul-2023 11:09:15 > Task :cloverHtmlReport
22-Jul-2023 11:09:15 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
22-Jul-2023 11:09:16 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/reports/clover'
22-Jul-2023 11:09:44 Done. Processed 107 packages in 28462ms (266ms per package).
22-Jul-2023 11:09:49
22-Jul-2023 11:09:49 > Task :cloverXmlReport
22-Jul-2023 11:09:49 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
22-Jul-2023 11:09:49 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/reports/clover/clover.xml'
22-Jul-2023 11:09:50
22-Jul-2023 11:09:50 > Task :cloverReport
22-Jul-2023 11:09:50
22-Jul-2023 11:09:50 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
22-Jul-2023 11:09:50
22-Jul-2023 11:09:50 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
22-Jul-2023 11:09:50
22-Jul-2023 11:09:50 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
22-Jul-2023 11:09:50
22-Jul-2023 11:09:50 BUILD SUCCESSFUL in 43s
22-Jul-2023 11:09:50 2 actionable tasks: 2 executed
22-Jul-2023 11:09:50 Finished task 'Clover Report' with result: Success
22-Jul-2023 11:09:50 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
22-Jul-2023 11:09:50 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1...
22-Jul-2023 11:09:50 Finished task 'TestNG Parser' with result: Success
22-Jul-2023 11:09:50 Running post build plugin 'NCover Results Collector'
22-Jul-2023 11:09:50 Running post build plugin 'Artifact Copier'
22-Jul-2023 11:09:50 Publishing an artifact: Clover Report (System)
22-Jul-2023 11:09:51 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.259 s
22-Jul-2023 11:09:51 Publishing an artifact: TestNG report
22-Jul-2023 11:09:51 Finished publishing of artifact Job artifact: [TestNG report], pattern: [**/*] anchored at: [build/reports/tests/test] in 87.43 ms
22-Jul-2023 11:09:51 Running post build plugin 'Artifactory Release Management Staging'
22-Jul-2023 11:09:51 Running post build plugin 'Artifactory Build Info Copier'
22-Jul-2023 11:09:51 Running post build plugin 'Artifactory Gradle Properties Info Copier'
22-Jul-2023 11:09:51 Running post build plugin 'npm Cache Cleanup'
22-Jul-2023 11:09:51 Running post build plugin 'Clover Results Collector'
22-Jul-2023 11:09:51 Running post build plugin 'Docker Container Cleanup'
22-Jul-2023 11:09:51 Finalising the build...
22-Jul-2023 11:09:51 Stopping timer.
22-Jul-2023 11:09:51 Build JB-GDB329-JOB1-64 completed.
22-Jul-2023 11:09:51 Running on server: post build plugin 'NCover Results Collector'
22-Jul-2023 11:09:51 Running on server: post build plugin 'Build Hanging Detection Configuration'
22-Jul-2023 11:09:51 Running on server: post build plugin 'Clover Delta Calculator'
22-Jul-2023 11:09:51 Running on server: post build plugin 'Maven Dependencies Postprocessor'
22-Jul-2023 11:09:51 All post build plugins have finished
22-Jul-2023 11:09:51 Generating build results summary...
22-Jul-2023 11:09:51 Saving build results to disk...
22-Jul-2023 11:09:51 Logging substituted variables...
22-Jul-2023 11:09:51 Indexing build results...
22-Jul-2023 11:09:51 Finished building JB-GDB329-JOB1-64.