simple	08-Dec-2025 13:21:22	Build Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #6 (JB-GDB731-JOB1-6) started building on agent Default Agent
simple	08-Dec-2025 13:21:22	
simple	08-Dec-2025 13:21:22	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1
simple	08-Dec-2025 13:21:22	Executing build Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #6 (JB-GDB731-JOB1-6)
simple	08-Dec-2025 13:21:22	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	08-Dec-2025 13:21:22	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1
simple	08-Dec-2025 13:21:22	Updating source code to revision: 3ad0f0a7896b330c0e763c467d1076bede27b59a
simple	08-Dec-2025 13:21:23	Fetching 'refs/heads/development/Release_2_11_5_Branch' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	08-Dec-2025 13:21:23	Checking out revision 3ad0f0a7896b330c0e763c467d1076bede27b59a.
simple	08-Dec-2025 13:21:23	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	08-Dec-2025 13:21:23	   a3717c0..3ad0f0a  development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch
simple	08-Dec-2025 13:21:23	Already on 'development/Release_2_11_5_Branch'
simple	08-Dec-2025 13:21:23	Your branch is behind 'origin/development/Release_2_11_5_Branch' by 1 commit, and can be fast-forwarded.
simple	08-Dec-2025 13:21:23	  (use "git pull" to update your local branch)
simple	08-Dec-2025 13:21:23	HEAD is now at 3ad0f0a JAL-4617 update release notes
simple	08-Dec-2025 13:21:23	Updated source code to revision: 3ad0f0a7896b330c0e763c467d1076bede27b59a
simple	08-Dec-2025 13:21:23	Finished task 'Checkout Default Repository' with result: Success
simple	08-Dec-2025 13:21:23	Running pre-build action: VCS Version Collector
simple	08-Dec-2025 13:21:23	Running pre-build action: Artifactory Release Staging
simple	08-Dec-2025 13:21:23	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	08-Dec-2025 13:21:23	Bamboo Artifactory Plugin version: 2.6.2
command	08-Dec-2025 13:21:23	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #6 (JB-GDB731-JOB1-6)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_11_5_Branch\nbamboo_repository_46498610_previous_revision_number=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_repository_revision_number=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB731-JOB1-6\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB731-JOB1\nbamboo_repository_46498610_git_username=\nbamboo_shortPlanName=development-Release_2_11_5_Branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=6\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB731-JOB1-6\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498610_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch\nbamboo_repository_46498610_revision_number=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_shortPlanKey=GDB731\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_buildTimeStamp=2025-12-08T13:21:22.944Z\nbamboo_repository_previous_revision_number=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_planRepository_previousRevision=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_repository_git_branch=development/Release_2_11_5_Branch\nbamboo_buildResultKey=JB-GDB731-JOB1-6\nbamboo_repository_branch_name=development/Release_2_11_5_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=3ad0f0a7896b330c0e763c467d1076bede27b59a\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46498610_branch_name=development/Release_2_11_5_Branch\nbamboo_planRepository_branch=development/Release_2_11_5_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_repository_46498610_git_branch=development/Release_2_11_5_Branch\nbamboo_planRepository_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=development/Release_2_11_5_Branch\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302791\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1\nbamboo_planKey=JB-GDB731\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498610_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=development/Release_2_11_5_Branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	08-Dec-2025 13:21:23	2414
build	08-Dec-2025 13:21:24	
build	08-Dec-2025 13:21:24	> Configure project :
build	08-Dec-2025 13:21:24	Using properties from file './utils/channels/default/channel_gradle.properties'
build	08-Dec-2025 13:21:24	JALVIEW_VERSION is set to '2.11.5.1'
build	08-Dec-2025 13:21:24	HEADLESS BUILD
build	08-Dec-2025 13:21:24	J2S ENABLED
build	08-Dec-2025 13:21:24	Using a LOCAL profile.
build	08-Dec-2025 13:21:24	eclipseDir exists
build	08-Dec-2025 13:21:25	
build	08-Dec-2025 13:21:25	> Task :clean
build	08-Dec-2025 13:21:25	> Task :cleanClover
build	08-Dec-2025 13:21:25	> Task :cleanTest UP-TO-DATE
build	08-Dec-2025 13:21:27	
build	08-Dec-2025 13:21:27	> Task :cloverInstrJava
build	08-Dec-2025 13:21:27	Clover: About to instrument 1109 files
build	08-Dec-2025 13:21:27	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	08-Dec-2025 13:21:27	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover.db'.
build	08-Dec-2025 13:21:27	Processing files at 1.9 source level.
error	08-Dec-2025 13:21:29	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	08-Dec-2025 13:21:29	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	08-Dec-2025 13:21:29	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	08-Dec-2025 13:21:29	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	08-Dec-2025 13:21:29	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	08-Dec-2025 13:21:29	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	08-Dec-2025 13:21:29	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
build	08-Dec-2025 13:21:35	Clover all over. Instrumented 1109 files (113 packages).
build	08-Dec-2025 13:21:38	
build	08-Dec-2025 13:21:38	> Task :cloverInstrTests
build	08-Dec-2025 13:21:38	Clover: About to instrument test files
build	08-Dec-2025 13:21:38	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	08-Dec-2025 13:21:38	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover.db'.
build	08-Dec-2025 13:21:38	Processing files at 1.9 source level.
build	08-Dec-2025 13:21:40	Clover all over. Instrumented 293 files (52 packages).
build	08-Dec-2025 13:21:40	1627 test methods detected.
build	08-Dec-2025 13:21:40	
build	08-Dec-2025 13:21:40	> Task :cloverInstr
build	08-Dec-2025 13:21:42	
build	08-Dec-2025 13:21:42	> Task :compileCloverJava
build	08-Dec-2025 13:21:42	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	08-Dec-2025 13:21:42	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:21:42	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:21:42	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:21:42	Setting target compatibility to 11
error	08-Dec-2025 13:21:55	Note: Some input files use or override a deprecated API.
error	08-Dec-2025 13:21:55	Note: Recompile with -Xlint:deprecation for details.
error	08-Dec-2025 13:21:55	Note: Some input files use unchecked or unsafe operations.
error	08-Dec-2025 13:21:55	Note: Recompile with -Xlint:unchecked for details.
build	08-Dec-2025 13:22:00	
build	08-Dec-2025 13:22:00	> Task :processCloverResources NO-SOURCE
build	08-Dec-2025 13:22:00	> Task :cloverClasses
build	08-Dec-2025 13:22:01	> Task :copyHelp
build	08-Dec-2025 13:22:02	> Task :buildIndices
build	08-Dec-2025 13:22:02	> Task :copyResources
build	08-Dec-2025 13:22:02	> Task :copyChannelResources
build	08-Dec-2025 13:22:02	
build	08-Dec-2025 13:22:02	> Task :createBuildProperties
build	08-Dec-2025 13:22:02	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	08-Dec-2025 13:22:02	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:22:02	
build	08-Dec-2025 13:22:02	> Task :buildResources
build	08-Dec-2025 13:22:02	> Task :copyDocs
build	08-Dec-2025 13:22:02	
build	08-Dec-2025 13:22:02	> Task :convertMdFiles
build	08-Dec-2025 13:22:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	08-Dec-2025 13:22:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	08-Dec-2025 13:22:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	08-Dec-2025 13:22:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/building.html
build	08-Dec-2025 13:22:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	08-Dec-2025 13:22:02	
build	08-Dec-2025 13:22:02	> Task :releasesTemplates
build	08-Dec-2025 13:22:02	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	08-Dec-2025 13:22:02	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:22:02	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:22:02	Stripping rc/test/etc for TEST
build	08-Dec-2025 13:22:02	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	08-Dec-2025 13:22:02	
build	08-Dec-2025 13:22:02	> Task :prepare
build	08-Dec-2025 13:22:04	
build	08-Dec-2025 13:22:04	> Task :compileJava
build	08-Dec-2025 13:22:04	Setting target compatibility to 11
error	08-Dec-2025 13:22:09	Note: Some input files use or override a deprecated API.
error	08-Dec-2025 13:22:09	Note: Recompile with -Xlint:deprecation for details.
error	08-Dec-2025 13:22:09	Note: Some input files use unchecked or unsafe operations.
error	08-Dec-2025 13:22:09	Note: Recompile with -Xlint:unchecked for details.
build	08-Dec-2025 13:22:11	
build	08-Dec-2025 13:22:11	> Task :compileTestJava
build	08-Dec-2025 13:22:11	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	08-Dec-2025 13:22:11	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:22:11	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:22:11	Setting target compatibility to 11
error	08-Dec-2025 13:22:14	Note: Some input files use or override a deprecated API.
error	08-Dec-2025 13:22:14	Note: Recompile with -Xlint:deprecation for details.
error	08-Dec-2025 13:22:14	Note: Some input files use unchecked or unsafe operations.
error	08-Dec-2025 13:22:14	Note: Recompile with -Xlint:unchecked for details.
build	08-Dec-2025 13:22:16	
build	08-Dec-2025 13:22:16	> Task :processTestResources
build	08-Dec-2025 13:22:16	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	08-Dec-2025 13:22:16	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:22:16	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:22:16	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:22:16	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:22:16	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:22:16	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:22:16	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:22:16	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
build	08-Dec-2025 13:22:16	
build	08-Dec-2025 13:22:16	> Task :testClasses
build	08-Dec-2025 13:22:18	
build	08-Dec-2025 13:22:18	> Task :testTask0
build	08-Dec-2025 13:22:18	Running tests WITH clover
error	08-Dec-2025 13:22:19	WARNING: An illegal reflective access operation has occurred
error	08-Dec-2025 13:22:19	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	08-Dec-2025 13:22:19	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	08-Dec-2025 13:22:19	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	08-Dec-2025 13:22:19	WARNING: All illegal access operations will be denied in a future release
build	08-Dec-2025 13:23:14	
build	08-Dec-2025 13:23:14	Gradle suite > Gradle test > jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy FAILED
build	08-Dec-2025 13:23:14	    java.lang.AssertionError: Expected occupancy to be non-null in column 5 expected object to not be null
build	08-Dec-2025 13:23:14	        at org.testng.Assert.fail(Assert.java:94)
build	08-Dec-2025 13:23:14	        at org.testng.Assert.assertNotNull(Assert.java:406)
build	08-Dec-2025 13:23:14	        at jalview.gui.AlignViewportTest.__CLR4_4_1lfq8443uue(AlignViewportTest.java:478)
build	08-Dec-2025 13:23:14	        at jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy(AlignViewportTest.java:446)
error	08-Dec-2025 13:26:32	
error	08-Dec-2025 13:26:32	1835 tests completed, 1 failed
build	08-Dec-2025 13:26:32	There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask0/index.html
build	08-Dec-2025 13:26:34	
build	08-Dec-2025 13:26:34	> Task :testTask1
build	08-Dec-2025 13:26:34	Running tests WITH clover
error	08-Dec-2025 13:26:36	WARNING: An illegal reflective access operation has occurred
error	08-Dec-2025 13:26:36	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	08-Dec-2025 13:26:36	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	08-Dec-2025 13:26:36	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	08-Dec-2025 13:26:36	WARNING: All illegal access operations will be denied in a future release
build	08-Dec-2025 13:28:46	
build	08-Dec-2025 13:28:46	> Task :testTask2
build	08-Dec-2025 13:28:46	Running tests WITH clover
build	08-Dec-2025 13:28:49	
build	08-Dec-2025 13:28:49	> Task :testTask3
build	08-Dec-2025 13:28:49	Running tests WITH clover
error	08-Dec-2025 13:28:51	WARNING: An illegal reflective access operation has occurred
error	08-Dec-2025 13:28:51	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	08-Dec-2025 13:28:51	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	08-Dec-2025 13:28:51	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	08-Dec-2025 13:28:51	WARNING: All illegal access operations will be denied in a future release
build	08-Dec-2025 13:29:38	
build	08-Dec-2025 13:29:38	> Task :test NO-SOURCE
build	08-Dec-2025 13:29:38	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	08-Dec-2025 13:29:38	│jalview:testTask0 results: FAILURE (1835 tests, 1834 successes, 1 failures, 0 skipped) in 4 minutes, 16.301 seconds   │
build	08-Dec-2025 13:29:38	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask0/index.html│
build	08-Dec-2025 13:29:38	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	08-Dec-2025 13:29:38	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 11.437 seconds       │
build	08-Dec-2025 13:29:38	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask1/index.html│
build	08-Dec-2025 13:29:38	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	08-Dec-2025 13:29:38	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.287 seconds                     │
error	08-Dec-2025 13:29:38	
error	08-Dec-2025 13:29:38	FAILURE: Build failed with an exception.
error	08-Dec-2025 13:29:38	
error	08-Dec-2025 13:29:38	* Where:
error	08-Dec-2025 13:29:38	Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build.gradle' line: 1967
error	08-Dec-2025 13:29:38	
error	08-Dec-2025 13:29:38	* What went wrong:
error	08-Dec-2025 13:29:38	Failed tests!
error	08-Dec-2025 13:29:38	
error	08-Dec-2025 13:29:38	* Try:
error	08-Dec-2025 13:29:38	> Run with --stacktrace option to get the stack trace.
error	08-Dec-2025 13:29:38	> Run with --info or --debug option to get more log output.
error	08-Dec-2025 13:29:38	> Run with --scan to get full insights.
error	08-Dec-2025 13:29:38	
build	08-Dec-2025 13:29:38	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask2/index.html│
build	08-Dec-2025 13:29:38	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	08-Dec-2025 13:29:38	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 50.770 seconds                  │
build	08-Dec-2025 13:29:38	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask3/index.html│
build	08-Dec-2025 13:29:38	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	08-Dec-2025 13:29:38	│OVERALL: results: FAILURE (1923 tests, 1922 successes, 1 failures, 0 skipped) in 6 minutes, 81.795 seconds            │
build	08-Dec-2025 13:29:38	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	08-Dec-2025 13:29:38	
build	08-Dec-2025 13:29:38	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	08-Dec-2025 13:29:38	
build	08-Dec-2025 13:29:38	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	08-Dec-2025 13:29:38	
build	08-Dec-2025 13:29:38	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	08-Dec-2025 13:29:38	
build	08-Dec-2025 13:29:38	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	08-Dec-2025 13:29:38	Please consult deprecation warnings for more details.
build	08-Dec-2025 13:29:38	21 actionable tasks: 20 executed, 1 up-to-date
error	08-Dec-2025 13:29:38	* Get more help at https://help.gradle.org
error	08-Dec-2025 13:29:38	
error	08-Dec-2025 13:29:38	BUILD FAILED in 8m 15s
simple	08-Dec-2025 13:29:39	
simple	08-Dec-2025 13:29:39	Failing task since return code of [/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test] was 1 while expected 0
simple	08-Dec-2025 13:29:39	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	08-Dec-2025 13:29:39	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	08-Dec-2025 13:29:39	Bamboo Artifactory Plugin version: 2.6.2
command	08-Dec-2025 13:29:39	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #6 (JB-GDB731-JOB1-6)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_11_5_Branch\nbamboo_repository_46498610_previous_revision_number=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_repository_revision_number=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB731-JOB1-6\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB731-JOB1\nbamboo_repository_46498610_git_username=\nbamboo_shortPlanName=development-Release_2_11_5_Branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=6\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB731-JOB1-6\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498610_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch\nbamboo_repository_46498610_revision_number=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_shortPlanKey=GDB731\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_buildTimeStamp=2025-12-08T13:21:22.944Z\nbamboo_repository_previous_revision_number=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_planRepository_previousRevision=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_repository_git_branch=development/Release_2_11_5_Branch\nbamboo_buildResultKey=JB-GDB731-JOB1-6\nbamboo_repository_branch_name=development/Release_2_11_5_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=3ad0f0a7896b330c0e763c467d1076bede27b59a\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_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\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=true\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46498610_branch_name=development/Release_2_11_5_Branch\nbamboo_planRepository_branch=development/Release_2_11_5_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_repository_46498610_git_branch=development/Release_2_11_5_Branch\nbamboo_planRepository_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=development/Release_2_11_5_Branch\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302791\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1\nbamboo_planKey=JB-GDB731\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498610_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=development/Release_2_11_5_Branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	08-Dec-2025 13:29:39	2414
build	08-Dec-2025 13:29:44	
build	08-Dec-2025 13:29:44	> Configure project :
build	08-Dec-2025 13:29:44	Using properties from file './utils/channels/default/channel_gradle.properties'
build	08-Dec-2025 13:29:44	JALVIEW_VERSION is set to '2.11.5.1'
build	08-Dec-2025 13:29:44	HEADLESS BUILD
build	08-Dec-2025 13:29:44	J2S ENABLED
build	08-Dec-2025 13:29:45	Using a LOCAL profile.
build	08-Dec-2025 13:29:45	eclipseDir exists
build	08-Dec-2025 13:29:48	
build	08-Dec-2025 13:29:48	> Task :cloverHtmlReport
build	08-Dec-2025 13:29:48	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	08-Dec-2025 13:29:49	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/clover'
build	08-Dec-2025 13:30:34	Done. Processed 117 packages in 44903ms (383ms per package).
build	08-Dec-2025 13:30:39	
build	08-Dec-2025 13:30:39	> Task :cloverXmlReport
build	08-Dec-2025 13:30:39	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	08-Dec-2025 13:30:39	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/clover/clover.xml'
build	08-Dec-2025 13:30:40	
build	08-Dec-2025 13:30:40	> Task :cloverReport
build	08-Dec-2025 13:30:40	
build	08-Dec-2025 13:30:40	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	08-Dec-2025 13:30:40	
build	08-Dec-2025 13:30:40	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	08-Dec-2025 13:30:40	
build	08-Dec-2025 13:30:40	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	08-Dec-2025 13:30:40	
build	08-Dec-2025 13:30:40	BUILD SUCCESSFUL in 1m
build	08-Dec-2025 13:30:40	2 actionable tasks: 2 executed
simple	08-Dec-2025 13:30:40	Finished task 'Clover Report' with result: Success
simple	08-Dec-2025 13:30:40	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	08-Dec-2025 13:30:40	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1...
simple	08-Dec-2025 13:30:40	Failing task since 1 failing test cases were found.
simple	08-Dec-2025 13:30:40	Finished task 'TestNG Parser' with result: Failed
simple	08-Dec-2025 13:30:40	Running post build plugin 'NCover Results Collector'
simple	08-Dec-2025 13:30:40	Running post build plugin 'Artifact Copier'
simple	08-Dec-2025 13:30:40	Publishing an artifact: Clover Report (System)
simple	08-Dec-2025 13:30:42	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.825 s
simple	08-Dec-2025 13:30:42	Publishing an artifact: TestNG report
error	08-Dec-2025 13:30:42	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/test does not exist.
simple	08-Dec-2025 13:30:42	The artifact hasn't been successfully published after 1.182 ms
simple	08-Dec-2025 13:30:42	Running post build plugin 'Artifactory Release Management Staging'
simple	08-Dec-2025 13:30:42	Running post build plugin 'Artifactory Build Info Copier'
simple	08-Dec-2025 13:30:42	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	08-Dec-2025 13:30:42	Running post build plugin 'npm Cache Cleanup'
simple	08-Dec-2025 13:30:42	Running post build plugin 'Clover Results Collector'
simple	08-Dec-2025 13:30:42	Running post build plugin 'Docker Container Cleanup'
simple	08-Dec-2025 13:30:42	Finalising the build...
simple	08-Dec-2025 13:30:42	Stopping timer.
simple	08-Dec-2025 13:30:42	Build JB-GDB731-JOB1-6 completed.
simple	08-Dec-2025 13:30:42	Running on server: post build plugin 'NCover Results Collector'
simple	08-Dec-2025 13:30:42	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	08-Dec-2025 13:30:42	Running on server: post build plugin 'Clover Delta Calculator'
simple	08-Dec-2025 13:30:42	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	08-Dec-2025 13:30:42	All post build plugins have finished
simple	08-Dec-2025 13:30:42	Generating build results summary...
simple	08-Dec-2025 13:30:42	Saving build results to disk...
simple	08-Dec-2025 13:30:42	Logging substituted variables...
simple	08-Dec-2025 13:30:42	Indexing build results...
simple	08-Dec-2025 13:30:42	Finished building JB-GDB731-JOB1-6.