simple	12-Dec-2025 14:18:15	Build Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS - Clover and Tests #1 (JB-GDB737-JOB1-1) started building on agent Default Agent
simple	12-Dec-2025 14:18:15	
simple	12-Dec-2025 14:18:15	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1
simple	12-Dec-2025 14:18:15	Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS - Clover and Tests #1 (JB-GDB737-JOB1-1)
simple	12-Dec-2025 14:18:15	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	12-Dec-2025 14:18:15	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1
simple	12-Dec-2025 14:18:15	Updating source code to revision: 3525096f6402fa9e390d4d0ee6718bda9344ac3f
simple	12-Dec-2025 14:18:15	Fetching 'refs/heads/bug/JAL-4623_JAL-4624_PCA_for_SS' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	12-Dec-2025 14:18:15	Checking out revision 3525096f6402fa9e390d4d0ee6718bda9344ac3f.
simple	12-Dec-2025 14:18:15	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/.git'.
simple	12-Dec-2025 14:18:15	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1'...
simple	12-Dec-2025 14:18:15	done.
simple	12-Dec-2025 14:18:21	Switched to a new branch 'bug/JAL-4623_JAL-4624_PCA_for_SS'
simple	12-Dec-2025 14:18:21	Branch bug/JAL-4623_JAL-4624_PCA_for_SS set up to track remote branch bug/JAL-4623_JAL-4624_PCA_for_SS from origin.
simple	12-Dec-2025 14:18:21	Updated source code to revision: 3525096f6402fa9e390d4d0ee6718bda9344ac3f
simple	12-Dec-2025 14:18:21	Finished task 'Checkout Default Repository' with result: Success
simple	12-Dec-2025 14:18:21	Running pre-build action: VCS Version Collector
simple	12-Dec-2025 14:18:21	Running pre-build action: Artifactory Release Staging
simple	12-Dec-2025 14:18:21	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	12-Dec-2025 14:18:21	Bamboo Artifactory Plugin version: 2.6.2
command	12-Dec-2025 14:18:21	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS - Clover and Tests #1 (JB-GDB737-JOB1-1)'\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-GDB737-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_repository_revision_number=3525096f6402fa9e390d4d0ee6718bda9344ac3f\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB737-JOB1-1\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-GDB737-JOB1\nbamboo_repository_48168968_git_username=\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB737-JOB1\nbamboo_shortPlanName=bug-JAL-4623_JAL-4624_PCA_for_SS\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\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-GDB737-JOB1-1\nbamboo_repository_48168968_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS\nbamboo_shortPlanKey=GDB737\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=3525096f6402fa9e390d4d0ee6718bda9344ac3f\nbamboo_buildTimeStamp=2025-12-12T14:18:15.262Z\nbamboo_repository_48168968_git_branch=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_repository_git_branch=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_buildResultKey=JB-GDB737-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_repository_48168968_branch_name=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=3525096f6402fa9e390d4d0ee6718bda9344ac3f\nSHLVL=1\nbamboo_repository_48168968_revision_number=3525096f6402fa9e390d4d0ee6718bda9344ac3f\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_planRepository_branch=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_48168968_name=Jalview Gitlab\nbamboo_planRepository_branchDisplayName=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4623_JAL-4624_PCA_for_SS\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-47972367\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-GDB737-JOB1\nbamboo_planKey=JB-GDB737\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4623_JAL-4624_PCA_for_SS\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	12-Dec-2025 14:18:21	2414
build	12-Dec-2025 14:18:22	Starting a Gradle Daemon (subsequent builds will be faster)
build	12-Dec-2025 14:18:28	
build	12-Dec-2025 14:18:28	> Configure project :
build	12-Dec-2025 14:18:28	Using properties from file './utils/channels/default/channel_gradle.properties'
build	12-Dec-2025 14:18:28	JALVIEW_VERSION is set to '2.11.5.1'
build	12-Dec-2025 14:18:28	HEADLESS BUILD
build	12-Dec-2025 14:18:28	J2S ENABLED
build	12-Dec-2025 14:18:28	Using a LOCAL profile.
build	12-Dec-2025 14:18:29	eclipseDir exists
build	12-Dec-2025 14:18:29	
build	12-Dec-2025 14:18:29	> Task :clean
build	12-Dec-2025 14:18:29	> Task :cleanClover
build	12-Dec-2025 14:18:29	> Task :cleanTest UP-TO-DATE
build	12-Dec-2025 14:18:32	
build	12-Dec-2025 14:18:32	> Task :cloverInstrJava
build	12-Dec-2025 14:18:32	Clover: About to instrument 1109 files
build	12-Dec-2025 14:18:32	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	12-Dec-2025 14:18:32	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/clover/clover.db'.
build	12-Dec-2025 14:18:32	Processing files at 1.9 source level.
error	12-Dec-2025 14:18:35	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	12-Dec-2025 14:18:35	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	12-Dec-2025 14:18:35	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	12-Dec-2025 14:18:35	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	12-Dec-2025 14:18:35	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	12-Dec-2025 14:18:35	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	12-Dec-2025 14:18:35	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	12-Dec-2025 14:18:41	Clover all over. Instrumented 1109 files (113 packages).
build	12-Dec-2025 14:18:43	
build	12-Dec-2025 14:18:43	> Task :cloverInstrTests
build	12-Dec-2025 14:18:43	Clover: About to instrument test files
build	12-Dec-2025 14:18:43	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	12-Dec-2025 14:18:43	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/clover/clover.db'.
build	12-Dec-2025 14:18:43	Processing files at 1.9 source level.
build	12-Dec-2025 14:18:45	Clover all over. Instrumented 293 files (52 packages).
build	12-Dec-2025 14:18:45	1627 test methods detected.
build	12-Dec-2025 14:18:45	
build	12-Dec-2025 14:18:45	> Task :cloverInstr
build	12-Dec-2025 14:18:48	
build	12-Dec-2025 14:18:48	> Task :compileCloverJava
build	12-Dec-2025 14:18:48	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	12-Dec-2025 14:18:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:18:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:18:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:18:48	Setting target compatibility to 11
error	12-Dec-2025 14:19:08	Note: Some input files use or override a deprecated API.
error	12-Dec-2025 14:19:08	Note: Recompile with -Xlint:deprecation for details.
error	12-Dec-2025 14:19:08	Note: Some input files use unchecked or unsafe operations.
error	12-Dec-2025 14:19:08	Note: Recompile with -Xlint:unchecked for details.
build	12-Dec-2025 14:19:14	
build	12-Dec-2025 14:19:14	> Task :processCloverResources NO-SOURCE
build	12-Dec-2025 14:19:14	> Task :cloverClasses
build	12-Dec-2025 14:19:14	> Task :copyHelp
build	12-Dec-2025 14:19:15	> Task :buildIndices
build	12-Dec-2025 14:19:15	> Task :copyResources
build	12-Dec-2025 14:19:15	> Task :copyChannelResources
build	12-Dec-2025 14:19:15	
build	12-Dec-2025 14:19:15	> Task :createBuildProperties
build	12-Dec-2025 14:19:15	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	12-Dec-2025 14:19:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:19:15	
build	12-Dec-2025 14:19:15	> Task :buildResources
build	12-Dec-2025 14:19:15	> Task :copyDocs
build	12-Dec-2025 14:19:15	
build	12-Dec-2025 14:19:15	> Task :convertMdFiles
build	12-Dec-2025 14:19:15	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	12-Dec-2025 14:19:15	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	12-Dec-2025 14:19:15	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	12-Dec-2025 14:19:15	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/resources/doc_build/doc/building.html
build	12-Dec-2025 14:19:15	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	12-Dec-2025 14:19:16	
build	12-Dec-2025 14:19:16	> Task :releasesTemplates
build	12-Dec-2025 14:19:16	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	12-Dec-2025 14:19:16	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:19:16	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:19:16	Stripping rc/test/etc for TEST
build	12-Dec-2025 14:19:16	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	12-Dec-2025 14:19:16	
build	12-Dec-2025 14:19:16	> Task :prepare
build	12-Dec-2025 14:19:18	
build	12-Dec-2025 14:19:18	> Task :compileJava
build	12-Dec-2025 14:19:18	Setting target compatibility to 11
error	12-Dec-2025 14:19:22	Note: Some input files use or override a deprecated API.
error	12-Dec-2025 14:19:22	Note: Recompile with -Xlint:deprecation for details.
error	12-Dec-2025 14:19:22	Note: Some input files use unchecked or unsafe operations.
error	12-Dec-2025 14:19:22	Note: Recompile with -Xlint:unchecked for details.
build	12-Dec-2025 14:19:26	
build	12-Dec-2025 14:19:26	> Task :compileTestJava
build	12-Dec-2025 14:19:26	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	12-Dec-2025 14:19:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:19:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:19:26	Setting target compatibility to 11
error	12-Dec-2025 14:19:30	Note: Some input files use or override a deprecated API.
error	12-Dec-2025 14:19:30	Note: Recompile with -Xlint:deprecation for details.
error	12-Dec-2025 14:19:30	Note: Some input files use unchecked or unsafe operations.
error	12-Dec-2025 14:19:30	Note: Recompile with -Xlint:unchecked for details.
build	12-Dec-2025 14:19:31	
build	12-Dec-2025 14:19:31	> Task :processTestResources
build	12-Dec-2025 14:19:31	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	12-Dec-2025 14:19:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:19:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:19:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:19:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:19:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:19:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:19:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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	12-Dec-2025 14:19:31	
build	12-Dec-2025 14:19:31	> Task :testClasses
build	12-Dec-2025 14:19:33	
build	12-Dec-2025 14:19:33	> Task :testTask0
build	12-Dec-2025 14:19:33	Running tests WITH clover
error	12-Dec-2025 14:19:35	WARNING: An illegal reflective access operation has occurred
error	12-Dec-2025 14:19:35	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	12-Dec-2025 14:19:35	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	12-Dec-2025 14:19:35	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	12-Dec-2025 14:19:35	WARNING: All illegal access operations will be denied in a future release
build	12-Dec-2025 14:20:34	
build	12-Dec-2025 14:20:34	Gradle suite > Gradle test > jalview.gui.StructureChooserTest.fetchStructuresInfoMockedTest FAILED
build	12-Dec-2025 14:20:34	    java.lang.ArrayIndexOutOfBoundsException: 0 >= 0
build	12-Dec-2025 14:20:34	        at java.base/java.util.Vector.removeElementAt(Vector.java:580)
build	12-Dec-2025 14:20:34	        at java.desktop/javax.swing.table.DefaultTableColumnModel.removeColumn(DefaultTableColumnModel.java:152)
build	12-Dec-2025 14:20:34	        at java.desktop/javax.swing.JTable.createDefaultColumnsFromModel(JTable.java:1293)
build	12-Dec-2025 14:20:34	        at java.desktop/javax.swing.JTable.tableChanged(JTable.java:4391)
build	12-Dec-2025 14:20:34	        at java.desktop/javax.swing.JTable.setModel(JTable.java:3693)
build	12-Dec-2025 14:20:34	        at jalview.gui.StructureChooser.fetchStructuresMetaData(StructureChooser.java:548)
build	12-Dec-2025 14:20:34	        at jalview.gui.StructureChooserTest.__CLR4_4_1gzvl9m3t5e(StructureChooserTest.java:233)
build	12-Dec-2025 14:20:34	        at jalview.gui.StructureChooserTest.fetchStructuresInfoMockedTest(StructureChooserTest.java:226)
error	12-Dec-2025 14:23:32	
error	12-Dec-2025 14:23:32	1835 tests completed, 1 failed
build	12-Dec-2025 14:23:32	There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/tests/testTask0/index.html
build	12-Dec-2025 14:23:34	
build	12-Dec-2025 14:23:34	> Task :testTask1
build	12-Dec-2025 14:23:34	Running tests WITH clover
error	12-Dec-2025 14:23:35	WARNING: An illegal reflective access operation has occurred
error	12-Dec-2025 14:23:35	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	12-Dec-2025 14:23:35	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	12-Dec-2025 14:23:35	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	12-Dec-2025 14:23:35	WARNING: All illegal access operations will be denied in a future release
build	12-Dec-2025 14:25:36	
build	12-Dec-2025 14:25:36	> Task :testTask2
build	12-Dec-2025 14:25:36	Running tests WITH clover
build	12-Dec-2025 14:25:39	
build	12-Dec-2025 14:25:39	> Task :testTask3
build	12-Dec-2025 14:25:39	Running tests WITH clover
error	12-Dec-2025 14:25:40	WARNING: An illegal reflective access operation has occurred
error	12-Dec-2025 14:25:40	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	12-Dec-2025 14:25:40	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	12-Dec-2025 14:25:40	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	12-Dec-2025 14:25:40	WARNING: All illegal access operations will be denied in a future release
build	12-Dec-2025 14:26:25	
build	12-Dec-2025 14:26:25	> Task :test NO-SOURCE
build	12-Dec-2025 14:26:25	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	12-Dec-2025 14:26:25	│jalview:testTask0 results: FAILURE (1835 tests, 1834 successes, 1 failures, 0 skipped) in 4 minutes, 0.498 seconds    │
build	12-Dec-2025 14:26:25	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/tests/testTask0/index.html│
build	12-Dec-2025 14:26:25	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	12-Dec-2025 14:26:25	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 1.690 seconds        │
build	12-Dec-2025 14:26:25	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/tests/testTask1/index.html│
build	12-Dec-2025 14:26:25	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	12-Dec-2025 14:26:25	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 2.933 seconds                     │
build	12-Dec-2025 14:26:25	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/tests/testTask2/index.html│
build	12-Dec-2025 14:26:25	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	12-Dec-2025 14:26:25	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 47.533 seconds                  │
build	12-Dec-2025 14:26:25	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/tests/testTask3/index.html│
build	12-Dec-2025 14:26:25	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	12-Dec-2025 14:26:25	│OVERALL: results: FAILURE (1923 tests, 1922 successes, 1 failures, 0 skipped) in 6 minutes, 52.654 seconds            │
build	12-Dec-2025 14:26:25	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	12-Dec-2025 14:26:25	
build	12-Dec-2025 14:26:25	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	12-Dec-2025 14:26:25	
build	12-Dec-2025 14:26:25	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	12-Dec-2025 14:26:25	
build	12-Dec-2025 14:26:25	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	12-Dec-2025 14:26:25	
build	12-Dec-2025 14:26:25	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	12-Dec-2025 14:26:25	Please consult deprecation warnings for more details.
build	12-Dec-2025 14:26:25	21 actionable tasks: 20 executed, 1 up-to-date
error	12-Dec-2025 14:26:25	
error	12-Dec-2025 14:26:25	FAILURE: Build failed with an exception.
error	12-Dec-2025 14:26:25	
error	12-Dec-2025 14:26:25	* Where:
error	12-Dec-2025 14:26:25	Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build.gradle' line: 1967
error	12-Dec-2025 14:26:25	
error	12-Dec-2025 14:26:25	* What went wrong:
error	12-Dec-2025 14:26:25	Failed tests!
error	12-Dec-2025 14:26:25	
error	12-Dec-2025 14:26:25	* Try:
error	12-Dec-2025 14:26:25	> Run with --stacktrace option to get the stack trace.
error	12-Dec-2025 14:26:25	> Run with --info or --debug option to get more log output.
error	12-Dec-2025 14:26:25	> Run with --scan to get full insights.
error	12-Dec-2025 14:26:25	
error	12-Dec-2025 14:26:25	* Get more help at https://help.gradle.org
error	12-Dec-2025 14:26:25	
error	12-Dec-2025 14:26:25	BUILD FAILED in 8m 3s
simple	12-Dec-2025 14:26:25	
simple	12-Dec-2025 14:26:25	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	12-Dec-2025 14:26:25	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	12-Dec-2025 14:26:25	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	12-Dec-2025 14:26:25	Bamboo Artifactory Plugin version: 2.6.2
command	12-Dec-2025 14:26:25	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS - Clover and Tests #1 (JB-GDB737-JOB1-1)'\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-GDB737-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_repository_revision_number=3525096f6402fa9e390d4d0ee6718bda9344ac3f\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB737-JOB1-1\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-GDB737-JOB1\nbamboo_repository_48168968_git_username=\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB737-JOB1\nbamboo_shortPlanName=bug-JAL-4623_JAL-4624_PCA_for_SS\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\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-GDB737-JOB1-1\nbamboo_repository_48168968_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS\nbamboo_shortPlanKey=GDB737\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=3525096f6402fa9e390d4d0ee6718bda9344ac3f\nbamboo_buildTimeStamp=2025-12-12T14:18:15.262Z\nbamboo_repository_48168968_git_branch=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_repository_git_branch=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_buildResultKey=JB-GDB737-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_repository_48168968_branch_name=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=3525096f6402fa9e390d4d0ee6718bda9344ac3f\nSHLVL=1\nbamboo_repository_48168968_revision_number=3525096f6402fa9e390d4d0ee6718bda9344ac3f\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_planRepository_branch=bug/JAL-4623_JAL-4624_PCA_for_SS\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_repository_48168968_name=Jalview Gitlab\nbamboo_planRepository_branchDisplayName=bug/JAL-4623_JAL-4624_PCA_for_SS\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4623_JAL-4624_PCA_for_SS\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-47972367\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-GDB737-JOB1\nbamboo_planKey=JB-GDB737\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4623_JAL-4624_PCA_for_SS\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	12-Dec-2025 14:26:25	2414
build	12-Dec-2025 14:26:30	
build	12-Dec-2025 14:26:30	> Configure project :
build	12-Dec-2025 14:26:30	Using properties from file './utils/channels/default/channel_gradle.properties'
build	12-Dec-2025 14:26:30	JALVIEW_VERSION is set to '2.11.5.1'
build	12-Dec-2025 14:26:30	HEADLESS BUILD
build	12-Dec-2025 14:26:30	J2S ENABLED
build	12-Dec-2025 14:26:30	Using a LOCAL profile.
build	12-Dec-2025 14:26:31	eclipseDir exists
build	12-Dec-2025 14:26:33	
build	12-Dec-2025 14:26:33	> Task :cloverHtmlReport
build	12-Dec-2025 14:26:33	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	12-Dec-2025 14:26:34	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/clover'
build	12-Dec-2025 14:27:18	Done. Processed 117 packages in 44528ms (380ms per package).
build	12-Dec-2025 14:27:23	
build	12-Dec-2025 14:27:23	> Task :cloverXmlReport
build	12-Dec-2025 14:27:23	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	12-Dec-2025 14:27:24	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/clover/clover.xml'
build	12-Dec-2025 14:27:24	
build	12-Dec-2025 14:27:24	> Task :cloverReport
build	12-Dec-2025 14:27:24	
build	12-Dec-2025 14:27:24	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	12-Dec-2025 14:27:24	
build	12-Dec-2025 14:27:24	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	12-Dec-2025 14:27:24	
build	12-Dec-2025 14:27:24	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	12-Dec-2025 14:27:24	
build	12-Dec-2025 14:27:24	BUILD SUCCESSFUL in 58s
build	12-Dec-2025 14:27:24	2 actionable tasks: 2 executed
simple	12-Dec-2025 14:27:24	Finished task 'Clover Report' with result: Success
simple	12-Dec-2025 14:27:24	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	12-Dec-2025 14:27:24	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1...
simple	12-Dec-2025 14:27:24	Failing task since 1 failing test cases were found.
simple	12-Dec-2025 14:27:24	Finished task 'TestNG Parser' with result: Failed
simple	12-Dec-2025 14:27:24	Running post build plugin 'NCover Results Collector'
simple	12-Dec-2025 14:27:24	Running post build plugin 'Artifact Copier'
simple	12-Dec-2025 14:27:24	Publishing an artifact: Clover Report (System)
simple	12-Dec-2025 14:27:27	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.430 s
simple	12-Dec-2025 14:27:27	Publishing an artifact: TestNG report
error	12-Dec-2025 14:27:27	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/tests/test does not exist.
simple	12-Dec-2025 14:27:27	The artifact hasn't been successfully published after 1.332 ms
simple	12-Dec-2025 14:27:27	Running post build plugin 'Artifactory Release Management Staging'
simple	12-Dec-2025 14:27:27	Running post build plugin 'Artifactory Build Info Copier'
simple	12-Dec-2025 14:27:27	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	12-Dec-2025 14:27:27	Running post build plugin 'npm Cache Cleanup'
simple	12-Dec-2025 14:27:27	Running post build plugin 'Clover Results Collector'
simple	12-Dec-2025 14:27:27	Running post build plugin 'Docker Container Cleanup'
simple	12-Dec-2025 14:27:27	Finalising the build...
simple	12-Dec-2025 14:27:27	Stopping timer.
simple	12-Dec-2025 14:27:27	Build JB-GDB737-JOB1-1 completed.
simple	12-Dec-2025 14:27:27	Running on server: post build plugin 'NCover Results Collector'
simple	12-Dec-2025 14:27:27	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	12-Dec-2025 14:27:27	Running on server: post build plugin 'Clover Delta Calculator'
simple	12-Dec-2025 14:27:27	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	12-Dec-2025 14:27:27	All post build plugins have finished
simple	12-Dec-2025 14:27:27	Generating build results summary...
simple	12-Dec-2025 14:27:27	Saving build results to disk...
simple	12-Dec-2025 14:27:27	Logging substituted variables...
simple	12-Dec-2025 14:27:27	Indexing build results...
simple	12-Dec-2025 14:27:27	Finished building JB-GDB737-JOB1-1.