simple	01-Apr-2026 13:13:14	Build Jalview Builds - Gradle Develop Build - feature-JAL-4478_multimer_pae_import - Clover and Tests #1 (JB-GDB750-JOB1-1) started building on agent Default Agent
simple	01-Apr-2026 13:13:14	
simple	01-Apr-2026 13:13:14	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1
simple	01-Apr-2026 13:13:14	Executing build Jalview Builds - Gradle Develop Build - feature-JAL-4478_multimer_pae_import - Clover and Tests #1 (JB-GDB750-JOB1-1)
simple	01-Apr-2026 13:13:14	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	01-Apr-2026 13:13:14	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1
simple	01-Apr-2026 13:13:14	Updating source code to revision: b1ad6c90376f94f7542bd2c69f7e944cd0f8f3b1
simple	01-Apr-2026 13:13:14	Fetching 'refs/heads/feature/JAL-4478_multimer_pae_import' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	01-Apr-2026 13:13:15	Checking out revision b1ad6c90376f94f7542bd2c69f7e944cd0f8f3b1.
simple	01-Apr-2026 13:13:15	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/.git'.
simple	01-Apr-2026 13:13:15	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1'...
simple	01-Apr-2026 13:13:15	done.
simple	01-Apr-2026 13:13:21	Branch feature/JAL-4478_multimer_pae_import set up to track remote branch feature/JAL-4478_multimer_pae_import from origin.
simple	01-Apr-2026 13:13:21	Switched to a new branch 'feature/JAL-4478_multimer_pae_import'
simple	01-Apr-2026 13:13:21	Updated source code to revision: b1ad6c90376f94f7542bd2c69f7e944cd0f8f3b1
simple	01-Apr-2026 13:13:21	Finished task 'Checkout Default Repository' with result: Success
simple	01-Apr-2026 13:13:21	Running pre-build action: VCS Version Collector
simple	01-Apr-2026 13:13:21	Running pre-build action: Artifactory Release Staging
simple	01-Apr-2026 13:13:21	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	01-Apr-2026 13:13:21	Bamboo Artifactory Plugin version: 2.6.2
command	01-Apr-2026 13:13:21	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4478_multimer_pae_import - Clover and Tests #1 (JB-GDB750-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-GDB750-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4478_multimer_pae_import\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4478_multimer_pae_import\nbamboo_repository_revision_number=b1ad6c90376f94f7542bd2c69f7e944cd0f8f3b1\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB750-JOB1-1\nbamboo_repository_48169046_branch_name=feature/JAL-4478_multimer_pae_import\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-GDB750-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_repository_48169046_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB750-JOB1\nbamboo_shortPlanName=feature-JAL-4478_multimer_pae_import\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-GDB750-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - feature-JAL-4478_multimer_pae_import\nbamboo_shortPlanKey=GDB750\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=b1ad6c90376f94f7542bd2c69f7e944cd0f8f3b1\nbamboo_buildTimeStamp=2026-04-01T13:13:14.631+01:00\nbamboo_repository_git_branch=feature/JAL-4478_multimer_pae_import\nbamboo_buildResultKey=JB-GDB750-JOB1-1\nbamboo_repository_branch_name=feature/JAL-4478_multimer_pae_import\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - feature-JAL-4478_multimer_pae_import - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=b1ad6c90376f94f7542bd2c69f7e944cd0f8f3b1\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169046_git_branch=feature/JAL-4478_multimer_pae_import\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=feature/JAL-4478_multimer_pae_import\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_48169046_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_branchDisplayName=feature/JAL-4478_multimer_pae_import\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-4478_multimer_pae_import\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-47972523\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_repository_48169046_revision_number=b1ad6c90376f94f7542bd2c69f7e944cd0f8f3b1\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_repository_48169046_git_username=\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-GDB750-JOB1\nbamboo_planKey=JB-GDB750\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=feature/JAL-4478_multimer_pae_import\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	01-Apr-2026 13:13:21	2414
build	01-Apr-2026 13:13:22	Starting a Gradle Daemon (subsequent builds will be faster)
build	01-Apr-2026 13:13:29	
build	01-Apr-2026 13:13:29	> Configure project :
build	01-Apr-2026 13:13:29	Using properties from file './utils/channels/default/channel_gradle.properties'
build	01-Apr-2026 13:13:29	JALVIEW_VERSION is set to '2.11.5.1'
build	01-Apr-2026 13:13:29	HEADLESS BUILD
build	01-Apr-2026 13:13:29	J2S ENABLED
build	01-Apr-2026 13:13:29	Using a LOCAL profile.
build	01-Apr-2026 13:13:30	eclipseDir exists
build	01-Apr-2026 13:13:31	
build	01-Apr-2026 13:13:31	> Task :clean
build	01-Apr-2026 13:13:31	> Task :cleanClover
build	01-Apr-2026 13:13:31	> Task :cleanTest UP-TO-DATE
build	01-Apr-2026 13:13:33	
build	01-Apr-2026 13:13:33	> Task :cloverInstrJava
build	01-Apr-2026 13:13:33	Clover: About to instrument 1110 files
build	01-Apr-2026 13:13:33	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	01-Apr-2026 13:13:33	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/clover/clover.db'.
build	01-Apr-2026 13:13:33	Processing files at 1.9 source level.
error	01-Apr-2026 13:13:37	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	01-Apr-2026 13:13:37	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	01-Apr-2026 13:13:37	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	01-Apr-2026 13:13:37	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	01-Apr-2026 13:13:37	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	01-Apr-2026 13:13:37	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	01-Apr-2026 13:13:37	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	01-Apr-2026 13:13:42	Clover all over. Instrumented 1110 files (113 packages).
build	01-Apr-2026 13:13:44	
build	01-Apr-2026 13:13:44	> Task :cloverInstrTests
build	01-Apr-2026 13:13:44	Clover: About to instrument test files
build	01-Apr-2026 13:13:44	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	01-Apr-2026 13:13:44	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/clover/clover.db'.
build	01-Apr-2026 13:13:44	Processing files at 1.9 source level.
build	01-Apr-2026 13:13:46	Clover all over. Instrumented 293 files (52 packages).
build	01-Apr-2026 13:13:46	1628 test methods detected.
build	01-Apr-2026 13:13:47	
build	01-Apr-2026 13:13:47	> Task :cloverInstr
build	01-Apr-2026 13:13:50	
build	01-Apr-2026 13:13:50	> Task :compileCloverJava
build	01-Apr-2026 13:13:50	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	01-Apr-2026 13:13:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:13:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:13:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:13:50	Setting target compatibility to 11
error	01-Apr-2026 13:14:12	Note: Some input files use or override a deprecated API.
error	01-Apr-2026 13:14:12	Note: Recompile with -Xlint:deprecation for details.
error	01-Apr-2026 13:14:12	Note: Some input files use unchecked or unsafe operations.
error	01-Apr-2026 13:14:12	Note: Recompile with -Xlint:unchecked for details.
build	01-Apr-2026 13:14:19	
build	01-Apr-2026 13:14:19	> Task :processCloverResources NO-SOURCE
build	01-Apr-2026 13:14:19	> Task :cloverClasses
build	01-Apr-2026 13:14:20	> Task :copyHelp
build	01-Apr-2026 13:14:21	> Task :buildIndices
build	01-Apr-2026 13:14:21	> Task :copyResources
build	01-Apr-2026 13:14:21	> Task :copyChannelResources
build	01-Apr-2026 13:14:21	
build	01-Apr-2026 13:14:21	> Task :createBuildProperties
build	01-Apr-2026 13:14:21	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	01-Apr-2026 13:14:21	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:14:21	
build	01-Apr-2026 13:14:21	> Task :buildResources
build	01-Apr-2026 13:14:21	> Task :copyDocs
build	01-Apr-2026 13:14:21	
build	01-Apr-2026 13:14:21	> Task :convertMdFiles
build	01-Apr-2026 13:14:21	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	01-Apr-2026 13:14:21	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	01-Apr-2026 13:14:21	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	01-Apr-2026 13:14:21	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/resources/doc_build/doc/building.html
build	01-Apr-2026 13:14:21	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	01-Apr-2026 13:14:22	
build	01-Apr-2026 13:14:22	> Task :releasesTemplates
build	01-Apr-2026 13:14:22	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	01-Apr-2026 13:14:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:14:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:14:22	Stripping rc/test/etc for TEST
build	01-Apr-2026 13:14:22	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	01-Apr-2026 13:14:22	
build	01-Apr-2026 13:14:22	> Task :prepare
build	01-Apr-2026 13:14:24	
build	01-Apr-2026 13:14:24	> Task :compileJava
build	01-Apr-2026 13:14:24	Setting target compatibility to 11
error	01-Apr-2026 13:14:29	Note: Some input files use or override a deprecated API.
error	01-Apr-2026 13:14:29	Note: Recompile with -Xlint:deprecation for details.
error	01-Apr-2026 13:14:29	Note: Some input files use unchecked or unsafe operations.
error	01-Apr-2026 13:14:29	Note: Recompile with -Xlint:unchecked for details.
build	01-Apr-2026 13:14:34	
build	01-Apr-2026 13:14:34	> Task :compileTestJava
build	01-Apr-2026 13:14:34	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	01-Apr-2026 13:14:34	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:14:34	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:14:34	Setting target compatibility to 11
error	01-Apr-2026 13:14:37	Note: Some input files use or override a deprecated API.
error	01-Apr-2026 13:14:37	Note: Recompile with -Xlint:deprecation for details.
error	01-Apr-2026 13:14:37	Note: Some input files use unchecked or unsafe operations.
error	01-Apr-2026 13:14:37	Note: Recompile with -Xlint:unchecked for details.
build	01-Apr-2026 13:14:39	
build	01-Apr-2026 13:14:39	> Task :processTestResources
build	01-Apr-2026 13:14:39	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	01-Apr-2026 13:14:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:14:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:14:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:14:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:14:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:14:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:14:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-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	01-Apr-2026 13:14:39	
build	01-Apr-2026 13:14:39	> Task :testClasses
build	01-Apr-2026 13:14:41	
build	01-Apr-2026 13:14:41	> Task :testTask0
build	01-Apr-2026 13:14:41	Running tests WITH clover
error	01-Apr-2026 13:14:43	WARNING: An illegal reflective access operation has occurred
error	01-Apr-2026 13:14:43	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	01-Apr-2026 13:14:43	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	01-Apr-2026 13:14:43	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	01-Apr-2026 13:14:43	WARNING: All illegal access operations will be denied in a future release
build	01-Apr-2026 13:15:12	
build	01-Apr-2026 13:15:12	Gradle suite > Gradle test > jalview.ext.jmol.JmolParserTest.testStructurePAE FAILED
build	01-Apr-2026 13:15:12	    java.lang.AssertionError: No PAE for second chain. expected:<1> but was:<0>
build	01-Apr-2026 13:15:12	        at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
build	01-Apr-2026 13:15:12	        at org.testng.AssertJUnit.failNotEquals(AssertJUnit.java:364)
build	01-Apr-2026 13:15:12	        at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:80)
build	01-Apr-2026 13:15:12	        at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:245)
build	01-Apr-2026 13:15:12	        at jalview.ext.jmol.JmolParserTest.__CLR4_4_16g3i9y3w2v(JmolParserTest.java:313)
build	01-Apr-2026 13:15:12	        at jalview.ext.jmol.JmolParserTest.testStructurePAE(JmolParserTest.java:306)
error	01-Apr-2026 13:18:46	
error	01-Apr-2026 13:18:46	1836 tests completed, 1 failed
build	01-Apr-2026 13:18:46	There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/reports/tests/testTask0/index.html
build	01-Apr-2026 13:18:48	
build	01-Apr-2026 13:18:48	> Task :testTask1
build	01-Apr-2026 13:18:48	Running tests WITH clover
error	01-Apr-2026 13:18:50	WARNING: An illegal reflective access operation has occurred
error	01-Apr-2026 13:18:50	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	01-Apr-2026 13:18:50	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	01-Apr-2026 13:18:50	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	01-Apr-2026 13:18:50	WARNING: All illegal access operations will be denied in a future release
build	01-Apr-2026 13:20:58	
build	01-Apr-2026 13:20:58	> Task :testTask2
build	01-Apr-2026 13:20:58	Running tests WITH clover
build	01-Apr-2026 13:21:02	
build	01-Apr-2026 13:21:02	> Task :testTask3
build	01-Apr-2026 13:21:02	Running tests WITH clover
error	01-Apr-2026 13:21:03	WARNING: An illegal reflective access operation has occurred
error	01-Apr-2026 13:21:03	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	01-Apr-2026 13:21:03	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	01-Apr-2026 13:21:03	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	01-Apr-2026 13:21:03	WARNING: All illegal access operations will be denied in a future release
build	01-Apr-2026 13:21:49	
build	01-Apr-2026 13:21:49	> Task :test NO-SOURCE
build	01-Apr-2026 13:21:49	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	01-Apr-2026 13:21:49	│jalview:testTask0 results: FAILURE (1836 tests, 1835 successes, 1 failures, 0 skipped) in 4 minutes, 7.079 seconds    │
build	01-Apr-2026 13:21:49	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/reports/tests/testTask0/index.html│
build	01-Apr-2026 13:21:49	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	01-Apr-2026 13:21:49	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 9.899 seconds        │
build	01-Apr-2026 13:21:49	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/reports/tests/testTask1/index.html│
build	01-Apr-2026 13:21:49	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	01-Apr-2026 13:21:49	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.399 seconds                     │
build	01-Apr-2026 13:21:49	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/reports/tests/testTask2/index.html│
build	01-Apr-2026 13:21:49	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	01-Apr-2026 13:21:49	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 48.811 seconds                  │
build	01-Apr-2026 13:21:49	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/reports/tests/testTask3/index.html│
build	01-Apr-2026 13:21:49	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	01-Apr-2026 13:21:49	│OVERALL: results: FAILURE (1924 tests, 1923 successes, 1 failures, 0 skipped) in 6 minutes, 69.188 seconds            │
build	01-Apr-2026 13:21:49	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	01-Apr-2026 13:21:49	
build	01-Apr-2026 13:21:49	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	01-Apr-2026 13:21:49	
build	01-Apr-2026 13:21:49	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	01-Apr-2026 13:21:49	
build	01-Apr-2026 13:21:49	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	01-Apr-2026 13:21:49	
build	01-Apr-2026 13:21:49	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	01-Apr-2026 13:21:49	Please consult deprecation warnings for more details.
build	01-Apr-2026 13:21:49	21 actionable tasks: 20 executed, 1 up-to-date
error	01-Apr-2026 13:21:49	
error	01-Apr-2026 13:21:49	FAILURE: Build failed with an exception.
error	01-Apr-2026 13:21:49	
error	01-Apr-2026 13:21:49	* Where:
error	01-Apr-2026 13:21:49	Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build.gradle' line: 1967
error	01-Apr-2026 13:21:49	
error	01-Apr-2026 13:21:49	* What went wrong:
error	01-Apr-2026 13:21:49	Failed tests!
error	01-Apr-2026 13:21:49	
error	01-Apr-2026 13:21:49	* Try:
error	01-Apr-2026 13:21:49	> Run with --stacktrace option to get the stack trace.
error	01-Apr-2026 13:21:49	> Run with --info or --debug option to get more log output.
error	01-Apr-2026 13:21:49	> Run with --scan to get full insights.
error	01-Apr-2026 13:21:49	
error	01-Apr-2026 13:21:49	* Get more help at https://help.gradle.org
error	01-Apr-2026 13:21:49	
error	01-Apr-2026 13:21:49	BUILD FAILED in 8m 27s
simple	01-Apr-2026 13:21:49	
simple	01-Apr-2026 13:21:49	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	01-Apr-2026 13:21:49	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	01-Apr-2026 13:21:49	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	01-Apr-2026 13:21:49	Bamboo Artifactory Plugin version: 2.6.2
command	01-Apr-2026 13:21:49	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4478_multimer_pae_import - Clover and Tests #1 (JB-GDB750-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-GDB750-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4478_multimer_pae_import\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4478_multimer_pae_import\nbamboo_repository_revision_number=b1ad6c90376f94f7542bd2c69f7e944cd0f8f3b1\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB750-JOB1-1\nbamboo_repository_48169046_branch_name=feature/JAL-4478_multimer_pae_import\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-GDB750-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_repository_48169046_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB750-JOB1\nbamboo_shortPlanName=feature-JAL-4478_multimer_pae_import\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-GDB750-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - feature-JAL-4478_multimer_pae_import\nbamboo_shortPlanKey=GDB750\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=b1ad6c90376f94f7542bd2c69f7e944cd0f8f3b1\nbamboo_buildTimeStamp=2026-04-01T13:13:14.631+01:00\nbamboo_repository_git_branch=feature/JAL-4478_multimer_pae_import\nbamboo_buildResultKey=JB-GDB750-JOB1-1\nbamboo_repository_branch_name=feature/JAL-4478_multimer_pae_import\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - feature-JAL-4478_multimer_pae_import - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=b1ad6c90376f94f7542bd2c69f7e944cd0f8f3b1\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169046_git_branch=feature/JAL-4478_multimer_pae_import\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=feature/JAL-4478_multimer_pae_import\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_48169046_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_branchDisplayName=feature/JAL-4478_multimer_pae_import\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-4478_multimer_pae_import\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-47972523\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_repository_48169046_revision_number=b1ad6c90376f94f7542bd2c69f7e944cd0f8f3b1\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_repository_48169046_git_username=\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-GDB750-JOB1\nbamboo_planKey=JB-GDB750\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=feature/JAL-4478_multimer_pae_import\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	01-Apr-2026 13:21:49	2414
build	01-Apr-2026 13:21:56	
build	01-Apr-2026 13:21:56	> Configure project :
build	01-Apr-2026 13:21:56	Using properties from file './utils/channels/default/channel_gradle.properties'
build	01-Apr-2026 13:21:56	JALVIEW_VERSION is set to '2.11.5.1'
build	01-Apr-2026 13:21:56	HEADLESS BUILD
build	01-Apr-2026 13:21:56	J2S ENABLED
build	01-Apr-2026 13:21:56	Using a LOCAL profile.
build	01-Apr-2026 13:21:57	eclipseDir exists
build	01-Apr-2026 13:21:59	
build	01-Apr-2026 13:21:59	> Task :cloverHtmlReport
build	01-Apr-2026 13:21:59	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	01-Apr-2026 13:22:00	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/reports/clover'
build	01-Apr-2026 13:22:48	Done. Processed 117 packages in 48252ms (412ms per package).
build	01-Apr-2026 13:22:53	
build	01-Apr-2026 13:22:53	> Task :cloverXmlReport
build	01-Apr-2026 13:22:53	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	01-Apr-2026 13:22:55	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/reports/clover/clover.xml'
build	01-Apr-2026 13:22:55	
build	01-Apr-2026 13:22:55	> Task :cloverReport
build	01-Apr-2026 13:22:55	
build	01-Apr-2026 13:22:55	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	01-Apr-2026 13:22:55	
build	01-Apr-2026 13:22:55	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	01-Apr-2026 13:22:55	
build	01-Apr-2026 13:22:55	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	01-Apr-2026 13:22:55	
build	01-Apr-2026 13:22:55	BUILD SUCCESSFUL in 1m 5s
build	01-Apr-2026 13:22:55	2 actionable tasks: 2 executed
simple	01-Apr-2026 13:22:55	Finished task 'Clover Report' with result: Success
simple	01-Apr-2026 13:22:55	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	01-Apr-2026 13:22:55	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1...
simple	01-Apr-2026 13:22:55	Failing task since 1 failing test cases were found.
simple	01-Apr-2026 13:22:55	Finished task 'TestNG Parser' with result: Failed
simple	01-Apr-2026 13:22:55	Running post build plugin 'NCover Results Collector'
simple	01-Apr-2026 13:22:55	Running post build plugin 'Artifact Copier'
simple	01-Apr-2026 13:22:55	Publishing an artifact: Clover Report (System)
simple	01-Apr-2026 13:22:57	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.615 s
simple	01-Apr-2026 13:22:57	Publishing an artifact: TestNG report
error	01-Apr-2026 13:22:57	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB750-JOB1/build/reports/tests/test does not exist.
simple	01-Apr-2026 13:22:57	The artifact hasn't been successfully published after 2.464 ms
simple	01-Apr-2026 13:22:57	Running post build plugin 'Artifactory Release Management Staging'
simple	01-Apr-2026 13:22:57	Running post build plugin 'Artifactory Build Info Copier'
simple	01-Apr-2026 13:22:57	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	01-Apr-2026 13:22:57	Running post build plugin 'npm Cache Cleanup'
simple	01-Apr-2026 13:22:57	Running post build plugin 'Clover Results Collector'
simple	01-Apr-2026 13:22:57	Running post build plugin 'Docker Container Cleanup'
simple	01-Apr-2026 13:22:57	Finalising the build...
simple	01-Apr-2026 13:22:57	Stopping timer.
simple	01-Apr-2026 13:22:57	Build JB-GDB750-JOB1-1 completed.
simple	01-Apr-2026 13:22:57	Running on server: post build plugin 'NCover Results Collector'
simple	01-Apr-2026 13:22:57	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	01-Apr-2026 13:22:57	Running on server: post build plugin 'Clover Delta Calculator'
simple	01-Apr-2026 13:22:57	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	01-Apr-2026 13:22:57	All post build plugins have finished
simple	01-Apr-2026 13:22:57	Generating build results summary...
simple	01-Apr-2026 13:22:57	Saving build results to disk...
simple	01-Apr-2026 13:22:57	Logging substituted variables...
simple	01-Apr-2026 13:22:57	Indexing build results...
simple	01-Apr-2026 13:22:57	Finished building JB-GDB750-JOB1-1.