simple	25-Mar-2026 16:53:02	Build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-JOB1-1) started building on agent Default Agent
simple	25-Mar-2026 16:53:02	
simple	25-Mar-2026 16:53:02	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1
simple	25-Mar-2026 16:53:02	Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-JOB1-1)
simple	25-Mar-2026 16:53:02	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	25-Mar-2026 16:53:02	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1
simple	25-Mar-2026 16:53:02	Updating source code to revision: 570cfd128c945bc7593ad75c31b9761ff81f5fee
simple	25-Mar-2026 16:53:02	Fetching 'refs/heads/patch/JAL-4410_multimers_from_3dbeacons' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	25-Mar-2026 16:53:03	Checking out revision 570cfd128c945bc7593ad75c31b9761ff81f5fee.
simple	25-Mar-2026 16:53:03	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/.git'.
simple	25-Mar-2026 16:53:03	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1'...
simple	25-Mar-2026 16:53:03	done.
simple	25-Mar-2026 16:53:09	Switched to a new branch 'patch/JAL-4410_multimers_from_3dbeacons'
simple	25-Mar-2026 16:53:09	Branch patch/JAL-4410_multimers_from_3dbeacons set up to track remote branch patch/JAL-4410_multimers_from_3dbeacons from origin.
simple	25-Mar-2026 16:53:09	Updated source code to revision: 570cfd128c945bc7593ad75c31b9761ff81f5fee
simple	25-Mar-2026 16:53:09	Finished task 'Checkout Default Repository' with result: Success
simple	25-Mar-2026 16:53:09	Running pre-build action: VCS Version Collector
simple	25-Mar-2026 16:53:09	Running pre-build action: Artifactory Release Staging
simple	25-Mar-2026 16:53:09	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	25-Mar-2026 16:53:09	Bamboo Artifactory Plugin version: 2.6.2
command	25-Mar-2026 16:53:09	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-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-GDB749-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-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-GDB749-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB749-JOB1\nbamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons\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_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-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 - patch-JAL-4410_multimers_from_3dbeacons\nbamboo_shortPlanKey=GDB749\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_buildTimeStamp=2026-03-25T16:53:02.888Z\nbamboo_repository_48169043_name=Jalview Gitlab\nbamboo_repository_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildResultKey=JB-GDB749-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee\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_planRepository_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_48169043_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4410_multimers_from_3dbeacons\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_48169043_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_repository_48169043_git_username=\nbamboo_plan_storageTag=plan-47972517\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-GDB749-JOB1\nbamboo_planKey=JB-GDB749\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4410_multimers_from_3dbeacons\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	25-Mar-2026 16:53:09	2414
build	25-Mar-2026 16:53:10	Starting a Gradle Daemon (subsequent builds will be faster)
build	25-Mar-2026 16:53:20	
build	25-Mar-2026 16:53:20	> Configure project :
build	25-Mar-2026 16:53:20	Using properties from file './utils/channels/default/channel_gradle.properties'
build	25-Mar-2026 16:53:20	JALVIEW_VERSION is set to '2.11.5.1'
build	25-Mar-2026 16:53:20	HEADLESS BUILD
build	25-Mar-2026 16:53:20	J2S ENABLED
build	25-Mar-2026 16:53:20	Using a LOCAL profile.
build	25-Mar-2026 16:53:21	eclipseDir exists
build	25-Mar-2026 16:53:21	
build	25-Mar-2026 16:53:21	> Task :clean
build	25-Mar-2026 16:53:21	> Task :cleanClover
build	25-Mar-2026 16:53:21	> Task :cleanTest UP-TO-DATE
build	25-Mar-2026 16:53:23	
build	25-Mar-2026 16:53:23	> Task :cloverInstrJava
build	25-Mar-2026 16:53:23	Clover: About to instrument 1110 files
build	25-Mar-2026 16:53:24	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	25-Mar-2026 16:53:24	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'.
build	25-Mar-2026 16:53:24	Processing files at 1.9 source level.
error	25-Mar-2026 16:53:27	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	25-Mar-2026 16:53:27	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	25-Mar-2026 16:53:27	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	25-Mar-2026 16:53:27	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	25-Mar-2026 16:53:27	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	25-Mar-2026 16:53:27	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	25-Mar-2026 16:53:27	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	25-Mar-2026 16:53:33	Clover all over. Instrumented 1110 files (113 packages).
build	25-Mar-2026 16:53:35	
build	25-Mar-2026 16:53:35	> Task :cloverInstrTests
build	25-Mar-2026 16:53:35	Clover: About to instrument test files
build	25-Mar-2026 16:53:35	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	25-Mar-2026 16:53:35	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'.
build	25-Mar-2026 16:53:35	Processing files at 1.9 source level.
build	25-Mar-2026 16:53:37	Clover all over. Instrumented 293 files (52 packages).
build	25-Mar-2026 16:53:37	1627 test methods detected.
build	25-Mar-2026 16:53:37	
build	25-Mar-2026 16:53:37	> Task :cloverInstr
build	25-Mar-2026 16:53:41	
build	25-Mar-2026 16:53:41	> Task :compileCloverJava
build	25-Mar-2026 16:53:41	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	25-Mar-2026 16:53:41	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:53:41	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:53:41	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:53:41	Setting target compatibility to 11
error	25-Mar-2026 16:54:01	Note: Some input files use or override a deprecated API.
error	25-Mar-2026 16:54:01	Note: Recompile with -Xlint:deprecation for details.
error	25-Mar-2026 16:54:01	Note: Some input files use unchecked or unsafe operations.
error	25-Mar-2026 16:54:01	Note: Recompile with -Xlint:unchecked for details.
build	25-Mar-2026 16:54:08	
build	25-Mar-2026 16:54:08	> Task :processCloverResources NO-SOURCE
build	25-Mar-2026 16:54:08	> Task :cloverClasses
build	25-Mar-2026 16:54:09	> Task :copyHelp
build	25-Mar-2026 16:54:10	> Task :buildIndices
build	25-Mar-2026 16:54:10	> Task :copyResources
build	25-Mar-2026 16:54:10	> Task :copyChannelResources
build	25-Mar-2026 16:54:10	
build	25-Mar-2026 16:54:10	> Task :createBuildProperties
build	25-Mar-2026 16:54:10	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	25-Mar-2026 16:54:10	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:54:10	
build	25-Mar-2026 16:54:10	> Task :buildResources
build	25-Mar-2026 16:54:10	> Task :copyDocs
build	25-Mar-2026 16:54:10	
build	25-Mar-2026 16:54:10	> Task :convertMdFiles
build	25-Mar-2026 16:54:10	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	25-Mar-2026 16:54:10	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	25-Mar-2026 16:54:10	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	25-Mar-2026 16:54:10	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/building.html
build	25-Mar-2026 16:54:10	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	25-Mar-2026 16:54:11	
build	25-Mar-2026 16:54:11	> Task :releasesTemplates
build	25-Mar-2026 16:54:11	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	25-Mar-2026 16:54:11	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:54:11	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:54:11	Stripping rc/test/etc for TEST
build	25-Mar-2026 16:54:11	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	25-Mar-2026 16:54:11	
build	25-Mar-2026 16:54:11	> Task :prepare
build	25-Mar-2026 16:54:13	
build	25-Mar-2026 16:54:13	> Task :compileJava
build	25-Mar-2026 16:54:13	Setting target compatibility to 11
error	25-Mar-2026 16:54:18	Note: Some input files use or override a deprecated API.
error	25-Mar-2026 16:54:18	Note: Recompile with -Xlint:deprecation for details.
error	25-Mar-2026 16:54:18	Note: Some input files use unchecked or unsafe operations.
error	25-Mar-2026 16:54:18	Note: Recompile with -Xlint:unchecked for details.
build	25-Mar-2026 16:54:23	
build	25-Mar-2026 16:54:23	> Task :compileTestJava
build	25-Mar-2026 16:54:23	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	25-Mar-2026 16:54:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:54:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:54:23	Setting target compatibility to 11
error	25-Mar-2026 16:54:26	Note: Some input files use or override a deprecated API.
error	25-Mar-2026 16:54:26	Note: Recompile with -Xlint:deprecation for details.
error	25-Mar-2026 16:54:26	Note: Some input files use unchecked or unsafe operations.
error	25-Mar-2026 16:54:26	Note: Recompile with -Xlint:unchecked for details.
build	25-Mar-2026 16:54:28	
build	25-Mar-2026 16:54:28	> Task :processTestResources
build	25-Mar-2026 16:54:28	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	25-Mar-2026 16:54:28	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:54:28	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:54:28	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:54:28	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:54:28	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:54:28	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:54:28	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	25-Mar-2026 16:54:28	
build	25-Mar-2026 16:54:28	> Task :testClasses
build	25-Mar-2026 16:54:30	
build	25-Mar-2026 16:54:30	> Task :testTask0
build	25-Mar-2026 16:54:30	Running tests WITH clover
error	25-Mar-2026 16:54:32	WARNING: An illegal reflective access operation has occurred
error	25-Mar-2026 16:54:32	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	25-Mar-2026 16:54:32	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	25-Mar-2026 16:54:32	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	25-Mar-2026 16:54:32	WARNING: All illegal access operations will be denied in a future release
build	25-Mar-2026 16:55:25	
build	25-Mar-2026 16:55:25	Gradle suite > Gradle test > jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy FAILED
build	25-Mar-2026 16:55:25	    java.lang.AssertionError: Expected occupancy to be non-null in column 5 expected object to not be null
build	25-Mar-2026 16:55:25	        at org.testng.Assert.fail(Assert.java:94)
build	25-Mar-2026 16:55:25	        at org.testng.Assert.assertNotNull(Assert.java:406)
build	25-Mar-2026 16:55:25	        at jalview.gui.AlignViewportTest.__CLR4_4_1lfq8443uvh(AlignViewportTest.java:478)
build	25-Mar-2026 16:55:25	        at jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy(AlignViewportTest.java:446)
build	25-Mar-2026 17:09:28	Requesting stop of task ':testTask0' as it has exceeded its configured timeout of 15m.
build	25-Mar-2026 17:09:28	
build	25-Mar-2026 17:09:28	> Task :testTask0 FAILED
build	25-Mar-2026 17:09:28	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	25-Mar-2026 17:09:28	│jalview:testTask0 results: FAILURE (975 tests, 973 successes, 1 failures, 1 skipped) in 14 minutes, 59.937 seconds    │
build	25-Mar-2026 17:09:28	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask0/index.html│
build	25-Mar-2026 17:09:28	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	25-Mar-2026 17:09:28	│OVERALL: results: FAILURE (975 tests, 973 successes, 1 failures, 1 skipped) in 14 minutes, 59.937 seconds             │
build	25-Mar-2026 17:09:28	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	25-Mar-2026 17:09:28	
build	25-Mar-2026 17:09:28	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	25-Mar-2026 17:09:28	
build	25-Mar-2026 17:09:28	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	25-Mar-2026 17:09:28	
build	25-Mar-2026 17:09:28	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	25-Mar-2026 17:09:28	
build	25-Mar-2026 17:09:28	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	25-Mar-2026 17:09:28	Please consult deprecation warnings for more details.
build	25-Mar-2026 17:09:28	18 actionable tasks: 17 executed, 1 up-to-date
error	25-Mar-2026 17:09:28	
error	25-Mar-2026 17:09:28	975 tests completed, 1 failed, 1 skipped
error	25-Mar-2026 17:09:28	
error	25-Mar-2026 17:09:28	FAILURE: Build completed with 2 failures.
error	25-Mar-2026 17:09:28	
error	25-Mar-2026 17:09:28	1: Task failed with an exception.
error	25-Mar-2026 17:09:28	-----------
error	25-Mar-2026 17:09:28	* What went wrong:
error	25-Mar-2026 17:09:28	Execution failed for task ':testTask0'.
error	25-Mar-2026 17:09:28	> Timeout has been exceeded
error	25-Mar-2026 17:09:28	
error	25-Mar-2026 17:09:28	* Try:
error	25-Mar-2026 17:09:28	> Run with --stacktrace option to get the stack trace.
error	25-Mar-2026 17:09:28	> Run with --info or --debug option to get more log output.
error	25-Mar-2026 17:09:28	> Run with --scan to get full insights.
error	25-Mar-2026 17:09:28	==============================================================================
error	25-Mar-2026 17:09:28	
error	25-Mar-2026 17:09:28	2: Task failed with an exception.
error	25-Mar-2026 17:09:28	-----------
error	25-Mar-2026 17:09:28	* Where:
error	25-Mar-2026 17:09:28	Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build.gradle' line: 1967
error	25-Mar-2026 17:09:28	
error	25-Mar-2026 17:09:28	* What went wrong:
error	25-Mar-2026 17:09:28	Failed tests!
error	25-Mar-2026 17:09:28	
error	25-Mar-2026 17:09:28	* Try:
error	25-Mar-2026 17:09:28	> Run with --stacktrace option to get the stack trace.
error	25-Mar-2026 17:09:28	> Run with --info or --debug option to get more log output.
error	25-Mar-2026 17:09:28	> Run with --scan to get full insights.
error	25-Mar-2026 17:09:28	==============================================================================
error	25-Mar-2026 17:09:28	
error	25-Mar-2026 17:09:28	* Get more help at https://help.gradle.org
error	25-Mar-2026 17:09:28	
error	25-Mar-2026 17:09:28	BUILD FAILED in 16m 18s
simple	25-Mar-2026 17:09:28	
simple	25-Mar-2026 17:09:28	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	25-Mar-2026 17:09:28	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	25-Mar-2026 17:09:28	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	25-Mar-2026 17:09:28	Bamboo Artifactory Plugin version: 2.6.2
command	25-Mar-2026 17:09:28	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-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-GDB749-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-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-GDB749-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB749-JOB1\nbamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons\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_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-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 - patch-JAL-4410_multimers_from_3dbeacons\nbamboo_shortPlanKey=GDB749\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_buildTimeStamp=2026-03-25T16:53:02.888Z\nbamboo_repository_48169043_name=Jalview Gitlab\nbamboo_repository_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildResultKey=JB-GDB749-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee\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_planRepository_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_48169043_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4410_multimers_from_3dbeacons\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_48169043_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_repository_48169043_git_username=\nbamboo_plan_storageTag=plan-47972517\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-GDB749-JOB1\nbamboo_planKey=JB-GDB749\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4410_multimers_from_3dbeacons\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	25-Mar-2026 17:09:28	2414
build	25-Mar-2026 17:09:33	
build	25-Mar-2026 17:09:33	> Configure project :
build	25-Mar-2026 17:09:33	Using properties from file './utils/channels/default/channel_gradle.properties'
build	25-Mar-2026 17:09:33	JALVIEW_VERSION is set to '2.11.5.1'
build	25-Mar-2026 17:09:33	HEADLESS BUILD
build	25-Mar-2026 17:09:33	J2S ENABLED
build	25-Mar-2026 17:09:34	Using a LOCAL profile.
build	25-Mar-2026 17:09:34	eclipseDir exists
build	25-Mar-2026 17:09:37	
build	25-Mar-2026 17:09:37	> Task :cloverHtmlReport
build	25-Mar-2026 17:09:37	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	25-Mar-2026 17:09:37	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/clover'
build	25-Mar-2026 17:10:05	Done. Processed 117 packages in 27582ms (235ms per package).
build	25-Mar-2026 17:10:09	
build	25-Mar-2026 17:10:09	> Task :cloverXmlReport
build	25-Mar-2026 17:10:09	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	25-Mar-2026 17:10:10	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/clover/clover.xml'
build	25-Mar-2026 17:10:10	
build	25-Mar-2026 17:10:10	> Task :cloverReport
build	25-Mar-2026 17:10:10	
build	25-Mar-2026 17:10:10	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	25-Mar-2026 17:10:10	
build	25-Mar-2026 17:10:10	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	25-Mar-2026 17:10:10	
build	25-Mar-2026 17:10:10	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	25-Mar-2026 17:10:10	
build	25-Mar-2026 17:10:10	BUILD SUCCESSFUL in 41s
build	25-Mar-2026 17:10:10	2 actionable tasks: 2 executed
simple	25-Mar-2026 17:10:10	Finished task 'Clover Report' with result: Success
simple	25-Mar-2026 17:10:10	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	25-Mar-2026 17:10:10	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1...
simple	25-Mar-2026 17:10:10	Failing task since test cases were expected but none were found.
simple	25-Mar-2026 17:10:10	Finished task 'TestNG Parser' with result: Failed
simple	25-Mar-2026 17:10:10	Running post build plugin 'NCover Results Collector'
simple	25-Mar-2026 17:10:10	Running post build plugin 'Artifact Copier'
simple	25-Mar-2026 17:10:10	Publishing an artifact: Clover Report (System)
simple	25-Mar-2026 17:10:11	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.421 s
simple	25-Mar-2026 17:10:11	Publishing an artifact: TestNG report
error	25-Mar-2026 17:10:11	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/test does not exist.
simple	25-Mar-2026 17:10:11	The artifact hasn't been successfully published after 2.510 ms
simple	25-Mar-2026 17:10:11	Running post build plugin 'Artifactory Release Management Staging'
simple	25-Mar-2026 17:10:11	Running post build plugin 'Artifactory Build Info Copier'
simple	25-Mar-2026 17:10:11	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	25-Mar-2026 17:10:11	Running post build plugin 'npm Cache Cleanup'
simple	25-Mar-2026 17:10:11	Running post build plugin 'Clover Results Collector'
simple	25-Mar-2026 17:10:11	Running post build plugin 'Docker Container Cleanup'
simple	25-Mar-2026 17:10:11	Finalising the build...
simple	25-Mar-2026 17:10:11	Stopping timer.
simple	25-Mar-2026 17:10:11	Build JB-GDB749-JOB1-1 completed.
simple	25-Mar-2026 17:10:11	Running on server: post build plugin 'NCover Results Collector'
simple	25-Mar-2026 17:10:11	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	25-Mar-2026 17:10:11	Running on server: post build plugin 'Clover Delta Calculator'
simple	25-Mar-2026 17:10:11	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	25-Mar-2026 17:10:11	All post build plugins have finished
simple	25-Mar-2026 17:10:11	Generating build results summary...
simple	25-Mar-2026 17:10:11	Saving build results to disk...
simple	25-Mar-2026 17:10:11	Logging substituted variables...
simple	25-Mar-2026 17:10:11	Indexing build results...
simple	25-Mar-2026 17:10:11	Finished building JB-GDB749-JOB1-1.
simple	26-Mar-2026 08:01:21	Build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-JOB1-1) started building on agent Default Agent
simple	26-Mar-2026 08:01:21	
simple	26-Mar-2026 08:01:21	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1
simple	26-Mar-2026 08:01:21	Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-JOB1-1)
simple	26-Mar-2026 08:01:21	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	26-Mar-2026 08:01:21	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1
simple	26-Mar-2026 08:01:21	Updating source code to revision: 570cfd128c945bc7593ad75c31b9761ff81f5fee
simple	26-Mar-2026 08:01:21	Fetching 'refs/heads/patch/JAL-4410_multimers_from_3dbeacons' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	26-Mar-2026 08:01:22	Checking out revision 570cfd128c945bc7593ad75c31b9761ff81f5fee.
simple	26-Mar-2026 08:01:23	Already on 'patch/JAL-4410_multimers_from_3dbeacons'
simple	26-Mar-2026 08:01:23	Updated source code to revision: 570cfd128c945bc7593ad75c31b9761ff81f5fee
simple	26-Mar-2026 08:01:23	Finished task 'Checkout Default Repository' with result: Success
simple	26-Mar-2026 08:01:23	Running pre-build action: VCS Version Collector
simple	26-Mar-2026 08:01:23	Running pre-build action: Artifactory Release Staging
simple	26-Mar-2026 08:01:23	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	26-Mar-2026 08:01:23	Bamboo Artifactory Plugin version: 2.6.2
command	26-Mar-2026 08:01:23	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-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-GDB749-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_CLOVER_ELEMENTS=171386\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_CLOVER_BUILD_COVERAGE=29.3\nbamboo_CLOVER_CLASSES=1419\nbamboo_CLOVER_METHODS=16228\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB749-JOB1\nbamboo_CLOVER_COVERED_STATEMENTS=33560\nbamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_CLOVER_COVERED_CONDITIONALS=11321\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-1\nbamboo_CLOVER_STATEMENTS=112778\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_ManualBuildTriggerReason_stageName=Default Stage\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons\nbamboo_shortPlanKey=GDB749\nbamboo_shortJobKey=JOB1\nbamboo_CLOVER_NCLOC=269847\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_buildTimeStamp=2026-03-26T08:01:21.888Z\nbamboo_repository_48169043_name=Jalview Gitlab\nbamboo_CLOVER_COVERED_METHODS=5339\nbamboo_CLOVER_CONDITIONALS=42380\nbamboo_repository_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildResultKey=JB-GDB749-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_4=/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\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/\nbamboo_CLOVER_PACKAGES=115\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=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_48169043_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4410_multimers_from_3dbeacons\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_48169043_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_repository_48169043_git_username=\nbamboo_plan_storageTag=plan-47972517\nbamboo_CLOVER_LOC=427989\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_CLOVER_FILES=1123\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_ManualBuildTriggerReason_userName=jprocter\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_CLOVER_COVERED_ELEMENTS=50220\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-GDB749-JOB1\nbamboo_planKey=JB-GDB749\nbamboo_RerunBuildTriggerReason_noOfRetries=1\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4410_multimers_from_3dbeacons\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	26-Mar-2026 08:01:23	2414
build	26-Mar-2026 08:01:24	Starting a Gradle Daemon (subsequent builds will be faster)
build	26-Mar-2026 08:01:30	
build	26-Mar-2026 08:01:30	> Configure project :
build	26-Mar-2026 08:01:30	Using properties from file './utils/channels/default/channel_gradle.properties'
build	26-Mar-2026 08:01:30	JALVIEW_VERSION is set to '2.11.5.1'
build	26-Mar-2026 08:01:30	HEADLESS BUILD
build	26-Mar-2026 08:01:30	J2S ENABLED
build	26-Mar-2026 08:01:30	Using a LOCAL profile.
build	26-Mar-2026 08:01:31	eclipseDir exists
build	26-Mar-2026 08:01:32	
build	26-Mar-2026 08:01:32	> Task :clean
build	26-Mar-2026 08:01:32	> Task :cleanClover
build	26-Mar-2026 08:01:32	> Task :cleanTest UP-TO-DATE
build	26-Mar-2026 08:01:34	
build	26-Mar-2026 08:01:34	> Task :cloverInstrJava
build	26-Mar-2026 08:01:34	Clover: About to instrument 1110 files
build	26-Mar-2026 08:01:34	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	26-Mar-2026 08:01:34	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'.
build	26-Mar-2026 08:01:34	Processing files at 1.9 source level.
error	26-Mar-2026 08:01:36	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	26-Mar-2026 08:01:36	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	26-Mar-2026 08:01:36	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	26-Mar-2026 08:01:36	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	26-Mar-2026 08:01:36	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	26-Mar-2026 08:01:36	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	26-Mar-2026 08:01:36	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	26-Mar-2026 08:01:42	Clover all over. Instrumented 1110 files (113 packages).
build	26-Mar-2026 08:01:45	
build	26-Mar-2026 08:01:45	> Task :cloverInstrTests
build	26-Mar-2026 08:01:45	Clover: About to instrument test files
build	26-Mar-2026 08:01:45	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	26-Mar-2026 08:01:45	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'.
build	26-Mar-2026 08:01:45	Processing files at 1.9 source level.
build	26-Mar-2026 08:01:47	Clover all over. Instrumented 293 files (52 packages).
build	26-Mar-2026 08:01:47	1627 test methods detected.
build	26-Mar-2026 08:01:47	
build	26-Mar-2026 08:01:47	> Task :cloverInstr
build	26-Mar-2026 08:01:49	
build	26-Mar-2026 08:01:49	> Task :compileCloverJava
build	26-Mar-2026 08:01:49	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	26-Mar-2026 08:01:49	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:01:49	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:01:49	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:01:49	Setting target compatibility to 11
error	26-Mar-2026 08:02:10	Note: Some input files use or override a deprecated API.
error	26-Mar-2026 08:02:10	Note: Recompile with -Xlint:deprecation for details.
error	26-Mar-2026 08:02:10	Note: Some input files use unchecked or unsafe operations.
error	26-Mar-2026 08:02:10	Note: Recompile with -Xlint:unchecked for details.
build	26-Mar-2026 08:02:16	
build	26-Mar-2026 08:02:16	> Task :processCloverResources NO-SOURCE
build	26-Mar-2026 08:02:16	> Task :cloverClasses
build	26-Mar-2026 08:02:17	> Task :copyHelp
build	26-Mar-2026 08:02:18	> Task :buildIndices
build	26-Mar-2026 08:02:18	> Task :copyResources
build	26-Mar-2026 08:02:18	> Task :copyChannelResources
build	26-Mar-2026 08:02:18	
build	26-Mar-2026 08:02:18	> Task :createBuildProperties
build	26-Mar-2026 08:02:18	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	26-Mar-2026 08:02:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:02:18	
build	26-Mar-2026 08:02:18	> Task :buildResources
build	26-Mar-2026 08:02:18	> Task :copyDocs
build	26-Mar-2026 08:02:18	
build	26-Mar-2026 08:02:18	> Task :convertMdFiles
build	26-Mar-2026 08:02:18	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	26-Mar-2026 08:02:18	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	26-Mar-2026 08:02:18	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	26-Mar-2026 08:02:18	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/building.html
build	26-Mar-2026 08:02:18	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	26-Mar-2026 08:02:19	
build	26-Mar-2026 08:02:19	> Task :releasesTemplates
build	26-Mar-2026 08:02:19	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	26-Mar-2026 08:02:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:02:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:02:19	Stripping rc/test/etc for TEST
build	26-Mar-2026 08:02:19	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	26-Mar-2026 08:02:19	
build	26-Mar-2026 08:02:19	> Task :prepare
build	26-Mar-2026 08:02:21	
build	26-Mar-2026 08:02:21	> Task :compileJava
build	26-Mar-2026 08:02:21	Setting target compatibility to 11
error	26-Mar-2026 08:02:26	Note: Some input files use or override a deprecated API.
error	26-Mar-2026 08:02:26	Note: Recompile with -Xlint:deprecation for details.
error	26-Mar-2026 08:02:26	Note: Some input files use unchecked or unsafe operations.
error	26-Mar-2026 08:02:26	Note: Recompile with -Xlint:unchecked for details.
build	26-Mar-2026 08:02:30	
build	26-Mar-2026 08:02:30	> Task :compileTestJava
build	26-Mar-2026 08:02:30	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	26-Mar-2026 08:02:30	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:02:30	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:02:30	Setting target compatibility to 11
error	26-Mar-2026 08:02:34	Note: Some input files use or override a deprecated API.
error	26-Mar-2026 08:02:34	Note: Recompile with -Xlint:deprecation for details.
error	26-Mar-2026 08:02:34	Note: Some input files use unchecked or unsafe operations.
error	26-Mar-2026 08:02:34	Note: Recompile with -Xlint:unchecked for details.
build	26-Mar-2026 08:02:35	
build	26-Mar-2026 08:02:35	> Task :processTestResources
build	26-Mar-2026 08:02:35	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	26-Mar-2026 08:02:35	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:02:35	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:02:35	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:02:35	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:02:35	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:02:35	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:02:35	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:02:35	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	26-Mar-2026 08:02:35	
build	26-Mar-2026 08:02:35	> Task :testClasses
build	26-Mar-2026 08:02:37	
build	26-Mar-2026 08:02:37	> Task :testTask0
build	26-Mar-2026 08:02:37	Running tests WITH clover
error	26-Mar-2026 08:02:39	WARNING: An illegal reflective access operation has occurred
error	26-Mar-2026 08:02:39	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	26-Mar-2026 08:02:39	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	26-Mar-2026 08:02:39	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	26-Mar-2026 08:02:39	WARNING: All illegal access operations will be denied in a future release
build	26-Mar-2026 08:06:56	
build	26-Mar-2026 08:06:56	> Task :testTask1
build	26-Mar-2026 08:06:56	Running tests WITH clover
error	26-Mar-2026 08:06:57	WARNING: An illegal reflective access operation has occurred
error	26-Mar-2026 08:06:57	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	26-Mar-2026 08:06:57	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	26-Mar-2026 08:06:57	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	26-Mar-2026 08:06:57	WARNING: All illegal access operations will be denied in a future release
build	26-Mar-2026 08:09:15	
build	26-Mar-2026 08:09:15	> Task :testTask2
build	26-Mar-2026 08:09:15	Running tests WITH clover
build	26-Mar-2026 08:09:18	
build	26-Mar-2026 08:09:18	> Task :testTask3
build	26-Mar-2026 08:09:18	Running tests WITH clover
error	26-Mar-2026 08:09:19	WARNING: An illegal reflective access operation has occurred
error	26-Mar-2026 08:09:19	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	26-Mar-2026 08:09:19	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	26-Mar-2026 08:09:19	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	26-Mar-2026 08:09:19	WARNING: All illegal access operations will be denied in a future release
build	26-Mar-2026 08:10:07	
build	26-Mar-2026 08:10:07	> Task :test NO-SOURCE
build	26-Mar-2026 08:10:07	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	26-Mar-2026 08:10:07	│jalview:testTask0 results: SUCCESS (1835 tests, 1835 successes, 0 failures, 0 skipped) in 4 minutes, 17.393 seconds   │
build	26-Mar-2026 08:10:07	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask0/index.html│
build	26-Mar-2026 08:10:07	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	26-Mar-2026 08:10:07	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 19.016 seconds       │
build	26-Mar-2026 08:10:07	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask1/index.html│
build	26-Mar-2026 08:10:07	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	26-Mar-2026 08:10:07	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.120 seconds                     │
build	26-Mar-2026 08:10:07	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask2/index.html│
build	26-Mar-2026 08:10:07	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	26-Mar-2026 08:10:07	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 50.678 seconds                  │
build	26-Mar-2026 08:10:07	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask3/index.html│
build	26-Mar-2026 08:10:07	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	26-Mar-2026 08:10:07	│OVERALL: results: SUCCESS (1923 tests, 1923 successes, 0 failures, 0 skipped) in 6 minutes, 90.207 seconds            │
build	26-Mar-2026 08:10:07	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	26-Mar-2026 08:10:07	
build	26-Mar-2026 08:10:07	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	26-Mar-2026 08:10:07	
build	26-Mar-2026 08:10:07	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	26-Mar-2026 08:10:07	
build	26-Mar-2026 08:10:07	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	26-Mar-2026 08:10:07	
build	26-Mar-2026 08:10:07	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	26-Mar-2026 08:10:07	Please consult deprecation warnings for more details.
build	26-Mar-2026 08:10:07	
build	26-Mar-2026 08:10:07	BUILD SUCCESSFUL in 8m 43s
build	26-Mar-2026 08:10:07	21 actionable tasks: 20 executed, 1 up-to-date
simple	26-Mar-2026 08:10:07	Finished task 'Run tests with openclover under gradle' with result: Success
simple	26-Mar-2026 08:10:07	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	26-Mar-2026 08:10:07	Bamboo Artifactory Plugin version: 2.6.2
command	26-Mar-2026 08:10:07	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-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-GDB749-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_CLOVER_ELEMENTS=171386\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_CLOVER_BUILD_COVERAGE=29.3\nbamboo_CLOVER_CLASSES=1419\nbamboo_CLOVER_METHODS=16228\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB749-JOB1\nbamboo_CLOVER_COVERED_STATEMENTS=33560\nbamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_CLOVER_COVERED_CONDITIONALS=11321\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-1\nbamboo_CLOVER_STATEMENTS=112778\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_ManualBuildTriggerReason_stageName=Default Stage\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons\nbamboo_shortPlanKey=GDB749\nbamboo_shortJobKey=JOB1\nbamboo_CLOVER_NCLOC=269847\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_buildTimeStamp=2026-03-26T08:01:21.888Z\nbamboo_repository_48169043_name=Jalview Gitlab\nbamboo_CLOVER_COVERED_METHODS=5339\nbamboo_CLOVER_CONDITIONALS=42380\nbamboo_repository_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildResultKey=JB-GDB749-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_4=/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\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/\nbamboo_CLOVER_PACKAGES=115\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=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_48169043_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4410_multimers_from_3dbeacons\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_48169043_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_repository_48169043_git_username=\nbamboo_plan_storageTag=plan-47972517\nbamboo_CLOVER_LOC=427989\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_CLOVER_FILES=1123\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_ManualBuildTriggerReason_userName=jprocter\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_CLOVER_COVERED_ELEMENTS=50220\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-GDB749-JOB1\nbamboo_planKey=JB-GDB749\nbamboo_RerunBuildTriggerReason_noOfRetries=1\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4410_multimers_from_3dbeacons\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	26-Mar-2026 08:10:07	2414
build	26-Mar-2026 08:10:13	
build	26-Mar-2026 08:10:13	> Configure project :
build	26-Mar-2026 08:10:13	Using properties from file './utils/channels/default/channel_gradle.properties'
build	26-Mar-2026 08:10:13	JALVIEW_VERSION is set to '2.11.5.1'
build	26-Mar-2026 08:10:13	HEADLESS BUILD
build	26-Mar-2026 08:10:13	J2S ENABLED
build	26-Mar-2026 08:10:13	Using a LOCAL profile.
build	26-Mar-2026 08:10:14	eclipseDir exists
build	26-Mar-2026 08:10:16	
build	26-Mar-2026 08:10:16	> Task :cloverHtmlReport
build	26-Mar-2026 08:10:16	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	26-Mar-2026 08:10:17	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/clover'
build	26-Mar-2026 08:11:02	Done. Processed 117 packages in 45267ms (386ms per package).
build	26-Mar-2026 08:11:07	
build	26-Mar-2026 08:11:07	> Task :cloverXmlReport
build	26-Mar-2026 08:11:07	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	26-Mar-2026 08:11:09	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/clover/clover.xml'
build	26-Mar-2026 08:11:09	
build	26-Mar-2026 08:11:09	> Task :cloverReport
build	26-Mar-2026 08:11:09	
build	26-Mar-2026 08:11:09	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	26-Mar-2026 08:11:09	
build	26-Mar-2026 08:11:09	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	26-Mar-2026 08:11:09	
build	26-Mar-2026 08:11:09	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	26-Mar-2026 08:11:09	
build	26-Mar-2026 08:11:09	BUILD SUCCESSFUL in 1m 1s
build	26-Mar-2026 08:11:09	2 actionable tasks: 2 executed
simple	26-Mar-2026 08:11:09	Finished task 'Clover Report' with result: Success
simple	26-Mar-2026 08:11:09	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	26-Mar-2026 08:11:09	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1...
simple	26-Mar-2026 08:11:10	Finished task 'TestNG Parser' with result: Success
simple	26-Mar-2026 08:11:10	Running post build plugin 'NCover Results Collector'
simple	26-Mar-2026 08:11:10	Running post build plugin 'Artifact Copier'
simple	26-Mar-2026 08:11:10	Publishing an artifact: Clover Report (System)
simple	26-Mar-2026 08:11:11	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.685 s
simple	26-Mar-2026 08:11:11	Publishing an artifact: TestNG report
error	26-Mar-2026 08:11:11	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/test does not exist.
simple	26-Mar-2026 08:11:11	The artifact hasn't been successfully published after 2.428 ms
simple	26-Mar-2026 08:11:11	Running post build plugin 'Artifactory Release Management Staging'
simple	26-Mar-2026 08:11:11	Running post build plugin 'Artifactory Build Info Copier'
simple	26-Mar-2026 08:11:11	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	26-Mar-2026 08:11:11	Running post build plugin 'npm Cache Cleanup'
simple	26-Mar-2026 08:11:11	Running post build plugin 'Clover Results Collector'
simple	26-Mar-2026 08:11:11	Running post build plugin 'Docker Container Cleanup'
simple	26-Mar-2026 08:11:11	Finalising the build...
simple	26-Mar-2026 08:11:11	Stopping timer.
simple	26-Mar-2026 08:11:11	Build JB-GDB749-JOB1-1 completed.
simple	26-Mar-2026 08:11:11	Running on server: post build plugin 'NCover Results Collector'
simple	26-Mar-2026 08:11:11	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	26-Mar-2026 08:11:11	Running on server: post build plugin 'Clover Delta Calculator'
simple	26-Mar-2026 08:11:11	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	26-Mar-2026 08:11:11	All post build plugins have finished
simple	26-Mar-2026 08:11:11	Generating build results summary...
simple	26-Mar-2026 08:11:12	Saving build results to disk...
simple	26-Mar-2026 08:11:12	Logging substituted variables...
simple	26-Mar-2026 08:11:12	Indexing build results...
simple	26-Mar-2026 08:11:12	Finished building JB-GDB749-JOB1-1.