simple	27-May-2026 17:26:37	Build Jalview Builds - Gradle Develop Build - patch-JAL-4478_r212_initialpatch - Clover and Tests #1 (JB-GDB751-JOB1-1) started building on agent Default Agent
simple	27-May-2026 17:26:37	
simple	27-May-2026 17:26:37	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1
simple	27-May-2026 17:26:37	Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4478_r212_initialpatch - Clover and Tests #1 (JB-GDB751-JOB1-1)
simple	27-May-2026 17:26:37	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	27-May-2026 17:26:37	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1
simple	27-May-2026 17:26:37	Updating source code to revision: a70ce030f9aceed3e3ee89984340187708c0a2a0
simple	27-May-2026 17:26:37	Fetching 'refs/heads/patch/JAL-4478_r212_initialpatch' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	27-May-2026 17:26:38	Checking out revision a70ce030f9aceed3e3ee89984340187708c0a2a0.
simple	27-May-2026 17:26:38	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/.git'.
simple	27-May-2026 17:26:38	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1'...
simple	27-May-2026 17:26:38	done.
simple	27-May-2026 17:26:44	Switched to a new branch 'patch/JAL-4478_r212_initialpatch'
simple	27-May-2026 17:26:44	Branch patch/JAL-4478_r212_initialpatch set up to track remote branch patch/JAL-4478_r212_initialpatch from origin.
simple	27-May-2026 17:26:44	Updated source code to revision: a70ce030f9aceed3e3ee89984340187708c0a2a0
simple	27-May-2026 17:26:44	Finished task 'Checkout Default Repository' with result: Success
simple	27-May-2026 17:26:44	Running pre-build action: VCS Version Collector
simple	27-May-2026 17:26:44	Running pre-build action: Artifactory Release Staging
simple	27-May-2026 17:26:44	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	27-May-2026 17:26:44	Bamboo Artifactory Plugin version: 2.6.2
command	27-May-2026 17:26:44	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4478_r212_initialpatch - Clover and Tests #1 (JB-GDB751-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-GDB751-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4478_r212_initialpatch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4478_r212_initialpatch\nbamboo_repository_revision_number=a70ce030f9aceed3e3ee89984340187708c0a2a0\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB751-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-GDB751-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB751-JOB1\nbamboo_shortPlanName=patch-JAL-4478_r212_initialpatch\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-GDB751-JOB1-1\nbamboo_repository_48169054_git_branch=patch/JAL-4478_r212_initialpatch\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-4478_r212_initialpatch\nbamboo_shortPlanKey=GDB751\nbamboo_repository_48169054_name=Jalview Gitlab\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a70ce030f9aceed3e3ee89984340187708c0a2a0\nbamboo_buildTimeStamp=2026-05-27T17:18:13.842+01:00\nbamboo_repository_git_branch=patch/JAL-4478_r212_initialpatch\nbamboo_buildResultKey=JB-GDB751-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4478_r212_initialpatch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4478_r212_initialpatch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=a70ce030f9aceed3e3ee89984340187708c0a2a0\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169054_git_username=\nbamboo_repository_48169054_branch_name=patch/JAL-4478_r212_initialpatch\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_48169054_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\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-4478_r212_initialpatch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_48169054_revision_number=a70ce030f9aceed3e3ee89984340187708c0a2a0\nbamboo_planRepository_branchDisplayName=patch/JAL-4478_r212_initialpatch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4478_r212_initialpatch\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-47972539\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-GDB751-JOB1\nbamboo_planKey=JB-GDB751\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4478_r212_initialpatch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	27-May-2026 17:26:44	2414
build	27-May-2026 17:26:46	
build	27-May-2026 17:26:46	> Configure project :
build	27-May-2026 17:26:46	Using properties from file './utils/channels/default/channel_gradle.properties'
build	27-May-2026 17:26:46	JALVIEW_VERSION is set to '2.12.0'
build	27-May-2026 17:26:46	HEADLESS BUILD
build	27-May-2026 17:26:46	J2S ENABLED
build	27-May-2026 17:26:46	Using a LOCAL profile.
build	27-May-2026 17:26:46	eclipseDir exists
build	27-May-2026 17:26:46	
build	27-May-2026 17:26:46	> Task :clean
build	27-May-2026 17:26:46	> Task :cleanClover
build	27-May-2026 17:26:46	> Task :cleanTest UP-TO-DATE
build	27-May-2026 17:26:48	
build	27-May-2026 17:26:48	> Task :cloverInstrJava
build	27-May-2026 17:26:48	Clover: About to instrument 1256 files
build	27-May-2026 17:26:49	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	27-May-2026 17:26:49	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/clover/clover.db'.
build	27-May-2026 17:26:49	Processing files at 1.9 source level.
error	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:53	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	27-May-2026 17:26:54	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	27-May-2026 17:26:54	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	27-May-2026 17:26:54	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	27-May-2026 17:26:54	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	27-May-2026 17:26:54	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	27-May-2026 17:26:54	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	27-May-2026 17:26:54	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	27-May-2026 17:26:54	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	27-May-2026 17:26:54	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	27-May-2026 17:26:54	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	27-May-2026 17:26:54	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	27-May-2026 17:26:54	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	27-May-2026 17:26:59	Clover all over. Instrumented 1256 files (133 packages).
build	27-May-2026 17:27:01	
build	27-May-2026 17:27:01	> Task :cloverInstrTests
build	27-May-2026 17:27:01	Clover: About to instrument test files
build	27-May-2026 17:27:01	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	27-May-2026 17:27:01	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/clover/clover.db'.
build	27-May-2026 17:27:01	Processing files at 1.9 source level.
build	27-May-2026 17:27:04	Clover all over. Instrumented 315 files (58 packages).
build	27-May-2026 17:27:04	1772 test methods detected.
build	27-May-2026 17:27:04	
build	27-May-2026 17:27:04	> Task :cloverInstr
build	27-May-2026 17:27:07	
build	27-May-2026 17:27:07	> Task :compileCloverJava
build	27-May-2026 17:27:07	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	27-May-2026 17:27:07	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:07	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:07	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:07	Setting target compatibility to 11
error	27-May-2026 17:27:22	Note: Some input files use or override a deprecated API.
error	27-May-2026 17:27:22	Note: Recompile with -Xlint:deprecation for details.
error	27-May-2026 17:27:22	Note: Some input files use unchecked or unsafe operations.
error	27-May-2026 17:27:22	Note: Recompile with -Xlint:unchecked for details.
build	27-May-2026 17:27:28	
build	27-May-2026 17:27:28	> Task :processCloverResources NO-SOURCE
build	27-May-2026 17:27:28	> Task :cloverClasses
build	27-May-2026 17:27:28	> Task :copyHelp
build	27-May-2026 17:27:29	> Task :buildIndices
build	27-May-2026 17:27:29	> Task :copyResources
build	27-May-2026 17:27:29	> Task :copyChannelResources
build	27-May-2026 17:27:29	
build	27-May-2026 17:27:29	> Task :createBuildProperties
build	27-May-2026 17:27:29	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	27-May-2026 17:27:29	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:29	
build	27-May-2026 17:27:29	> Task :buildResources
build	27-May-2026 17:27:29	> Task :copyDocs
build	27-May-2026 17:27:29	
build	27-May-2026 17:27:29	> Task :convertMdFiles
build	27-May-2026 17:27:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	27-May-2026 17:27:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	27-May-2026 17:27:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	27-May-2026 17:27:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
build	27-May-2026 17:27:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/resources/doc_build/doc/building.html
build	27-May-2026 17:27:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/resources/doc_build/doc/addingWebClient.html
build	27-May-2026 17:27:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	27-May-2026 17:27:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
build	27-May-2026 17:27:29	
build	27-May-2026 17:27:29	> Task :releasesTemplates
build	27-May-2026 17:27:29	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	27-May-2026 17:27:29	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:29	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:29	Stripping rc/test/etc for TEST
build	27-May-2026 17:27:29	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	27-May-2026 17:27:29	
build	27-May-2026 17:27:29	> Task :prepare
build	27-May-2026 17:27:31	
build	27-May-2026 17:27:31	> Task :compileJava
build	27-May-2026 17:27:31	Setting target compatibility to 11
error	27-May-2026 17:27:37	Note: Some input files use or override a deprecated API.
error	27-May-2026 17:27:37	Note: Recompile with -Xlint:deprecation for details.
error	27-May-2026 17:27:37	Note: Some input files use unchecked or unsafe operations.
error	27-May-2026 17:27:37	Note: Recompile with -Xlint:unchecked for details.
build	27-May-2026 17:27:39	
build	27-May-2026 17:27:39	> Task :compileTestJava
build	27-May-2026 17:27:39	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	27-May-2026 17:27:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:39	Setting target compatibility to 11
error	27-May-2026 17:27:45	Note: Some input files use or override a deprecated API.
error	27-May-2026 17:27:45	Note: Recompile with -Xlint:deprecation for details.
error	27-May-2026 17:27:45	Note: Some input files use unchecked or unsafe operations.
error	27-May-2026 17:27:45	Note: Recompile with -Xlint:unchecked for details.
build	27-May-2026 17:27:46	
build	27-May-2026 17:27:46	> Task :processTestResources
build	27-May-2026 17:27:46	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	27-May-2026 17:27:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-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	27-May-2026 17:27:46	
build	27-May-2026 17:27:46	> Task :testClasses
build	27-May-2026 17:27:48	
build	27-May-2026 17:27:48	> Task :testTask0
build	27-May-2026 17:27:48	Running tests WITH clover
error	27-May-2026 17:27:50	WARNING: An illegal reflective access operation has occurred
error	27-May-2026 17:27:50	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	27-May-2026 17:27:50	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	27-May-2026 17:27:50	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	27-May-2026 17:27:50	WARNING: All illegal access operations will be denied in a future release
build	27-May-2026 17:29:42	
build	27-May-2026 17:29:42	Gradle suite > Gradle test > jalview.gui.CalculationChooserTest > testGetApplicableScoreModels FAILED
build	27-May-2026 17:29:42	    java.lang.AssertionError: expected [5] but found [6]
build	27-May-2026 17:29:42	        at org.testng.Assert.fail(Assert.java:110)
build	27-May-2026 17:29:42	        at org.testng.Assert.failNotEquals(Assert.java:1413)
build	27-May-2026 17:29:42	        at org.testng.Assert.assertEqualsImpl(Assert.java:149)
build	27-May-2026 17:29:42	        at org.testng.Assert.assertEquals(Assert.java:131)
build	27-May-2026 17:29:42	        at org.testng.Assert.assertEquals(Assert.java:1240)
build	27-May-2026 17:29:42	        at org.testng.Assert.assertEquals(Assert.java:1274)
build	27-May-2026 17:29:42	        at jalview.gui.CalculationChooserTest.__CLR4_4_1p7y2xs446s(CalculationChooserTest.java:59)
build	27-May-2026 17:29:42	        at jalview.gui.CalculationChooserTest.testGetApplicableScoreModels(CalculationChooserTest.java:48)
build	27-May-2026 17:30:19	[152.084s][warning][gc,alloc] AWT-EventQueue-0: Retried waiting for GCLocker too often allocating 135080516 words
error	27-May-2026 17:32:34	
error	27-May-2026 17:32:34	2105 tests completed, 1 failed
build	27-May-2026 17:32:34	There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/reports/tests/testTask0/index.html
build	27-May-2026 17:32:37	
build	27-May-2026 17:32:37	> Task :testTask1
build	27-May-2026 17:32:37	Running tests WITH clover
error	27-May-2026 17:32:38	WARNING: An illegal reflective access operation has occurred
error	27-May-2026 17:32:38	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	27-May-2026 17:32:38	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	27-May-2026 17:32:38	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	27-May-2026 17:32:38	WARNING: All illegal access operations will be denied in a future release
build	27-May-2026 17:34:45	
build	27-May-2026 17:34:45	> Task :testTask2
build	27-May-2026 17:34:45	Running tests WITH clover
error	27-May-2026 17:34:46	WARNING: An illegal reflective access operation has occurred
error	27-May-2026 17:34:46	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	27-May-2026 17:34:46	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	27-May-2026 17:34:46	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	27-May-2026 17:34:46	WARNING: All illegal access operations will be denied in a future release
build	27-May-2026 17:34:50	
build	27-May-2026 17:34:50	> Task :testTask3
build	27-May-2026 17:34:50	Running tests WITH clover
error	27-May-2026 17:34:51	WARNING: An illegal reflective access operation has occurred
error	27-May-2026 17:34:51	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	27-May-2026 17:34:51	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	27-May-2026 17:34:51	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	27-May-2026 17:34:51	WARNING: All illegal access operations will be denied in a future release
build	27-May-2026 17:35:12	
build	27-May-2026 17:35:12	> Task :test NO-SOURCE
error	27-May-2026 17:35:12	
error	27-May-2026 17:35:12	FAILURE: Build failed with an exception.
error	27-May-2026 17:35:12	
error	27-May-2026 17:35:12	* Where:
error	27-May-2026 17:35:12	Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build.gradle' line: 1964
error	27-May-2026 17:35:12	
error	27-May-2026 17:35:12	* What went wrong:
error	27-May-2026 17:35:12	Failed tests!
error	27-May-2026 17:35:12	
error	27-May-2026 17:35:12	* Try:
error	27-May-2026 17:35:12	> Run with --stacktrace option to get the stack trace.
error	27-May-2026 17:35:12	> Run with --info or --debug option to get more log output.
error	27-May-2026 17:35:12	> Run with --scan to get full insights.
error	27-May-2026 17:35:12	
error	27-May-2026 17:35:12	* Get more help at https://help.gradle.org
error	27-May-2026 17:35:12	
error	27-May-2026 17:35:12	BUILD FAILED in 8m 27s
build	27-May-2026 17:35:12	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	27-May-2026 17:35:12	│jalview:testTask0 results: FAILURE (2105 tests, 2104 successes, 1 failures, 0 skipped) in 4 minutes, 47.805 seconds   │
build	27-May-2026 17:35:12	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/reports/tests/testTask0/index.html│
build	27-May-2026 17:35:12	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	27-May-2026 17:35:12	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 8.410 seconds        │
build	27-May-2026 17:35:12	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/reports/tests/testTask1/index.html│
build	27-May-2026 17:35:12	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	27-May-2026 17:35:12	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.935 seconds                     │
build	27-May-2026 17:35:12	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/reports/tests/testTask2/index.html│
build	27-May-2026 17:35:12	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	27-May-2026 17:35:12	│jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 23.428 seconds                  │
build	27-May-2026 17:35:12	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/reports/tests/testTask3/index.html│
build	27-May-2026 17:35:12	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	27-May-2026 17:35:12	│OVERALL: results: FAILURE (2182 tests, 2180 successes, 1 failures, 1 skipped) in 6 minutes, 84.578 seconds            │
build	27-May-2026 17:35:12	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	27-May-2026 17:35:12	
build	27-May-2026 17:35:12	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	27-May-2026 17:35:12	
build	27-May-2026 17:35:12	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	27-May-2026 17:35:12	
build	27-May-2026 17:35:12	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	27-May-2026 17:35:12	
build	27-May-2026 17:35:12	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	27-May-2026 17:35:12	Please consult deprecation warnings for more details.
build	27-May-2026 17:35:12	21 actionable tasks: 20 executed, 1 up-to-date
simple	27-May-2026 17:35:12	
simple	27-May-2026 17:35:12	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	27-May-2026 17:35:12	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	27-May-2026 17:35:12	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	27-May-2026 17:35:12	Bamboo Artifactory Plugin version: 2.6.2
command	27-May-2026 17:35:12	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4478_r212_initialpatch - Clover and Tests #1 (JB-GDB751-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-GDB751-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4478_r212_initialpatch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4478_r212_initialpatch\nbamboo_repository_revision_number=a70ce030f9aceed3e3ee89984340187708c0a2a0\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB751-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-GDB751-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB751-JOB1\nbamboo_shortPlanName=patch-JAL-4478_r212_initialpatch\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-GDB751-JOB1-1\nbamboo_repository_48169054_git_branch=patch/JAL-4478_r212_initialpatch\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-4478_r212_initialpatch\nbamboo_shortPlanKey=GDB751\nbamboo_repository_48169054_name=Jalview Gitlab\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a70ce030f9aceed3e3ee89984340187708c0a2a0\nbamboo_buildTimeStamp=2026-05-27T17:18:13.842+01:00\nbamboo_repository_git_branch=patch/JAL-4478_r212_initialpatch\nbamboo_buildResultKey=JB-GDB751-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4478_r212_initialpatch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4478_r212_initialpatch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=a70ce030f9aceed3e3ee89984340187708c0a2a0\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169054_git_username=\nbamboo_repository_48169054_branch_name=patch/JAL-4478_r212_initialpatch\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_repository_48169054_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\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-4478_r212_initialpatch\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_48169054_revision_number=a70ce030f9aceed3e3ee89984340187708c0a2a0\nbamboo_planRepository_branchDisplayName=patch/JAL-4478_r212_initialpatch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4478_r212_initialpatch\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-47972539\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-GDB751-JOB1\nbamboo_planKey=JB-GDB751\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4478_r212_initialpatch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	27-May-2026 17:35:12	2414
build	27-May-2026 17:35:19	
build	27-May-2026 17:35:19	> Configure project :
build	27-May-2026 17:35:19	Using properties from file './utils/channels/default/channel_gradle.properties'
build	27-May-2026 17:35:19	JALVIEW_VERSION is set to '2.12.0'
build	27-May-2026 17:35:19	HEADLESS BUILD
build	27-May-2026 17:35:19	J2S ENABLED
build	27-May-2026 17:35:19	Using a LOCAL profile.
build	27-May-2026 17:35:20	eclipseDir exists
build	27-May-2026 17:35:22	
build	27-May-2026 17:35:22	> Task :cloverHtmlReport
build	27-May-2026 17:35:22	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	27-May-2026 17:35:24	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/reports/clover'
build	27-May-2026 17:36:19	Done. Processed 137 packages in 55343ms (403ms per package).
build	27-May-2026 17:36:25	
build	27-May-2026 17:36:25	> Task :cloverXmlReport
build	27-May-2026 17:36:25	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	27-May-2026 17:36:26	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/reports/clover/clover.xml'
build	27-May-2026 17:36:27	
build	27-May-2026 17:36:27	> Task :cloverReport
build	27-May-2026 17:36:27	
build	27-May-2026 17:36:27	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	27-May-2026 17:36:27	
build	27-May-2026 17:36:27	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	27-May-2026 17:36:27	
build	27-May-2026 17:36:27	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	27-May-2026 17:36:27	
build	27-May-2026 17:36:27	BUILD SUCCESSFUL in 1m 14s
build	27-May-2026 17:36:27	2 actionable tasks: 2 executed
simple	27-May-2026 17:36:27	Finished task 'Clover Report' with result: Success
simple	27-May-2026 17:36:27	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	27-May-2026 17:36:27	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1...
simple	27-May-2026 17:36:27	Failing task since 1 failing test cases were found.
simple	27-May-2026 17:36:27	Finished task 'TestNG Parser' with result: Failed
simple	27-May-2026 17:36:27	Running post build plugin 'NCover Results Collector'
simple	27-May-2026 17:36:27	Running post build plugin 'Artifact Copier'
simple	27-May-2026 17:36:27	Publishing an artifact: Clover Report (System)
simple	27-May-2026 17:36:29	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.672 s
simple	27-May-2026 17:36:29	Publishing an artifact: TestNG report
error	27-May-2026 17:36:29	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB751-JOB1/build/reports/tests/test does not exist.
simple	27-May-2026 17:36:29	The artifact hasn't been successfully published after 3.829 ms
simple	27-May-2026 17:36:29	Running post build plugin 'Artifactory Release Management Staging'
simple	27-May-2026 17:36:29	Running post build plugin 'Artifactory Build Info Copier'
simple	27-May-2026 17:36:29	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	27-May-2026 17:36:29	Running post build plugin 'npm Cache Cleanup'
simple	27-May-2026 17:36:29	Running post build plugin 'Clover Results Collector'
simple	27-May-2026 17:36:29	Running post build plugin 'Docker Container Cleanup'
simple	27-May-2026 17:36:29	Finalising the build...
simple	27-May-2026 17:36:29	Stopping timer.
simple	27-May-2026 17:36:29	Build JB-GDB751-JOB1-1 completed.
simple	27-May-2026 17:36:29	Running on server: post build plugin 'NCover Results Collector'
simple	27-May-2026 17:36:30	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	27-May-2026 17:36:30	Running on server: post build plugin 'Clover Delta Calculator'
simple	27-May-2026 17:36:30	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	27-May-2026 17:36:30	All post build plugins have finished
simple	27-May-2026 17:36:30	Generating build results summary...
simple	27-May-2026 17:36:30	Saving build results to disk...
simple	27-May-2026 17:36:30	Logging substituted variables...
simple	27-May-2026 17:36:30	Indexing build results...
simple	27-May-2026 17:36:30	Finished building JB-GDB751-JOB1-1.