simple	19-Nov-2025 14:59:46	Build Jalview Builds - Gradle Develop Build - test-JAL-4603_test_for_JAL-4603_in_progress - Clover and Tests #1 (JB-GDB728-JOB1-1) started building on agent Default Agent
simple	19-Nov-2025 14:59:46	
simple	19-Nov-2025 14:59:46	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1
simple	19-Nov-2025 14:59:46	Executing build Jalview Builds - Gradle Develop Build - test-JAL-4603_test_for_JAL-4603_in_progress - Clover and Tests #1 (JB-GDB728-JOB1-1)
simple	19-Nov-2025 14:59:46	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	19-Nov-2025 14:59:46	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1
simple	19-Nov-2025 14:59:46	Updating source code to revision: f2e7b59cf6631a630c80ace1fe1a10902b9f549c
simple	19-Nov-2025 14:59:47	Fetching 'refs/heads/test/JAL-4603_test_for_JAL-4603_in_progress' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	19-Nov-2025 14:59:47	Checking out revision f2e7b59cf6631a630c80ace1fe1a10902b9f549c.
simple	19-Nov-2025 14:59:47	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/.git'.
simple	19-Nov-2025 14:59:47	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1'...
simple	19-Nov-2025 14:59:47	done.
simple	19-Nov-2025 14:59:55	Switched to a new branch 'test/JAL-4603_test_for_JAL-4603_in_progress'
simple	19-Nov-2025 14:59:55	Branch test/JAL-4603_test_for_JAL-4603_in_progress set up to track remote branch test/JAL-4603_test_for_JAL-4603_in_progress from origin.
simple	19-Nov-2025 14:59:55	Updated source code to revision: f2e7b59cf6631a630c80ace1fe1a10902b9f549c
simple	19-Nov-2025 14:59:55	Finished task 'Checkout Default Repository' with result: Success
simple	19-Nov-2025 14:59:55	Running pre-build action: VCS Version Collector
simple	19-Nov-2025 14:59:55	Running pre-build action: Artifactory Release Staging
simple	19-Nov-2025 14:59:55	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	19-Nov-2025 14:59:55	Bamboo Artifactory Plugin version: 2.6.2
command	19-Nov-2025 14:59:55	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - test-JAL-4603_test_for_JAL-4603_in_progress - Clover and Tests #1 (JB-GDB728-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-GDB728-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_repository_revision_number=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB728-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-GDB728-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB728-JOB1\nbamboo_shortPlanName=test-JAL-4603_test_for_JAL-4603_in_progress\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-GDB728-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 - test-JAL-4603_test_for_JAL-4603_in_progress\nbamboo_shortPlanKey=GDB728\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nbamboo_repository_previous_revision_number=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nbamboo_buildTimeStamp=2025-11-19T14:51:38.032Z\nbamboo_planRepository_previousRevision=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nbamboo_repository_git_branch=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_buildResultKey=JB-GDB728-JOB1-1\nbamboo_repository_branch_name=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - test-JAL-4603_test_for_JAL-4603_in_progress - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498593_previous_revision_number=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_repository_46498593_revision_number=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_repository_46498593_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nbamboo_planRepository_branchDisplayName=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=test/JAL-4603_test_for_JAL-4603_in_progress\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-46302757\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_repository_46498593_git_branch=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498593_branch_name=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_repository_46498593_git_username=\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1\nbamboo_planKey=JB-GDB728\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498593_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=test/JAL-4603_test_for_JAL-4603_in_progress\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	19-Nov-2025 14:59:55	444
build	19-Nov-2025 14:59:57	
build	19-Nov-2025 14:59:57	> Configure project :
build	19-Nov-2025 14:59:57	Using properties from file './utils/channels/default/channel_gradle.properties'
build	19-Nov-2025 14:59:57	JALVIEW_VERSION is set to '2.11.5.0'
build	19-Nov-2025 14:59:57	HEADLESS BUILD
build	19-Nov-2025 14:59:57	J2S ENABLED
build	19-Nov-2025 14:59:57	Using a LOCAL profile.
build	19-Nov-2025 14:59:57	eclipseDir exists
build	19-Nov-2025 14:59:57	
build	19-Nov-2025 14:59:57	> Task :clean
build	19-Nov-2025 14:59:57	> Task :cleanClover
build	19-Nov-2025 14:59:57	> Task :cleanTest UP-TO-DATE
build	19-Nov-2025 15:00:01	
build	19-Nov-2025 15:00:01	> Task :cloverInstrJava
build	19-Nov-2025 15:00:01	Clover: About to instrument 1106 files
build	19-Nov-2025 15:00:01	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Nov-2025 15:00:01	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/clover/clover.db'.
build	19-Nov-2025 15:00:01	Processing files at 1.9 source level.
error	19-Nov-2025 15:00:07	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	19-Nov-2025 15:00:07	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	19-Nov-2025 15:00:07	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	19-Nov-2025 15:00:07	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	19-Nov-2025 15:00:07	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	19-Nov-2025 15:00:07	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	19-Nov-2025 15:00:07	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	19-Nov-2025 15:00:14	Clover all over. Instrumented 1106 files (112 packages).
build	19-Nov-2025 15:00:16	
build	19-Nov-2025 15:00:16	> Task :cloverInstrTests
build	19-Nov-2025 15:00:16	Clover: About to instrument test files
build	19-Nov-2025 15:00:16	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Nov-2025 15:00:16	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/clover/clover.db'.
build	19-Nov-2025 15:00:16	Processing files at 1.9 source level.
build	19-Nov-2025 15:00:19	Clover all over. Instrumented 294 files (52 packages).
build	19-Nov-2025 15:00:19	1619 test methods detected.
build	19-Nov-2025 15:00:19	
build	19-Nov-2025 15:00:19	> Task :cloverInstr
build	19-Nov-2025 15:00:23	
build	19-Nov-2025 15:00:23	> Task :compileCloverJava
build	19-Nov-2025 15:00:23	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:00:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:00:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:00:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:00:23	Setting target compatibility to 11
error	19-Nov-2025 15:00:39	Note: Some input files use or override a deprecated API.
error	19-Nov-2025 15:00:39	Note: Recompile with -Xlint:deprecation for details.
error	19-Nov-2025 15:00:39	Note: Some input files use unchecked or unsafe operations.
error	19-Nov-2025 15:00:39	Note: Recompile with -Xlint:unchecked for details.
build	19-Nov-2025 15:00:46	
build	19-Nov-2025 15:00:46	> Task :processCloverResources NO-SOURCE
build	19-Nov-2025 15:00:46	> Task :cloverClasses
build	19-Nov-2025 15:00:46	> Task :copyHelp
build	19-Nov-2025 15:00:47	> Task :buildIndices
build	19-Nov-2025 15:00:47	> Task :copyResources
build	19-Nov-2025 15:00:48	> Task :copyChannelResources
build	19-Nov-2025 15:00:48	
build	19-Nov-2025 15:00:48	> Task :createBuildProperties
build	19-Nov-2025 15:00:48	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:00:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:00:48	
build	19-Nov-2025 15:00:48	> Task :buildResources
build	19-Nov-2025 15:00:48	> Task :copyDocs
build	19-Nov-2025 15:00:48	
build	19-Nov-2025 15:00:48	> Task :convertMdFiles
build	19-Nov-2025 15:00:48	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	19-Nov-2025 15:00:48	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	19-Nov-2025 15:00:48	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	19-Nov-2025 15:00:48	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/resources/doc_build/doc/building.html
build	19-Nov-2025 15:00:48	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	19-Nov-2025 15:00:48	
build	19-Nov-2025 15:00:48	> Task :releasesTemplates
build	19-Nov-2025 15:00:48	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:00:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:00:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:00:48	Stripping rc/test/etc for TEST
build	19-Nov-2025 15:00:48	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	19-Nov-2025 15:00:48	
build	19-Nov-2025 15:00:48	> Task :prepare
build	19-Nov-2025 15:00:50	
build	19-Nov-2025 15:00:50	> Task :compileJava
build	19-Nov-2025 15:00:50	Setting target compatibility to 11
error	19-Nov-2025 15:00:57	Note: Some input files use or override a deprecated API.
error	19-Nov-2025 15:00:57	Note: Recompile with -Xlint:deprecation for details.
error	19-Nov-2025 15:00:57	Note: Some input files use unchecked or unsafe operations.
error	19-Nov-2025 15:00:57	Note: Recompile with -Xlint:unchecked for details.
build	19-Nov-2025 15:00:59	
build	19-Nov-2025 15:00:59	> Task :compileTestJava
build	19-Nov-2025 15:00:59	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:00:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:00:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:00:59	Setting target compatibility to 11
error	19-Nov-2025 15:01:03	Note: Some input files use or override a deprecated API.
error	19-Nov-2025 15:01:03	Note: Recompile with -Xlint:deprecation for details.
error	19-Nov-2025 15:01:03	Note: Some input files use unchecked or unsafe operations.
error	19-Nov-2025 15:01:03	Note: Recompile with -Xlint:unchecked for details.
build	19-Nov-2025 15:01:04	
build	19-Nov-2025 15:01:04	> Task :processTestResources
build	19-Nov-2025 15:01:04	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:01:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:01:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:01:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:01:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:01:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:01:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:01:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-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	19-Nov-2025 15:01:04	
build	19-Nov-2025 15:01:04	> Task :testClasses
build	19-Nov-2025 15:01:06	
build	19-Nov-2025 15:01:06	> Task :testTask0
build	19-Nov-2025 15:01:06	Running tests WITH clover
error	19-Nov-2025 15:01:09	WARNING: An illegal reflective access operation has occurred
error	19-Nov-2025 15:01:09	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	19-Nov-2025 15:01:09	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	19-Nov-2025 15:01:09	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	19-Nov-2025 15:01:09	WARNING: All illegal access operations will be denied in a future release
build	19-Nov-2025 15:02:04	
build	19-Nov-2025 15:02:04	Gradle suite > Gradle test > jalview.gui.ImageExporterTest.testExportSVG FAILED
build	19-Nov-2025 15:02:04	    java.lang.AssertionError: Exported file size (0) is not as big as it should be (>122880000) expected [true] but found [false]
build	19-Nov-2025 15:02:04	        at org.testng.Assert.fail(Assert.java:94)
build	19-Nov-2025 15:02:04	        at org.testng.Assert.failNotEquals(Assert.java:496)
build	19-Nov-2025 15:02:04	        at org.testng.Assert.assertTrue(Assert.java:42)
build	19-Nov-2025 15:02:04	        at jalview.gui.ImageExporterTest.__CLR4_4_1ogm5ln3tu1(ImageExporterTest.java:193)
build	19-Nov-2025 15:02:04	        at jalview.gui.ImageExporterTest.testExportSVG(ImageExporterTest.java:87)
build	19-Nov-2025 15:06:36	There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/reports/tests/testTask0/index.html
error	19-Nov-2025 15:06:36	
error	19-Nov-2025 15:06:36	1820 tests completed, 1 failed
build	19-Nov-2025 15:06:38	
build	19-Nov-2025 15:06:38	> Task :testTask1
build	19-Nov-2025 15:06:38	Running tests WITH clover
error	19-Nov-2025 15:06:41	WARNING: An illegal reflective access operation has occurred
error	19-Nov-2025 15:06:41	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	19-Nov-2025 15:06:41	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	19-Nov-2025 15:06:41	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	19-Nov-2025 15:06:41	WARNING: All illegal access operations will be denied in a future release
build	19-Nov-2025 15:09:35	
build	19-Nov-2025 15:09:35	> Task :testTask2
build	19-Nov-2025 15:09:35	Running tests WITH clover
build	19-Nov-2025 15:09:39	
build	19-Nov-2025 15:09:39	> Task :testTask3
build	19-Nov-2025 15:09:39	Running tests WITH clover
error	19-Nov-2025 15:09:42	WARNING: An illegal reflective access operation has occurred
error	19-Nov-2025 15:09:42	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	19-Nov-2025 15:09:42	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	19-Nov-2025 15:09:42	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	19-Nov-2025 15:09:42	WARNING: All illegal access operations will be denied in a future release
build	19-Nov-2025 15:10:44	
build	19-Nov-2025 15:10:44	> Task :test NO-SOURCE
build	19-Nov-2025 15:10:45	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	19-Nov-2025 15:10:45	│jalview:testTask0 results: FAILURE (1820 tests, 1819 successes, 1 failures, 0 skipped) in 5 minutes, 31.100 seconds   │
build	19-Nov-2025 15:10:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/reports/tests/testTask0/index.html│
build	19-Nov-2025 15:10:45	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Nov-2025 15:10:45	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 56.483 seconds       │
build	19-Nov-2025 15:10:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/reports/tests/testTask1/index.html│
build	19-Nov-2025 15:10:45	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Nov-2025 15:10:45	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.768 seconds                     │
build	19-Nov-2025 15:10:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/reports/tests/testTask2/index.html│
build	19-Nov-2025 15:10:45	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Nov-2025 15:10:45	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 7.241 seconds        │
build	19-Nov-2025 15:10:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/reports/tests/testTask3/index.html│
build	19-Nov-2025 15:10:45	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Nov-2025 15:10:45	│OVERALL: results: FAILURE (1908 tests, 1907 successes, 1 failures, 0 skipped) in 8 minutes, 99.592 seconds            │
build	19-Nov-2025 15:10:45	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
error	19-Nov-2025 15:10:45	
build	19-Nov-2025 15:10:45	
build	19-Nov-2025 15:10:45	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
error	19-Nov-2025 15:10:45	FAILURE: Build failed with an exception.
error	19-Nov-2025 15:10:45	
error	19-Nov-2025 15:10:45	* Where:
error	19-Nov-2025 15:10:45	Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build.gradle' line: 1967
error	19-Nov-2025 15:10:45	
error	19-Nov-2025 15:10:45	* What went wrong:
build	19-Nov-2025 15:10:45	
error	19-Nov-2025 15:10:45	Failed tests!
build	19-Nov-2025 15:10:45	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	19-Nov-2025 15:10:45	
build	19-Nov-2025 15:10:45	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	19-Nov-2025 15:10:45	
build	19-Nov-2025 15:10:45	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	19-Nov-2025 15:10:45	Please consult deprecation warnings for more details.
build	19-Nov-2025 15:10:45	21 actionable tasks: 20 executed, 1 up-to-date
error	19-Nov-2025 15:10:45	
error	19-Nov-2025 15:10:45	* Try:
error	19-Nov-2025 15:10:45	> Run with --stacktrace option to get the stack trace.
error	19-Nov-2025 15:10:45	> Run with --info or --debug option to get more log output.
error	19-Nov-2025 15:10:45	> Run with --scan to get full insights.
error	19-Nov-2025 15:10:45	
error	19-Nov-2025 15:10:45	* Get more help at https://help.gradle.org
error	19-Nov-2025 15:10:45	
error	19-Nov-2025 15:10:45	BUILD FAILED in 10m 49s
simple	19-Nov-2025 15:10:45	
simple	19-Nov-2025 15:10:45	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	19-Nov-2025 15:10:45	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	19-Nov-2025 15:10:45	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	19-Nov-2025 15:10:45	Bamboo Artifactory Plugin version: 2.6.2
command	19-Nov-2025 15:10:45	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - test-JAL-4603_test_for_JAL-4603_in_progress - Clover and Tests #1 (JB-GDB728-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-GDB728-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_repository_revision_number=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB728-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-GDB728-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB728-JOB1\nbamboo_shortPlanName=test-JAL-4603_test_for_JAL-4603_in_progress\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-GDB728-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 - test-JAL-4603_test_for_JAL-4603_in_progress\nbamboo_shortPlanKey=GDB728\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nbamboo_repository_previous_revision_number=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nbamboo_buildTimeStamp=2025-11-19T14:51:38.032Z\nbamboo_planRepository_previousRevision=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nbamboo_repository_git_branch=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_buildResultKey=JB-GDB728-JOB1-1\nbamboo_repository_branch_name=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - test-JAL-4603_test_for_JAL-4603_in_progress - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498593_previous_revision_number=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\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_repository_46498593_revision_number=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nbamboo_buildFailed=true\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_repository_46498593_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=f2e7b59cf6631a630c80ace1fe1a10902b9f549c\nbamboo_planRepository_branchDisplayName=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=test/JAL-4603_test_for_JAL-4603_in_progress\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-46302757\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_repository_46498593_git_branch=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498593_branch_name=test/JAL-4603_test_for_JAL-4603_in_progress\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_repository_46498593_git_username=\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1\nbamboo_planKey=JB-GDB728\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498593_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=test/JAL-4603_test_for_JAL-4603_in_progress\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	19-Nov-2025 15:10:45	444
build	19-Nov-2025 15:10:53	
build	19-Nov-2025 15:10:53	> Configure project :
build	19-Nov-2025 15:10:53	Using properties from file './utils/channels/default/channel_gradle.properties'
build	19-Nov-2025 15:10:53	JALVIEW_VERSION is set to '2.11.5.0'
build	19-Nov-2025 15:10:53	HEADLESS BUILD
build	19-Nov-2025 15:10:53	J2S ENABLED
build	19-Nov-2025 15:10:53	Using a LOCAL profile.
build	19-Nov-2025 15:10:54	eclipseDir exists
build	19-Nov-2025 15:10:57	
build	19-Nov-2025 15:10:57	> Task :cloverHtmlReport
build	19-Nov-2025 15:10:57	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Nov-2025 15:10:59	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/reports/clover'
build	19-Nov-2025 15:11:57	Done. Processed 116 packages in 58721ms (506ms per package).
build	19-Nov-2025 15:12:05	
build	19-Nov-2025 15:12:05	> Task :cloverXmlReport
build	19-Nov-2025 15:12:05	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Nov-2025 15:12:07	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/reports/clover/clover.xml'
build	19-Nov-2025 15:12:07	
build	19-Nov-2025 15:12:07	> Task :cloverReport
build	19-Nov-2025 15:12:07	
build	19-Nov-2025 15:12:07	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	19-Nov-2025 15:12:07	
build	19-Nov-2025 15:12:07	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	19-Nov-2025 15:12:07	
build	19-Nov-2025 15:12:07	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	19-Nov-2025 15:12:07	
build	19-Nov-2025 15:12:07	BUILD SUCCESSFUL in 1m 22s
build	19-Nov-2025 15:12:07	2 actionable tasks: 2 executed
simple	19-Nov-2025 15:12:07	Finished task 'Clover Report' with result: Success
simple	19-Nov-2025 15:12:07	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	19-Nov-2025 15:12:07	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1...
simple	19-Nov-2025 15:12:07	Failing task since 1 failing test cases were found.
simple	19-Nov-2025 15:12:07	Finished task 'TestNG Parser' with result: Failed
simple	19-Nov-2025 15:12:07	Running post build plugin 'NCover Results Collector'
simple	19-Nov-2025 15:12:07	Running post build plugin 'Artifact Copier'
simple	19-Nov-2025 15:12:07	Publishing an artifact: Clover Report (System)
simple	19-Nov-2025 15:12:15	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 7.397 s
simple	19-Nov-2025 15:12:15	Publishing an artifact: TestNG report
error	19-Nov-2025 15:12:15	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB728-JOB1/build/reports/tests/test does not exist.
simple	19-Nov-2025 15:12:15	The artifact hasn't been successfully published after 5.635 ms
simple	19-Nov-2025 15:12:15	Running post build plugin 'Artifactory Release Management Staging'
simple	19-Nov-2025 15:12:15	Running post build plugin 'Artifactory Build Info Copier'
simple	19-Nov-2025 15:12:15	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	19-Nov-2025 15:12:15	Running post build plugin 'npm Cache Cleanup'
simple	19-Nov-2025 15:12:15	Running post build plugin 'Clover Results Collector'
simple	19-Nov-2025 15:12:15	Running post build plugin 'Docker Container Cleanup'
simple	19-Nov-2025 15:12:15	Finalising the build...
simple	19-Nov-2025 15:12:15	Stopping timer.
simple	19-Nov-2025 15:12:15	Build JB-GDB728-JOB1-1 completed.
simple	19-Nov-2025 15:12:15	Running on server: post build plugin 'NCover Results Collector'
simple	19-Nov-2025 15:12:15	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	19-Nov-2025 15:12:15	Running on server: post build plugin 'Clover Delta Calculator'
simple	19-Nov-2025 15:12:15	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	19-Nov-2025 15:12:15	All post build plugins have finished
simple	19-Nov-2025 15:12:15	Generating build results summary...
simple	19-Nov-2025 15:12:15	Saving build results to disk...
simple	19-Nov-2025 15:12:16	Logging substituted variables...
simple	19-Nov-2025 15:12:16	Indexing build results...
simple	19-Nov-2025 15:12:16	Finished building JB-GDB728-JOB1-1.