simple	18-Nov-2024 09:37:50	Build Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests #2 (JB-GDB647-JOB1-2) started building on agent Default Agent
simple	18-Nov-2024 09:37:50	
simple	18-Nov-2024 09:37:50	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1
simple	18-Nov-2024 09:37:50	Executing build Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests #2 (JB-GDB647-JOB1-2)
simple	18-Nov-2024 09:37:50	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	18-Nov-2024 09:37:50	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1
simple	18-Nov-2024 09:37:50	Updating source code to revision: 5e8bd075739b756cac8f741a47a7de952c45f879
simple	18-Nov-2024 09:37:50	Fetching 'refs/heads/spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure' from 'http://source.jalview.org/git/jalview.git'.
simple	18-Nov-2024 09:37:50	Checking out revision 5e8bd075739b756cac8f741a47a7de952c45f879.
simple	18-Nov-2024 09:37:51	Already on 'spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure'
simple	18-Nov-2024 09:37:51	Updated source code to revision: 5e8bd075739b756cac8f741a47a7de952c45f879
simple	18-Nov-2024 09:37:51	Finished task 'Checkout Default Repository' with result: Success
simple	18-Nov-2024 09:37:51	Running pre-build action: VCS Version Collector
simple	18-Nov-2024 09:37:51	Running pre-build action: Artifactory Release Staging
simple	18-Nov-2024 09:37:52	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	18-Nov-2024 09:37:52	Bamboo Artifactory Plugin version: 2.6.2
command	18-Nov-2024 09:37:52	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests #2 (JB-GDB647-JOB1-2)'\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-GDB647-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_46498215_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB647-JOB1-2\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-GDB647-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB647-JOB1\nbamboo_shortPlanName=spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_46498215_name=Jalview Git\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=2\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-GDB647-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_repository_46498215_git_username=\nbamboo_planName=Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_shortPlanKey=GDB647\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_buildTimeStamp=2024-11-18T09:37:49.999Z\nbamboo_repository_previous_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_planRepository_previousRevision=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_repository_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_buildResultKey=JB-GDB647-JOB1-2\nbamboo_repository_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_46498215_previous_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498215_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_planRepository_1_revision=5e8bd075739b756cac8f741a47a7de952c45f879\nSHLVL=1\nbamboo_repository_46498215_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_dependenciesDisabled=false\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=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_repository_46498215_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\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-46302029\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_ManualBuildTriggerReason_userName=jprocter\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/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-GDB647-JOB1\nbamboo_planKey=JB-GDB647\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	18-Nov-2024 09:37:52	444
build	18-Nov-2024 09:37:52	Starting a Gradle Daemon (subsequent builds will be faster)
build	18-Nov-2024 09:38:04	
build	18-Nov-2024 09:38:04	> Configure project :
build	18-Nov-2024 09:38:04	Using properties from file './utils/channels/default/channel_gradle.properties'
build	18-Nov-2024 09:38:04	JALVIEW_VERSION is set to '2.11.4.2'
build	18-Nov-2024 09:38:04	HEADLESS BUILD
build	18-Nov-2024 09:38:04	J2S ENABLED
build	18-Nov-2024 09:38:04	Using a LOCAL profile.
build	18-Nov-2024 09:38:06	eclipseDir exists
build	18-Nov-2024 09:38:07	
build	18-Nov-2024 09:38:07	> Task :clean
build	18-Nov-2024 09:38:07	> Task :cleanClover
build	18-Nov-2024 09:38:07	> Task :cleanTest UP-TO-DATE
build	18-Nov-2024 09:38:09	
build	18-Nov-2024 09:38:09	> Task :cloverInstrJava
build	18-Nov-2024 09:38:09	Clover: About to instrument 1105 files
build	18-Nov-2024 09:38:09	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	18-Nov-2024 09:38:09	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/clover/clover.db'.
build	18-Nov-2024 09:38:09	Processing files at 1.9 source level.
error	18-Nov-2024 09:38:12	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	18-Nov-2024 09:38:12	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	18-Nov-2024 09:38:12	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	18-Nov-2024 09:38:12	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	18-Nov-2024 09:38:12	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	18-Nov-2024 09:38:12	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	18-Nov-2024 09:38:12	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	18-Nov-2024 09:38:19	Clover all over. Instrumented 1105 files (112 packages).
build	18-Nov-2024 09:38:22	
build	18-Nov-2024 09:38:22	> Task :cloverInstrTests
build	18-Nov-2024 09:38:22	Clover: About to instrument test files
build	18-Nov-2024 09:38:22	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	18-Nov-2024 09:38:22	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/clover/clover.db'.
build	18-Nov-2024 09:38:22	Processing files at 1.9 source level.
build	18-Nov-2024 09:38:25	Clover all over. Instrumented 292 files (52 packages).
build	18-Nov-2024 09:38:25	1600 test methods detected.
build	18-Nov-2024 09:38:25	
build	18-Nov-2024 09:38:25	> Task :cloverInstr
build	18-Nov-2024 09:38:27	
build	18-Nov-2024 09:38:27	> Task :compileCloverJava
build	18-Nov-2024 09:38:27	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	18-Nov-2024 09:38:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:38:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:38:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:38:27	Setting target compatibility to 11
error	18-Nov-2024 09:38:49	Note: Some input files use or override a deprecated API.
error	18-Nov-2024 09:38:49	Note: Recompile with -Xlint:deprecation for details.
error	18-Nov-2024 09:38:49	Note: Some input files use unchecked or unsafe operations.
error	18-Nov-2024 09:38:49	Note: Recompile with -Xlint:unchecked for details.
build	18-Nov-2024 09:38:54	
build	18-Nov-2024 09:38:54	> Task :processCloverResources NO-SOURCE
build	18-Nov-2024 09:38:54	> Task :cloverClasses
build	18-Nov-2024 09:38:55	> Task :copyHelp
build	18-Nov-2024 09:38:56	> Task :buildIndices
build	18-Nov-2024 09:38:56	> Task :copyResources
build	18-Nov-2024 09:38:56	> Task :copyChannelResources
build	18-Nov-2024 09:38:56	
build	18-Nov-2024 09:38:56	> Task :createBuildProperties
build	18-Nov-2024 09:38:56	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	18-Nov-2024 09:38:56	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:38:56	
build	18-Nov-2024 09:38:56	> Task :buildResources
build	18-Nov-2024 09:38:56	> Task :copyDocs
build	18-Nov-2024 09:38:57	
build	18-Nov-2024 09:38:57	> Task :convertMdFiles
build	18-Nov-2024 09:38:57	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	18-Nov-2024 09:38:57	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	18-Nov-2024 09:38:57	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	18-Nov-2024 09:38:57	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/building.html
build	18-Nov-2024 09:38:57	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	18-Nov-2024 09:38:57	
build	18-Nov-2024 09:38:57	> Task :releasesTemplates
build	18-Nov-2024 09:38:57	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	18-Nov-2024 09:38:57	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:38:57	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:38:57	Stripping rc/test/etc for TEST
build	18-Nov-2024 09:38:57	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	18-Nov-2024 09:38:57	
build	18-Nov-2024 09:38:57	> Task :prepare
build	18-Nov-2024 09:38:59	
build	18-Nov-2024 09:38:59	> Task :compileJava
build	18-Nov-2024 09:38:59	Setting target compatibility to 11
error	18-Nov-2024 09:39:05	Note: Some input files use or override a deprecated API.
error	18-Nov-2024 09:39:05	Note: Recompile with -Xlint:deprecation for details.
error	18-Nov-2024 09:39:05	Note: Some input files use unchecked or unsafe operations.
error	18-Nov-2024 09:39:05	Note: Recompile with -Xlint:unchecked for details.
build	18-Nov-2024 09:39:08	
build	18-Nov-2024 09:39:08	> Task :compileTestJava
build	18-Nov-2024 09:39:08	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	18-Nov-2024 09:39:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:39:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:39:08	Setting target compatibility to 11
error	18-Nov-2024 09:39:14	Note: Some input files use or override a deprecated API.
error	18-Nov-2024 09:39:14	Note: Recompile with -Xlint:deprecation for details.
error	18-Nov-2024 09:39:14	Note: Some input files use unchecked or unsafe operations.
error	18-Nov-2024 09:39:14	Note: Recompile with -Xlint:unchecked for details.
build	18-Nov-2024 09:39:15	
build	18-Nov-2024 09:39:15	> Task :processTestResources
build	18-Nov-2024 09:39:15	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	18-Nov-2024 09:39:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	18-Nov-2024 09:39:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:39:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:39:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:39:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:39:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:39:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:39:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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	18-Nov-2024 09:39:15	
build	18-Nov-2024 09:39:15	> Task :testClasses
build	18-Nov-2024 09:39:17	
build	18-Nov-2024 09:39:17	> Task :testTask0
build	18-Nov-2024 09:39:17	Running tests WITH clover
error	18-Nov-2024 09:39:20	WARNING: An illegal reflective access operation has occurred
error	18-Nov-2024 09:39:20	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	18-Nov-2024 09:39:20	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	18-Nov-2024 09:39:20	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	18-Nov-2024 09:39:20	WARNING: All illegal access operations will be denied in a future release
build	18-Nov-2024 09:40:25	
build	18-Nov-2024 09:40:25	Gradle suite > Gradle test > jalview.io.cache.JvCacheableInputBoxTest.updateCacheTest FAILED
build	18-Nov-2024 09:40:25	    java.lang.AssertionError: Giving up after 1.4s waiting for cache to be updated.
build	18-Nov-2024 09:40:25	        at org.junit.Assert.fail(Assert.java:88)
build	18-Nov-2024 09:40:25	        at jalview.io.cache.JvCacheableInputBoxTest.__CLR4_4_1shislu47c8(JvCacheableInputBoxTest.java:107)
build	18-Nov-2024 09:40:25	        at jalview.io.cache.JvCacheableInputBoxTest.updateCacheTest(JvCacheableInputBoxTest.java:82)
build	18-Nov-2024 09:54:15	Requesting stop of task ':testTask0' as it has exceeded its configured timeout of 15m.
build	18-Nov-2024 09:54:15	
error	18-Nov-2024 09:54:15	
error	18-Nov-2024 09:54:15	1157 tests completed, 1 failed, 1 skipped
build	18-Nov-2024 09:54:15	> Task :testTask0 FAILED
error	18-Nov-2024 09:54:15	
error	18-Nov-2024 09:54:15	FAILURE: Build completed with 2 failures.
error	18-Nov-2024 09:54:15	
error	18-Nov-2024 09:54:15	1: Task failed with an exception.
error	18-Nov-2024 09:54:15	-----------
error	18-Nov-2024 09:54:15	* What went wrong:
error	18-Nov-2024 09:54:15	Execution failed for task ':testTask0'.
error	18-Nov-2024 09:54:15	> Timeout has been exceeded
error	18-Nov-2024 09:54:15	
error	18-Nov-2024 09:54:15	* Try:
error	18-Nov-2024 09:54:15	> Run with --stacktrace option to get the stack trace.
error	18-Nov-2024 09:54:15	> Run with --info or --debug option to get more log output.
error	18-Nov-2024 09:54:15	> Run with --scan to get full insights.
error	18-Nov-2024 09:54:15	==============================================================================
error	18-Nov-2024 09:54:15	
error	18-Nov-2024 09:54:15	2: Task failed with an exception.
error	18-Nov-2024 09:54:15	-----------
error	18-Nov-2024 09:54:15	* Where:
error	18-Nov-2024 09:54:15	Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build.gradle' line: 1967
error	18-Nov-2024 09:54:15	
error	18-Nov-2024 09:54:15	* What went wrong:
error	18-Nov-2024 09:54:15	Failed tests!
error	18-Nov-2024 09:54:15	
error	18-Nov-2024 09:54:15	* Try:
build	18-Nov-2024 09:54:15	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	18-Nov-2024 09:54:15	│jalview:testTask0 results: FAILURE (1157 tests, 1155 successes, 1 failures, 1 skipped) in 14 minutes, 59.934 seconds  │
build	18-Nov-2024 09:54:15	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/tests/testTask0/index.html│
build	18-Nov-2024 09:54:15	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	18-Nov-2024 09:54:15	│OVERALL: results: FAILURE (1157 tests, 1155 successes, 1 failures, 1 skipped) in 14 minutes, 59.934 seconds           │
build	18-Nov-2024 09:54:15	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	18-Nov-2024 09:54:15	
build	18-Nov-2024 09:54:15	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	18-Nov-2024 09:54:15	
build	18-Nov-2024 09:54:15	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	18-Nov-2024 09:54:15	
build	18-Nov-2024 09:54:15	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	18-Nov-2024 09:54:15	
build	18-Nov-2024 09:54:15	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	18-Nov-2024 09:54:15	Please consult deprecation warnings for more details.
build	18-Nov-2024 09:54:15	18 actionable tasks: 17 executed, 1 up-to-date
error	18-Nov-2024 09:54:15	> Run with --stacktrace option to get the stack trace.
error	18-Nov-2024 09:54:15	> Run with --info or --debug option to get more log output.
error	18-Nov-2024 09:54:15	> Run with --scan to get full insights.
error	18-Nov-2024 09:54:15	==============================================================================
error	18-Nov-2024 09:54:15	
error	18-Nov-2024 09:54:15	* Get more help at https://help.gradle.org
error	18-Nov-2024 09:54:15	
error	18-Nov-2024 09:54:15	BUILD FAILED in 16m 23s
simple	18-Nov-2024 09:54:15	
simple	18-Nov-2024 09:54:15	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	18-Nov-2024 09:54:15	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	18-Nov-2024 09:54:15	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	18-Nov-2024 09:54:15	Bamboo Artifactory Plugin version: 2.6.2
command	18-Nov-2024 09:54:15	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests #2 (JB-GDB647-JOB1-2)'\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-GDB647-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_46498215_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB647-JOB1-2\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-GDB647-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB647-JOB1\nbamboo_shortPlanName=spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_46498215_name=Jalview Git\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=2\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-GDB647-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_repository_46498215_git_username=\nbamboo_planName=Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_shortPlanKey=GDB647\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_buildTimeStamp=2024-11-18T09:37:49.999Z\nbamboo_repository_previous_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_planRepository_previousRevision=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_repository_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_buildResultKey=JB-GDB647-JOB1-2\nbamboo_repository_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_46498215_previous_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498215_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_planRepository_1_revision=5e8bd075739b756cac8f741a47a7de952c45f879\nSHLVL=1\nbamboo_repository_46498215_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\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_dependenciesDisabled=false\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=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\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_planRepository_1_previousRevision=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_repository_46498215_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\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-46302029\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_ManualBuildTriggerReason_userName=jprocter\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/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-GDB647-JOB1\nbamboo_planKey=JB-GDB647\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	18-Nov-2024 09:54:15	444
build	18-Nov-2024 09:54:22	
build	18-Nov-2024 09:54:22	> Configure project :
build	18-Nov-2024 09:54:22	Using properties from file './utils/channels/default/channel_gradle.properties'
build	18-Nov-2024 09:54:22	JALVIEW_VERSION is set to '2.11.4.2'
build	18-Nov-2024 09:54:22	HEADLESS BUILD
build	18-Nov-2024 09:54:22	J2S ENABLED
build	18-Nov-2024 09:54:22	Using a LOCAL profile.
build	18-Nov-2024 09:54:23	eclipseDir exists
build	18-Nov-2024 09:54:25	
build	18-Nov-2024 09:54:25	> Task :cloverHtmlReport
build	18-Nov-2024 09:54:25	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	18-Nov-2024 09:54:26	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/clover'
build	18-Nov-2024 09:54:53	Done. Processed 116 packages in 26769ms (230ms per package).
build	18-Nov-2024 09:54:57	
build	18-Nov-2024 09:54:57	> Task :cloverXmlReport
build	18-Nov-2024 09:54:57	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	18-Nov-2024 09:54:58	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/clover/clover.xml'
build	18-Nov-2024 09:54:58	
build	18-Nov-2024 09:54:58	> Task :cloverReport
build	18-Nov-2024 09:54:58	
build	18-Nov-2024 09:54:58	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	18-Nov-2024 09:54:58	
build	18-Nov-2024 09:54:58	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	18-Nov-2024 09:54:58	
build	18-Nov-2024 09:54:58	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	18-Nov-2024 09:54:58	
build	18-Nov-2024 09:54:58	BUILD SUCCESSFUL in 42s
build	18-Nov-2024 09:54:58	2 actionable tasks: 2 executed
simple	18-Nov-2024 09:55:00	Finished task 'Clover Report' with result: Success
simple	18-Nov-2024 09:55:00	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	18-Nov-2024 09:55:00	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1...
simple	18-Nov-2024 09:55:00	Failing task since test cases were expected but none were found.
simple	18-Nov-2024 09:55:00	Finished task 'TestNG Parser' with result: Failed
simple	18-Nov-2024 09:55:00	Running post build plugin 'NCover Results Collector'
simple	18-Nov-2024 09:55:00	Running post build plugin 'Artifact Copier'
simple	18-Nov-2024 09:55:00	Publishing an artifact: Clover Report (System)
simple	18-Nov-2024 09:55:01	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.322 s
simple	18-Nov-2024 09:55:01	Publishing an artifact: TestNG report
error	18-Nov-2024 09:55:01	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/tests/test does not exist.
simple	18-Nov-2024 09:55:01	The artifact hasn't been successfully published after 1.434 ms
simple	18-Nov-2024 09:55:01	Running post build plugin 'Artifactory Release Management Staging'
simple	18-Nov-2024 09:55:01	Running post build plugin 'Artifactory Build Info Copier'
simple	18-Nov-2024 09:55:01	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	18-Nov-2024 09:55:01	Running post build plugin 'npm Cache Cleanup'
simple	18-Nov-2024 09:55:01	Running post build plugin 'Clover Results Collector'
simple	18-Nov-2024 09:55:01	Running post build plugin 'Docker Container Cleanup'
simple	18-Nov-2024 09:55:01	Finalising the build...
simple	18-Nov-2024 09:55:01	Stopping timer.
simple	18-Nov-2024 09:55:01	Build JB-GDB647-JOB1-2 completed.
simple	18-Nov-2024 09:55:01	Running on server: post build plugin 'NCover Results Collector'
simple	18-Nov-2024 09:55:01	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	18-Nov-2024 09:55:01	Running on server: post build plugin 'Clover Delta Calculator'
simple	18-Nov-2024 09:55:01	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	18-Nov-2024 09:55:01	All post build plugins have finished
simple	18-Nov-2024 09:55:01	Generating build results summary...
simple	18-Nov-2024 09:55:01	Saving build results to disk...
simple	18-Nov-2024 09:55:01	Logging substituted variables...
simple	18-Nov-2024 09:55:01	Indexing build results...
simple	18-Nov-2024 09:55:01	Finished building JB-GDB647-JOB1-2.