simple	13-Nov-2024 18:27:09	Build Jalview Builds - Gradle Develop Build - Clover and Tests #698 (JB-GDB-JOB1-698) started building on agent Default Agent
simple	13-Nov-2024 18:27:09	
simple	13-Nov-2024 18:27:09	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1
simple	13-Nov-2024 18:27:09	Executing build Jalview Builds - Gradle Develop Build - Clover and Tests #698 (JB-GDB-JOB1-698)
simple	13-Nov-2024 18:27:09	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	13-Nov-2024 18:27:09	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1
simple	13-Nov-2024 18:27:09	Updating source code to revision: 544bd63f8e2c0122da4f309bdc415162fc1da737
simple	13-Nov-2024 18:27:10	Fetching 'refs/heads/develop' from 'http://source.jalview.org/git/jalview.git'.
simple	13-Nov-2024 18:27:10	Checking out revision 544bd63f8e2c0122da4f309bdc415162fc1da737.
simple	13-Nov-2024 18:27:10	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164
simple	13-Nov-2024 18:27:10	   a3bb626..544bd63  develop    -> origin/develop
simple	13-Nov-2024 18:27:11	Already on 'develop'
simple	13-Nov-2024 18:27:11	Your branch is behind 'origin/develop' by 10 commits, and can be fast-forwarded.
simple	13-Nov-2024 18:27:11	  (use "git pull" to update your local branch)
simple	13-Nov-2024 18:27:11	HEAD is now at 544bd63 JAL-2275 JAL-3921 JAL-4077 release notes JAL-4090
simple	13-Nov-2024 18:27:11	Updated source code to revision: 544bd63f8e2c0122da4f309bdc415162fc1da737
simple	13-Nov-2024 18:27:11	Finished task 'Checkout Default Repository' with result: Success
simple	13-Nov-2024 18:27:11	Running pre-build action: VCS Version Collector
simple	13-Nov-2024 18:27:11	Running pre-build action: Artifactory Release Staging
simple	13-Nov-2024 18:27:11	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	13-Nov-2024 18:27:11	Bamboo Artifactory Plugin version: 2.6.2
command	13-Nov-2024 18:27:11	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - Clover and Tests #698 (JB-GDB-JOB1-698)'\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-GDB-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=544bd63f8e2c0122da4f309bdc415162fc1da737\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB-JOB1-698\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-GDB-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB-JOB1\nbamboo_shortPlanName=Gradle Develop Build\nbamboo_repository_8060939_revision_number=544bd63f8e2c0122da4f309bdc415162fc1da737\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_8060939_git_username=\nLOGNAME=bamboo\nbamboo_buildNumber=698\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-GDB-JOB1-698\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build\nbamboo_shortPlanKey=GDB\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=544bd63f8e2c0122da4f309bdc415162fc1da737\nbamboo_buildTimeStamp=2024-11-13T18:26:46.655Z\nbamboo_repository_previous_revision_number=a3bb626cf79d42346add84b85a593d20253e723a\nbamboo_repository_8060939_branch_name=develop\nbamboo_planRepository_previousRevision=a3bb626cf79d42346add84b85a593d20253e723a\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-GDB-JOB1-698\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - Clover and Tests\nbamboo_repository_8060939_name=Jalview Git\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=544bd63f8e2c0122da4f309bdc415162fc1da737\nSHLVL=1\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/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_8060939_git_branch=develop\nbamboo_planRepository_branch=develop\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=a3bb626cf79d42346add84b85a593d20253e723a\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\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-7864341\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_8060939_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_repository_8060939_previous_revision_number=a3bb626cf79d42346add84b85a593d20253e723a\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=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-GDB-JOB1\nbamboo_planKey=JB-GDB\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	13-Nov-2024 18:27:11	444
build	13-Nov-2024 18:27:13	
build	13-Nov-2024 18:27:13	> Configure project :
build	13-Nov-2024 18:27:13	Using properties from file './utils/channels/default/channel_gradle.properties'
build	13-Nov-2024 18:27:13	JALVIEW_VERSION is set to '2.11.4.2'
build	13-Nov-2024 18:27:13	HEADLESS BUILD
build	13-Nov-2024 18:27:13	J2S ENABLED
build	13-Nov-2024 18:27:13	Using a LOCAL profile.
build	13-Nov-2024 18:27:13	eclipseDir exists
build	13-Nov-2024 18:27:13	
build	13-Nov-2024 18:27:13	> Task :clean
build	13-Nov-2024 18:27:13	> Task :cleanClover
build	13-Nov-2024 18:27:13	> Task :cleanTest UP-TO-DATE
build	13-Nov-2024 18:27:15	
build	13-Nov-2024 18:27:15	> Task :cloverInstrJava
build	13-Nov-2024 18:27:15	Clover: About to instrument 1103 files
build	13-Nov-2024 18:27:16	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	13-Nov-2024 18:27:16	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover.db'.
build	13-Nov-2024 18:27:16	Processing files at 1.9 source level.
error	13-Nov-2024 18:27:23	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	13-Nov-2024 18:27:23	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	13-Nov-2024 18:27:23	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	13-Nov-2024 18:27:23	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	13-Nov-2024 18:27:23	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	13-Nov-2024 18:27:23	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	13-Nov-2024 18:27:23	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	13-Nov-2024 18:27:32	Clover all over. Instrumented 1103 files (112 packages).
build	13-Nov-2024 18:27:34	
build	13-Nov-2024 18:27:34	> Task :cloverInstrTests
build	13-Nov-2024 18:27:34	Clover: About to instrument test files
build	13-Nov-2024 18:27:34	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	13-Nov-2024 18:27:34	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover.db'.
build	13-Nov-2024 18:27:34	Processing files at 1.9 source level.
build	13-Nov-2024 18:27:39	Clover all over. Instrumented 291 files (52 packages).
build	13-Nov-2024 18:27:39	1597 test methods detected.
build	13-Nov-2024 18:27:39	
build	13-Nov-2024 18:27:39	> Task :cloverInstr
build	13-Nov-2024 18:27:41	
build	13-Nov-2024 18:27:41	> Task :compileCloverJava
build	13-Nov-2024 18:27:41	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	13-Nov-2024 18:27:41	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:27:41	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:27:41	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:27:41	Setting target compatibility to 11
error	13-Nov-2024 18:27:55	Note: Some input files use or override a deprecated API.
error	13-Nov-2024 18:27:55	Note: Recompile with -Xlint:deprecation for details.
error	13-Nov-2024 18:27:55	Note: Some input files use unchecked or unsafe operations.
error	13-Nov-2024 18:27:55	Note: Recompile with -Xlint:unchecked for details.
build	13-Nov-2024 18:28:00	
build	13-Nov-2024 18:28:00	> Task :processCloverResources NO-SOURCE
build	13-Nov-2024 18:28:00	> Task :cloverClasses
build	13-Nov-2024 18:28:01	> Task :copyHelp
build	13-Nov-2024 18:28:02	> Task :buildIndices
build	13-Nov-2024 18:28:03	> Task :copyResources
build	13-Nov-2024 18:28:03	> Task :copyChannelResources
build	13-Nov-2024 18:28:03	
build	13-Nov-2024 18:28:03	> Task :createBuildProperties
build	13-Nov-2024 18:28:03	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	13-Nov-2024 18:28:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:28:03	
build	13-Nov-2024 18:28:03	> Task :buildResources
build	13-Nov-2024 18:28:03	> Task :copyDocs
build	13-Nov-2024 18:28:03	
build	13-Nov-2024 18:28:03	> Task :convertMdFiles
build	13-Nov-2024 18:28:03	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	13-Nov-2024 18:28:03	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	13-Nov-2024 18:28:03	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	13-Nov-2024 18:28:03	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/building.html
build	13-Nov-2024 18:28:03	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	13-Nov-2024 18:28:04	
build	13-Nov-2024 18:28:04	> Task :releasesTemplates
build	13-Nov-2024 18:28:04	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	13-Nov-2024 18:28:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:28:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:28:04	Stripping rc/test/etc for TEST
build	13-Nov-2024 18:28:04	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	13-Nov-2024 18:28:04	
build	13-Nov-2024 18:28:04	> Task :prepare
build	13-Nov-2024 18:28:06	
build	13-Nov-2024 18:28:06	> Task :compileJava
build	13-Nov-2024 18:28:06	Setting target compatibility to 11
error	13-Nov-2024 18:28:11	Note: Some input files use or override a deprecated API.
error	13-Nov-2024 18:28:11	Note: Recompile with -Xlint:deprecation for details.
error	13-Nov-2024 18:28:11	Note: Some input files use unchecked or unsafe operations.
error	13-Nov-2024 18:28:11	Note: Recompile with -Xlint:unchecked for details.
build	13-Nov-2024 18:28:13	
build	13-Nov-2024 18:28:13	> Task :compileTestJava
build	13-Nov-2024 18:28:13	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	13-Nov-2024 18:28:13	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:28:13	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:28:13	Setting target compatibility to 11
error	13-Nov-2024 18:28:18	Note: Some input files use or override a deprecated API.
error	13-Nov-2024 18:28:18	Note: Recompile with -Xlint:deprecation for details.
error	13-Nov-2024 18:28:18	Note: Some input files use unchecked or unsafe operations.
error	13-Nov-2024 18:28:18	Note: Recompile with -Xlint:unchecked for details.
build	13-Nov-2024 18:28:19	
build	13-Nov-2024 18:28:19	> Task :processTestResources
build	13-Nov-2024 18:28:19	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	13-Nov-2024 18:28:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:28:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:28:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:28:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:28:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:28:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:28:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:28:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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	13-Nov-2024 18:28:19	
build	13-Nov-2024 18:28:19	> Task :testClasses
build	13-Nov-2024 18:28:21	
build	13-Nov-2024 18:28:21	> Task :testTask0
build	13-Nov-2024 18:28:21	Running tests WITH clover
error	13-Nov-2024 18:28:23	WARNING: An illegal reflective access operation has occurred
error	13-Nov-2024 18:28:23	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	13-Nov-2024 18:28:23	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	13-Nov-2024 18:28:23	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	13-Nov-2024 18:28:23	WARNING: All illegal access operations will be denied in a future release
build	13-Nov-2024 18:32:21	
build	13-Nov-2024 18:32:21	> Task :testTask1
build	13-Nov-2024 18:32:21	Running tests WITH clover
error	13-Nov-2024 18:32:23	WARNING: An illegal reflective access operation has occurred
error	13-Nov-2024 18:32:23	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	13-Nov-2024 18:32:23	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	13-Nov-2024 18:32:23	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	13-Nov-2024 18:32:23	WARNING: All illegal access operations will be denied in a future release
build	13-Nov-2024 18:33:56	
build	13-Nov-2024 18:33:56	> Task :testTask2
build	13-Nov-2024 18:33:56	Running tests WITH clover
build	13-Nov-2024 18:33:59	
build	13-Nov-2024 18:33:59	> Task :testTask3
build	13-Nov-2024 18:33:59	Running tests WITH clover
error	13-Nov-2024 18:34:01	WARNING: An illegal reflective access operation has occurred
error	13-Nov-2024 18:34:01	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	13-Nov-2024 18:34:01	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	13-Nov-2024 18:34:01	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	13-Nov-2024 18:34:01	WARNING: All illegal access operations will be denied in a future release
build	13-Nov-2024 18:34:45	
build	13-Nov-2024 18:34:45	> Task :test NO-SOURCE
build	13-Nov-2024 18:34:45	┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	13-Nov-2024 18:34:45	│jalview:testTask0 results: SUCCESS (1746 tests, 1746 successes, 0 failures, 0 skipped) in 3 minutes, 59.981 seconds│
build	13-Nov-2024 18:34:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask0/index.html│
build	13-Nov-2024 18:34:45	├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	13-Nov-2024 18:34:45	│jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 35.046 seconds    │
build	13-Nov-2024 18:34:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask1/index.html│
build	13-Nov-2024 18:34:45	├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	13-Nov-2024 18:34:45	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.175 seconds                  │
build	13-Nov-2024 18:34:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask2/index.html│
build	13-Nov-2024 18:34:45	├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	13-Nov-2024 18:34:45	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 47.608 seconds               │
build	13-Nov-2024 18:34:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask3/index.html│
build	13-Nov-2024 18:34:45	├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	13-Nov-2024 18:34:45	│OVERALL: results: SUCCESS (1821 tests, 1821 successes, 0 failures, 0 skipped) in 4 minutes, 145.810 seconds        │
build	13-Nov-2024 18:34:45	└───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	13-Nov-2024 18:34:45	
build	13-Nov-2024 18:34:45	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	13-Nov-2024 18:34:45	
build	13-Nov-2024 18:34:45	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	13-Nov-2024 18:34:45	
build	13-Nov-2024 18:34:45	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	13-Nov-2024 18:34:45	
build	13-Nov-2024 18:34:45	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	13-Nov-2024 18:34:45	Please consult deprecation warnings for more details.
build	13-Nov-2024 18:34:45	
build	13-Nov-2024 18:34:45	BUILD SUCCESSFUL in 7m 33s
build	13-Nov-2024 18:34:45	21 actionable tasks: 20 executed, 1 up-to-date
simple	13-Nov-2024 18:34:45	Finished task 'Run tests with openclover under gradle' with result: Success
simple	13-Nov-2024 18:34:45	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	13-Nov-2024 18:34:45	Bamboo Artifactory Plugin version: 2.6.2
command	13-Nov-2024 18:34:45	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - Clover and Tests #698 (JB-GDB-JOB1-698)'\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-GDB-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=544bd63f8e2c0122da4f309bdc415162fc1da737\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB-JOB1-698\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-GDB-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB-JOB1\nbamboo_shortPlanName=Gradle Develop Build\nbamboo_repository_8060939_revision_number=544bd63f8e2c0122da4f309bdc415162fc1da737\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_8060939_git_username=\nLOGNAME=bamboo\nbamboo_buildNumber=698\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-GDB-JOB1-698\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build\nbamboo_shortPlanKey=GDB\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=544bd63f8e2c0122da4f309bdc415162fc1da737\nbamboo_buildTimeStamp=2024-11-13T18:26:46.655Z\nbamboo_repository_previous_revision_number=a3bb626cf79d42346add84b85a593d20253e723a\nbamboo_repository_8060939_branch_name=develop\nbamboo_planRepository_previousRevision=a3bb626cf79d42346add84b85a593d20253e723a\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-GDB-JOB1-698\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - Clover and Tests\nbamboo_repository_8060939_name=Jalview Git\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=544bd63f8e2c0122da4f309bdc415162fc1da737\nSHLVL=1\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/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_8060939_git_branch=develop\nbamboo_planRepository_branch=develop\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=a3bb626cf79d42346add84b85a593d20253e723a\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\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-7864341\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_8060939_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_repository_8060939_previous_revision_number=a3bb626cf79d42346add84b85a593d20253e723a\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=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-GDB-JOB1\nbamboo_planKey=JB-GDB\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	13-Nov-2024 18:34:45	444
build	13-Nov-2024 18:34:59	
build	13-Nov-2024 18:34:59	> Configure project :
build	13-Nov-2024 18:34:59	Using properties from file './utils/channels/default/channel_gradle.properties'
build	13-Nov-2024 18:34:59	JALVIEW_VERSION is set to '2.11.4.2'
build	13-Nov-2024 18:34:59	HEADLESS BUILD
build	13-Nov-2024 18:34:59	J2S ENABLED
build	13-Nov-2024 18:35:00	Using a LOCAL profile.
build	13-Nov-2024 18:35:01	eclipseDir exists
build	13-Nov-2024 18:35:03	
build	13-Nov-2024 18:35:03	> Task :cloverHtmlReport
build	13-Nov-2024 18:35:03	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	13-Nov-2024 18:35:05	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/clover'
build	13-Nov-2024 18:35:43	Done. Processed 116 packages in 38881ms (335ms per package).
build	13-Nov-2024 18:35:49	
build	13-Nov-2024 18:35:49	> Task :cloverXmlReport
build	13-Nov-2024 18:35:49	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	13-Nov-2024 18:35:49	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/clover/clover.xml'
build	13-Nov-2024 18:35:49	
build	13-Nov-2024 18:35:49	> Task :cloverReport
build	13-Nov-2024 18:35:49	
build	13-Nov-2024 18:35:49	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	13-Nov-2024 18:35:49	
build	13-Nov-2024 18:35:49	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	13-Nov-2024 18:35:49	
build	13-Nov-2024 18:35:49	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	13-Nov-2024 18:35:49	
build	13-Nov-2024 18:35:49	BUILD SUCCESSFUL in 1m 3s
build	13-Nov-2024 18:35:49	2 actionable tasks: 2 executed
simple	13-Nov-2024 18:35:49	Finished task 'Clover Report' with result: Success
simple	13-Nov-2024 18:35:49	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	13-Nov-2024 18:35:49	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1...
simple	13-Nov-2024 18:35:49	Finished task 'TestNG Parser' with result: Success
simple	13-Nov-2024 18:35:49	Running post build plugin 'NCover Results Collector'
simple	13-Nov-2024 18:35:49	Running post build plugin 'Artifact Copier'
simple	13-Nov-2024 18:35:49	Publishing an artifact: Clover Report (System)
simple	13-Nov-2024 18:35:51	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.448 s
simple	13-Nov-2024 18:35:51	Publishing an artifact: TestNG report
error	13-Nov-2024 18:35:51	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/test does not exist.
simple	13-Nov-2024 18:35:51	The artifact hasn't been successfully published after 1.357 ms
simple	13-Nov-2024 18:35:51	Running post build plugin 'Artifactory Release Management Staging'
simple	13-Nov-2024 18:35:51	Running post build plugin 'Artifactory Build Info Copier'
simple	13-Nov-2024 18:35:51	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	13-Nov-2024 18:35:51	Running post build plugin 'npm Cache Cleanup'
simple	13-Nov-2024 18:35:51	Running post build plugin 'Clover Results Collector'
simple	13-Nov-2024 18:35:51	Running post build plugin 'Docker Container Cleanup'
simple	13-Nov-2024 18:35:51	Finalising the build...
simple	13-Nov-2024 18:35:51	Stopping timer.
simple	13-Nov-2024 18:35:51	Build JB-GDB-JOB1-698 completed.
simple	13-Nov-2024 18:35:51	Running on server: post build plugin 'NCover Results Collector'
simple	13-Nov-2024 18:35:51	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	13-Nov-2024 18:35:51	Running on server: post build plugin 'Clover Delta Calculator'
simple	13-Nov-2024 18:35:51	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	13-Nov-2024 18:35:51	All post build plugins have finished
simple	13-Nov-2024 18:35:51	Generating build results summary...
simple	13-Nov-2024 18:35:51	Saving build results to disk...
simple	13-Nov-2024 18:35:51	Logging substituted variables...
simple	13-Nov-2024 18:35:51	Indexing build results...
simple	13-Nov-2024 18:35:51	Finished building JB-GDB-JOB1-698.