simple	06-Nov-2024 14:47:00	Build Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop - Clover and Tests #5 (JB-GDB639-JOB1-5) started building on agent Default Agent
simple	06-Nov-2024 14:47:00	
simple	06-Nov-2024 14:47:00	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1
simple	06-Nov-2024 14:47:00	Executing build Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop - Clover and Tests #5 (JB-GDB639-JOB1-5)
simple	06-Nov-2024 14:47:00	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	06-Nov-2024 14:47:00	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1
simple	06-Nov-2024 14:47:00	Updating source code to revision: c6c46de559211c83d7e8bdf450d17628ae534af4
simple	06-Nov-2024 14:47:00	Fetching 'refs/heads/improvement/JAL-4485_not_finding_chimerax_on_managed_desktop' from 'http://source.jalview.org/git/jalview.git'.
simple	06-Nov-2024 14:47:01	Checking out revision c6c46de559211c83d7e8bdf450d17628ae534af4.
simple	06-Nov-2024 14:47:01	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164
simple	06-Nov-2024 14:47:01	   5ef2e9a..c6c46de  improvement/JAL-4485_not_finding_chimerax_on_managed_desktop -> origin/improvement/JAL-4485_not_finding_chimerax_on_managed_desktop
simple	06-Nov-2024 14:47:01	Already on 'improvement/JAL-4485_not_finding_chimerax_on_managed_desktop'
simple	06-Nov-2024 14:47:01	Your branch is behind 'origin/improvement/JAL-4485_not_finding_chimerax_on_managed_desktop' by 4 commits, and can be fast-forwarded.
simple	06-Nov-2024 14:47:01	  (use "git pull" to update your local branch)
simple	06-Nov-2024 14:47:01	HEAD is now at c6c46de JAL-4485 Tests for FileUtils.getMatchingVersionedFilesTest()
simple	06-Nov-2024 14:47:01	Updated source code to revision: c6c46de559211c83d7e8bdf450d17628ae534af4
simple	06-Nov-2024 14:47:01	Finished task 'Checkout Default Repository' with result: Success
simple	06-Nov-2024 14:47:01	Running pre-build action: VCS Version Collector
simple	06-Nov-2024 14:47:01	Running pre-build action: Artifactory Release Staging
simple	06-Nov-2024 14:47:01	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	06-Nov-2024 14:47:01	Bamboo Artifactory Plugin version: 2.6.2
command	06-Nov-2024 14:47:01	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop - Clover and Tests #5 (JB-GDB639-JOB1-5)'\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-GDB639-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_repository_revision_number=c6c46de559211c83d7e8bdf450d17628ae534af4\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB639-JOB1-5\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-GDB639-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB639-JOB1\nbamboo_shortPlanName=improvement-JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=5\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-GDB639-JOB1-5\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498170_previous_revision_number=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_shortPlanKey=GDB639\nbamboo_repository_46498170_name=Jalview Git\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=c6c46de559211c83d7e8bdf450d17628ae534af4\nbamboo_buildTimeStamp=2024-11-06T14:47:00.883Z\nbamboo_repository_previous_revision_number=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_repository_46498170_git_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_planRepository_previousRevision=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_repository_git_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_buildResultKey=JB-GDB639-JOB1-5\nbamboo_repository_branch_name=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=c6c46de559211c83d7e8bdf450d17628ae534af4\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_46498170_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\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=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_planRepository_branchDisplayName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_repository_46498170_revision_number=c6c46de559211c83d7e8bdf450d17628ae534af4\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498170_branch_name=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301939\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_46498170_git_username=\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-GDB639-JOB1\nbamboo_planKey=JB-GDB639\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	06-Nov-2024 14:47:01	444
build	06-Nov-2024 14:47:01	Starting a Gradle Daemon (subsequent builds will be faster)
build	06-Nov-2024 14:47:07	
build	06-Nov-2024 14:47:07	> Configure project :
build	06-Nov-2024 14:47:07	Using properties from file './utils/channels/default/channel_gradle.properties'
build	06-Nov-2024 14:47:07	JALVIEW_VERSION is set to '2.11.4.1'
build	06-Nov-2024 14:47:07	HEADLESS BUILD
build	06-Nov-2024 14:47:07	J2S ENABLED
build	06-Nov-2024 14:47:07	Using a LOCAL profile.
build	06-Nov-2024 14:47:08	eclipseDir exists
build	06-Nov-2024 14:47:09	
build	06-Nov-2024 14:47:09	> Task :clean
build	06-Nov-2024 14:47:09	> Task :cleanClover
build	06-Nov-2024 14:47:09	> Task :cleanTest UP-TO-DATE
build	06-Nov-2024 14:47:11	
build	06-Nov-2024 14:47:11	> Task :cloverInstrJava
build	06-Nov-2024 14:47:11	Clover: About to instrument 1103 files
build	06-Nov-2024 14:47:11	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	06-Nov-2024 14:47:11	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/clover/clover.db'.
build	06-Nov-2024 14:47:11	Processing files at 1.9 source level.
error	06-Nov-2024 14:47:14	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	06-Nov-2024 14:47:14	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	06-Nov-2024 14:47:14	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	06-Nov-2024 14:47:14	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	06-Nov-2024 14:47:14	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	06-Nov-2024 14:47:14	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	06-Nov-2024 14:47:14	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	06-Nov-2024 14:47:20	Clover all over. Instrumented 1103 files (112 packages).
build	06-Nov-2024 14:47:23	
build	06-Nov-2024 14:47:23	> Task :cloverInstrTests
build	06-Nov-2024 14:47:23	Clover: About to instrument test files
build	06-Nov-2024 14:47:23	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	06-Nov-2024 14:47:23	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/clover/clover.db'.
build	06-Nov-2024 14:47:23	Processing files at 1.9 source level.
build	06-Nov-2024 14:47:25	Clover all over. Instrumented 291 files (52 packages).
build	06-Nov-2024 14:47:25	1595 test methods detected.
build	06-Nov-2024 14:47:25	
build	06-Nov-2024 14:47:25	> Task :cloverInstr
build	06-Nov-2024 14:47:27	
build	06-Nov-2024 14:47:27	> Task :compileCloverJava
build	06-Nov-2024 14:47:27	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	06-Nov-2024 14:47:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:47:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:47:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:47:27	Setting target compatibility to 11
error	06-Nov-2024 14:47:49	Note: Some input files use or override a deprecated API.
error	06-Nov-2024 14:47:49	Note: Recompile with -Xlint:deprecation for details.
error	06-Nov-2024 14:47:49	Note: Some input files use unchecked or unsafe operations.
error	06-Nov-2024 14:47:49	Note: Recompile with -Xlint:unchecked for details.
build	06-Nov-2024 14:47:55	
build	06-Nov-2024 14:47:55	> Task :processCloverResources NO-SOURCE
build	06-Nov-2024 14:47:55	> Task :cloverClasses
build	06-Nov-2024 14:47:55	> Task :copyHelp
build	06-Nov-2024 14:47:57	> Task :buildIndices
build	06-Nov-2024 14:47:57	> Task :copyResources
build	06-Nov-2024 14:47:57	> Task :copyChannelResources
build	06-Nov-2024 14:47:57	
build	06-Nov-2024 14:47:57	> Task :createBuildProperties
build	06-Nov-2024 14:47:57	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	06-Nov-2024 14:47:57	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:47:57	
build	06-Nov-2024 14:47:57	> Task :buildResources
build	06-Nov-2024 14:47:57	> Task :copyDocs
build	06-Nov-2024 14:47:58	
build	06-Nov-2024 14:47:58	> Task :convertMdFiles
build	06-Nov-2024 14:47:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	06-Nov-2024 14:47:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	06-Nov-2024 14:47:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	06-Nov-2024 14:47:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/resources/doc_build/doc/building.html
build	06-Nov-2024 14:47:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	06-Nov-2024 14:47:58	
build	06-Nov-2024 14:47:58	> Task :releasesTemplates
build	06-Nov-2024 14:47:58	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	06-Nov-2024 14:47:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:47:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:47:58	Stripping rc/test/etc for TEST
build	06-Nov-2024 14:47:58	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	06-Nov-2024 14:47:58	
build	06-Nov-2024 14:47:58	> Task :prepare
build	06-Nov-2024 14:48:00	
build	06-Nov-2024 14:48:00	> Task :compileJava
build	06-Nov-2024 14:48:00	Setting target compatibility to 11
error	06-Nov-2024 14:48:06	Note: Some input files use or override a deprecated API.
error	06-Nov-2024 14:48:06	Note: Recompile with -Xlint:deprecation for details.
error	06-Nov-2024 14:48:06	Note: Some input files use unchecked or unsafe operations.
error	06-Nov-2024 14:48:06	Note: Recompile with -Xlint:unchecked for details.
build	06-Nov-2024 14:48:09	
build	06-Nov-2024 14:48:09	> Task :compileTestJava
build	06-Nov-2024 14:48:09	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	06-Nov-2024 14:48:09	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:48:09	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:48:09	Setting target compatibility to 11
error	06-Nov-2024 14:48:14	Note: Some input files use or override a deprecated API.
error	06-Nov-2024 14:48:14	Note: Recompile with -Xlint:deprecation for details.
error	06-Nov-2024 14:48:14	Note: Some input files use unchecked or unsafe operations.
error	06-Nov-2024 14:48:14	Note: Recompile with -Xlint:unchecked for details.
build	06-Nov-2024 14:48:15	
build	06-Nov-2024 14:48:15	> Task :processTestResources
build	06-Nov-2024 14:48:15	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	06-Nov-2024 14:48:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:48:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:48:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:48:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:48:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:48:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:48:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:48:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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	06-Nov-2024 14:48:15	
build	06-Nov-2024 14:48:15	> Task :testClasses
build	06-Nov-2024 14:48:17	
build	06-Nov-2024 14:48:17	> Task :testTask0
build	06-Nov-2024 14:48:17	Running tests WITH clover
error	06-Nov-2024 14:48:20	WARNING: An illegal reflective access operation has occurred
error	06-Nov-2024 14:48:20	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	06-Nov-2024 14:48:20	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	06-Nov-2024 14:48:20	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	06-Nov-2024 14:48:20	WARNING: All illegal access operations will be denied in a future release
build	06-Nov-2024 14:52:15	
build	06-Nov-2024 14:52:15	> Task :testTask1
build	06-Nov-2024 14:52:15	Running tests WITH clover
error	06-Nov-2024 14:52:16	WARNING: An illegal reflective access operation has occurred
error	06-Nov-2024 14:52:16	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	06-Nov-2024 14:52:16	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	06-Nov-2024 14:52:16	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	06-Nov-2024 14:52:16	WARNING: All illegal access operations will be denied in a future release
build	06-Nov-2024 14:53:51	
build	06-Nov-2024 14:53:51	> Task :testTask2
build	06-Nov-2024 14:53:51	Running tests WITH clover
build	06-Nov-2024 14:53:54	
build	06-Nov-2024 14:53:54	> Task :testTask3
build	06-Nov-2024 14:53:54	Running tests WITH clover
error	06-Nov-2024 14:53:56	WARNING: An illegal reflective access operation has occurred
error	06-Nov-2024 14:53:56	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	06-Nov-2024 14:53:56	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	06-Nov-2024 14:53:56	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	06-Nov-2024 14:53:56	WARNING: All illegal access operations will be denied in a future release
build	06-Nov-2024 14:54:41	
build	06-Nov-2024 14:54:41	> Task :test NO-SOURCE
build	06-Nov-2024 14:54:41	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	06-Nov-2024 14:54:41	│jalview:testTask0 results: SUCCESS (1735 tests, 1735 successes, 0 failures, 0 skipped) in 3 minutes, 56.803 seconds   │
build	06-Nov-2024 14:54:41	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/tests/testTask0/index.html│
build	06-Nov-2024 14:54:41	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	06-Nov-2024 14:54:41	│jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 35.988 seconds       │
build	06-Nov-2024 14:54:41	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/tests/testTask1/index.html│
build	06-Nov-2024 14:54:41	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	06-Nov-2024 14:54:41	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.309 seconds                     │
build	06-Nov-2024 14:54:41	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/tests/testTask2/index.html│
build	06-Nov-2024 14:54:41	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	06-Nov-2024 14:54:41	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 48.498 seconds                  │
build	06-Nov-2024 14:54:41	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/tests/testTask3/index.html│
build	06-Nov-2024 14:54:41	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	06-Nov-2024 14:54:41	│OVERALL: results: SUCCESS (1810 tests, 1810 successes, 0 failures, 0 skipped) in 4 minutes, 144.598 seconds           │
build	06-Nov-2024 14:54:41	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	06-Nov-2024 14:54:41	
build	06-Nov-2024 14:54:41	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	06-Nov-2024 14:54:41	
build	06-Nov-2024 14:54:41	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	06-Nov-2024 14:54:41	
build	06-Nov-2024 14:54:41	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	06-Nov-2024 14:54:41	
build	06-Nov-2024 14:54:41	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	06-Nov-2024 14:54:41	Please consult deprecation warnings for more details.
build	06-Nov-2024 14:54:41	
build	06-Nov-2024 14:54:41	BUILD SUCCESSFUL in 7m 39s
build	06-Nov-2024 14:54:41	21 actionable tasks: 20 executed, 1 up-to-date
simple	06-Nov-2024 14:54:41	Finished task 'Run tests with openclover under gradle' with result: Success
simple	06-Nov-2024 14:54:41	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	06-Nov-2024 14:54:41	Bamboo Artifactory Plugin version: 2.6.2
command	06-Nov-2024 14:54:41	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop - Clover and Tests #5 (JB-GDB639-JOB1-5)'\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-GDB639-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_repository_revision_number=c6c46de559211c83d7e8bdf450d17628ae534af4\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB639-JOB1-5\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-GDB639-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB639-JOB1\nbamboo_shortPlanName=improvement-JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=5\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-GDB639-JOB1-5\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498170_previous_revision_number=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_shortPlanKey=GDB639\nbamboo_repository_46498170_name=Jalview Git\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=c6c46de559211c83d7e8bdf450d17628ae534af4\nbamboo_buildTimeStamp=2024-11-06T14:47:00.883Z\nbamboo_repository_previous_revision_number=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_repository_46498170_git_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_planRepository_previousRevision=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_repository_git_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_buildResultKey=JB-GDB639-JOB1-5\nbamboo_repository_branch_name=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=c6c46de559211c83d7e8bdf450d17628ae534af4\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_46498170_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\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=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_planRepository_branchDisplayName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_repository_46498170_revision_number=c6c46de559211c83d7e8bdf450d17628ae534af4\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498170_branch_name=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301939\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_46498170_git_username=\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-GDB639-JOB1\nbamboo_planKey=JB-GDB639\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	06-Nov-2024 14:54:41	444
build	06-Nov-2024 14:54:46	
build	06-Nov-2024 14:54:46	> Configure project :
build	06-Nov-2024 14:54:46	Using properties from file './utils/channels/default/channel_gradle.properties'
build	06-Nov-2024 14:54:46	JALVIEW_VERSION is set to '2.11.4.1'
build	06-Nov-2024 14:54:46	HEADLESS BUILD
build	06-Nov-2024 14:54:46	J2S ENABLED
build	06-Nov-2024 14:54:47	Using a LOCAL profile.
build	06-Nov-2024 14:54:47	eclipseDir exists
build	06-Nov-2024 14:54:50	
build	06-Nov-2024 14:54:50	> Task :cloverHtmlReport
build	06-Nov-2024 14:54:50	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	06-Nov-2024 14:54:51	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/clover'
build	06-Nov-2024 14:55:30	Done. Processed 116 packages in 39478ms (340ms per package).
build	06-Nov-2024 14:55:36	
build	06-Nov-2024 14:55:36	> Task :cloverXmlReport
build	06-Nov-2024 14:55:36	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	06-Nov-2024 14:55:36	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/clover/clover.xml'
build	06-Nov-2024 14:55:37	
build	06-Nov-2024 14:55:37	> Task :cloverReport
build	06-Nov-2024 14:55:37	
build	06-Nov-2024 14:55:37	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	06-Nov-2024 14:55:37	
build	06-Nov-2024 14:55:37	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	06-Nov-2024 14:55:37	
build	06-Nov-2024 14:55:37	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	06-Nov-2024 14:55:37	
build	06-Nov-2024 14:55:37	BUILD SUCCESSFUL in 55s
build	06-Nov-2024 14:55:37	2 actionable tasks: 2 executed
simple	06-Nov-2024 14:55:37	Finished task 'Clover Report' with result: Success
simple	06-Nov-2024 14:55:37	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	06-Nov-2024 14:55:37	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1...
simple	06-Nov-2024 14:55:37	Finished task 'TestNG Parser' with result: Success
simple	06-Nov-2024 14:55:37	Running post build plugin 'NCover Results Collector'
simple	06-Nov-2024 14:55:37	Running post build plugin 'Artifact Copier'
simple	06-Nov-2024 14:55:37	Publishing an artifact: Clover Report (System)
simple	06-Nov-2024 14:55:38	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.422 s
simple	06-Nov-2024 14:55:38	Publishing an artifact: TestNG report
error	06-Nov-2024 14:55:38	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/tests/test does not exist.
simple	06-Nov-2024 14:55:38	The artifact hasn't been successfully published after 1.289 ms
simple	06-Nov-2024 14:55:38	Running post build plugin 'Artifactory Release Management Staging'
simple	06-Nov-2024 14:55:38	Running post build plugin 'Artifactory Build Info Copier'
simple	06-Nov-2024 14:55:38	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	06-Nov-2024 14:55:38	Running post build plugin 'npm Cache Cleanup'
simple	06-Nov-2024 14:55:38	Running post build plugin 'Clover Results Collector'
simple	06-Nov-2024 14:55:38	Running post build plugin 'Docker Container Cleanup'
simple	06-Nov-2024 14:55:38	Finalising the build...
simple	06-Nov-2024 14:55:38	Stopping timer.
simple	06-Nov-2024 14:55:38	Build JB-GDB639-JOB1-5 completed.
simple	06-Nov-2024 14:55:38	Running on server: post build plugin 'NCover Results Collector'
simple	06-Nov-2024 14:55:38	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	06-Nov-2024 14:55:38	Running on server: post build plugin 'Clover Delta Calculator'
simple	06-Nov-2024 14:55:38	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	06-Nov-2024 14:55:38	All post build plugins have finished
simple	06-Nov-2024 14:55:38	Generating build results summary...
simple	06-Nov-2024 14:55:38	Saving build results to disk...
simple	06-Nov-2024 14:55:38	Logging substituted variables...
simple	06-Nov-2024 14:55:38	Indexing build results...
simple	06-Nov-2024 14:55:38	Finished building JB-GDB639-JOB1-5.