simple	11-Nov-2024 15:13:53	Build Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests #3 (JB-GDB642-JOB1-3) started building on agent Default Agent
simple	11-Nov-2024 15:13:53	
simple	11-Nov-2024 15:13:53	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1
simple	11-Nov-2024 15:13:53	Executing build Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests #3 (JB-GDB642-JOB1-3)
simple	11-Nov-2024 15:13:53	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	11-Nov-2024 15:13:53	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1
simple	11-Nov-2024 15:13:53	Updating source code to revision: f6be36d7152321642e41db9d8bdbd2580431541e
simple	11-Nov-2024 15:13:54	Fetching 'refs/heads/features/JAL-4489_cluster_pca_and_pasimap' from 'http://source.jalview.org/git/jalview.git'.
simple	11-Nov-2024 15:13:55	Checking out revision f6be36d7152321642e41db9d8bdbd2580431541e.
simple	11-Nov-2024 15:13:55	Already on 'features/JAL-4489_cluster_pca_and_pasimap'
simple	11-Nov-2024 15:13:55	Updated source code to revision: f6be36d7152321642e41db9d8bdbd2580431541e
simple	11-Nov-2024 15:13:55	Finished task 'Checkout Default Repository' with result: Success
simple	11-Nov-2024 15:13:55	Running pre-build action: VCS Version Collector
simple	11-Nov-2024 15:13:55	Running pre-build action: Artifactory Release Staging
simple	11-Nov-2024 15:13:55	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	11-Nov-2024 15:13:55	Bamboo Artifactory Plugin version: 2.6.2
command	11-Nov-2024 15:13:55	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests #3 (JB-GDB642-JOB1-3)'\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-GDB642-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_repository_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB642-JOB1-3\nbamboo_repository_46498184_git_branch=features/JAL-4489_cluster_pca_and_pasimap\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-GDB642-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB642-JOB1\nbamboo_shortPlanName=features-JAL-4489_cluster_pca_and_pasimap\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=3\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-GDB642-JOB1-3\nbamboo_repository_46498184_name=Jalview Git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498184_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap\nbamboo_shortPlanKey=GDB642\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_repository_46498184_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_buildTimeStamp=2024-11-11T15:13:53.873Z\nbamboo_repository_previous_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_planRepository_previousRevision=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_repository_git_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_buildResultKey=JB-GDB642-JOB1-3\nbamboo_repository_branch_name=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=f6be36d7152321642e41db9d8bdbd2580431541e\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/\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=features/JAL-4489_cluster_pca_and_pasimap\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=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_repository_46498184_git_username=\nbamboo_planRepository_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=features/JAL-4489_cluster_pca_and_pasimap\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498184_previous_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301967\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-GDB642-JOB1\nbamboo_planKey=JB-GDB642\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498184_branch_name=features/JAL-4489_cluster_pca_and_pasimap\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=features/JAL-4489_cluster_pca_and_pasimap\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	11-Nov-2024 15:13:55	444
build	11-Nov-2024 15:13:58	
build	11-Nov-2024 15:13:58	> Configure project :
build	11-Nov-2024 15:13:58	Using properties from file './utils/channels/default/channel_gradle.properties'
build	11-Nov-2024 15:13:58	JALVIEW_VERSION is set to '2.11.4.1'
build	11-Nov-2024 15:13:58	HEADLESS BUILD
build	11-Nov-2024 15:13:58	J2S ENABLED
build	11-Nov-2024 15:13:58	Using a LOCAL profile.
build	11-Nov-2024 15:13:58	eclipseDir exists
build	11-Nov-2024 15:13:58	
build	11-Nov-2024 15:13:58	> Task :clean
build	11-Nov-2024 15:13:58	> Task :cleanClover
build	11-Nov-2024 15:13:58	> Task :cleanTest UP-TO-DATE
build	11-Nov-2024 15:14:00	
build	11-Nov-2024 15:14:00	> Task :cloverInstrJava
build	11-Nov-2024 15:14:00	Clover: About to instrument 1106 files
build	11-Nov-2024 15:14:00	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	11-Nov-2024 15:14:00	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover.db'.
build	11-Nov-2024 15:14:00	Processing files at 1.9 source level.
error	11-Nov-2024 15:14:04	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	11-Nov-2024 15:14:04	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	11-Nov-2024 15:14:04	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	11-Nov-2024 15:14:04	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	11-Nov-2024 15:14:04	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	11-Nov-2024 15:14:04	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	11-Nov-2024 15:14:04	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	11-Nov-2024 15:14:11	Clover all over. Instrumented 1106 files (112 packages).
build	11-Nov-2024 15:14:13	
build	11-Nov-2024 15:14:13	> Task :cloverInstrTests
build	11-Nov-2024 15:14:13	Clover: About to instrument test files
build	11-Nov-2024 15:14:13	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	11-Nov-2024 15:14:13	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover.db'.
build	11-Nov-2024 15:14:13	Processing files at 1.9 source level.
build	11-Nov-2024 15:14:16	Clover all over. Instrumented 291 files (52 packages).
build	11-Nov-2024 15:14:16	1594 test methods detected.
build	11-Nov-2024 15:14:16	
build	11-Nov-2024 15:14:16	> Task :cloverInstr
build	11-Nov-2024 15:14:18	
build	11-Nov-2024 15:14:18	> Task :compileCloverJava
build	11-Nov-2024 15:14:18	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:14:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:18	Setting target compatibility to 11
error	11-Nov-2024 15:14:31	Note: Some input files use or override a deprecated API.
error	11-Nov-2024 15:14:31	Note: Recompile with -Xlint:deprecation for details.
error	11-Nov-2024 15:14:31	Note: Some input files use unchecked or unsafe operations.
error	11-Nov-2024 15:14:31	Note: Recompile with -Xlint:unchecked for details.
build	11-Nov-2024 15:14:35	
build	11-Nov-2024 15:14:35	> Task :processCloverResources NO-SOURCE
build	11-Nov-2024 15:14:35	> Task :cloverClasses
build	11-Nov-2024 15:14:35	> Task :copyHelp
build	11-Nov-2024 15:14:36	> Task :buildIndices
build	11-Nov-2024 15:14:36	> Task :copyResources
build	11-Nov-2024 15:14:36	> Task :copyChannelResources
build	11-Nov-2024 15:14:36	
build	11-Nov-2024 15:14:36	> Task :createBuildProperties
build	11-Nov-2024 15:14:36	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:14:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:36	
build	11-Nov-2024 15:14:36	> Task :buildResources
build	11-Nov-2024 15:14:36	> Task :copyDocs
build	11-Nov-2024 15:14:36	
build	11-Nov-2024 15:14:36	> Task :convertMdFiles
build	11-Nov-2024 15:14:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	11-Nov-2024 15:14:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	11-Nov-2024 15:14:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	11-Nov-2024 15:14:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/building.html
build	11-Nov-2024 15:14:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	11-Nov-2024 15:14:37	
build	11-Nov-2024 15:14:37	> Task :releasesTemplates
build	11-Nov-2024 15:14:37	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:14:37	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:37	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:37	Stripping rc/test/etc for TEST
build	11-Nov-2024 15:14:37	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	11-Nov-2024 15:14:37	
build	11-Nov-2024 15:14:37	> Task :prepare
build	11-Nov-2024 15:14:39	
build	11-Nov-2024 15:14:39	> Task :compileJava
build	11-Nov-2024 15:14:39	Setting target compatibility to 11
error	11-Nov-2024 15:14:44	Note: Some input files use or override a deprecated API.
error	11-Nov-2024 15:14:44	Note: Recompile with -Xlint:deprecation for details.
error	11-Nov-2024 15:14:44	Note: Some input files use unchecked or unsafe operations.
error	11-Nov-2024 15:14:44	Note: Recompile with -Xlint:unchecked for details.
build	11-Nov-2024 15:14:46	
build	11-Nov-2024 15:14:46	> Task :compileTestJava
build	11-Nov-2024 15:14:46	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:14:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:46	Setting target compatibility to 11
error	11-Nov-2024 15:14:51	Note: Some input files use or override a deprecated API.
error	11-Nov-2024 15:14:51	Note: Recompile with -Xlint:deprecation for details.
error	11-Nov-2024 15:14:51	Note: Some input files use unchecked or unsafe operations.
error	11-Nov-2024 15:14:51	Note: Recompile with -Xlint:unchecked for details.
build	11-Nov-2024 15:14:52	
build	11-Nov-2024 15:14:52	> Task :processTestResources
build	11-Nov-2024 15:14:52	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:14:52	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:52	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:52	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:52	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:52	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:52	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:52	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:52	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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	11-Nov-2024 15:14:52	
build	11-Nov-2024 15:14:52	> Task :testClasses
build	11-Nov-2024 15:14:54	
build	11-Nov-2024 15:14:54	> Task :testTask0
build	11-Nov-2024 15:14:54	Running tests WITH clover
error	11-Nov-2024 15:14:57	WARNING: An illegal reflective access operation has occurred
error	11-Nov-2024 15:14:57	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	11-Nov-2024 15:14:57	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	11-Nov-2024 15:14:57	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	11-Nov-2024 15:14:57	WARNING: All illegal access operations will be denied in a future release
build	11-Nov-2024 15:18:53	
build	11-Nov-2024 15:18:53	> Task :testTask1
build	11-Nov-2024 15:18:53	Running tests WITH clover
error	11-Nov-2024 15:18:55	WARNING: An illegal reflective access operation has occurred
error	11-Nov-2024 15:18:55	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	11-Nov-2024 15:18:55	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	11-Nov-2024 15:18:55	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	11-Nov-2024 15:18:55	WARNING: All illegal access operations will be denied in a future release
build	11-Nov-2024 15:20:30	
build	11-Nov-2024 15:20:30	> Task :testTask2
build	11-Nov-2024 15:20:30	Running tests WITH clover
build	11-Nov-2024 15:20:33	
build	11-Nov-2024 15:20:33	> Task :testTask3
build	11-Nov-2024 15:20:33	Running tests WITH clover
error	11-Nov-2024 15:20:35	WARNING: An illegal reflective access operation has occurred
error	11-Nov-2024 15:20:35	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	11-Nov-2024 15:20:35	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	11-Nov-2024 15:20:35	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	11-Nov-2024 15:20:35	WARNING: All illegal access operations will be denied in a future release
build	11-Nov-2024 15:21:20	
build	11-Nov-2024 15:21:20	> Task :test NO-SOURCE
build	11-Nov-2024 15:21:20	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	11-Nov-2024 15:21:20	│jalview:testTask0 results: SUCCESS (1728 tests, 1728 successes, 0 failures, 0 skipped) in 3 minutes, 58.742 seconds   │
build	11-Nov-2024 15:21:20	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask0/index.html│
build	11-Nov-2024 15:21:20	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	11-Nov-2024 15:21:20	│jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 36.146 seconds       │
build	11-Nov-2024 15:21:20	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask1/index.html│
build	11-Nov-2024 15:21:20	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	11-Nov-2024 15:21:20	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.641 seconds                     │
build	11-Nov-2024 15:21:20	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask2/index.html│
build	11-Nov-2024 15:21:20	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	11-Nov-2024 15:21:20	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 48.443 seconds                  │
build	11-Nov-2024 15:21:20	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask3/index.html│
build	11-Nov-2024 15:21:20	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	11-Nov-2024 15:21:20	│OVERALL: results: SUCCESS (1803 tests, 1803 successes, 0 failures, 0 skipped) in 4 minutes, 146.972 seconds           │
build	11-Nov-2024 15:21:20	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	11-Nov-2024 15:21:20	
build	11-Nov-2024 15:21:20	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	11-Nov-2024 15:21:20	
build	11-Nov-2024 15:21:20	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	11-Nov-2024 15:21:20	
build	11-Nov-2024 15:21:20	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	11-Nov-2024 15:21:20	
build	11-Nov-2024 15:21:20	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	11-Nov-2024 15:21:20	Please consult deprecation warnings for more details.
build	11-Nov-2024 15:21:20	
build	11-Nov-2024 15:21:20	BUILD SUCCESSFUL in 7m 24s
build	11-Nov-2024 15:21:20	21 actionable tasks: 20 executed, 1 up-to-date
simple	11-Nov-2024 15:21:20	Finished task 'Run tests with openclover under gradle' with result: Success
simple	11-Nov-2024 15:21:20	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	11-Nov-2024 15:21:20	Bamboo Artifactory Plugin version: 2.6.2
command	11-Nov-2024 15:21:20	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests #3 (JB-GDB642-JOB1-3)'\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-GDB642-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_repository_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB642-JOB1-3\nbamboo_repository_46498184_git_branch=features/JAL-4489_cluster_pca_and_pasimap\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-GDB642-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB642-JOB1\nbamboo_shortPlanName=features-JAL-4489_cluster_pca_and_pasimap\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=3\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-GDB642-JOB1-3\nbamboo_repository_46498184_name=Jalview Git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498184_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap\nbamboo_shortPlanKey=GDB642\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_repository_46498184_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_buildTimeStamp=2024-11-11T15:13:53.873Z\nbamboo_repository_previous_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_planRepository_previousRevision=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_repository_git_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_buildResultKey=JB-GDB642-JOB1-3\nbamboo_repository_branch_name=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=f6be36d7152321642e41db9d8bdbd2580431541e\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/\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=features/JAL-4489_cluster_pca_and_pasimap\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=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_repository_46498184_git_username=\nbamboo_planRepository_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=features/JAL-4489_cluster_pca_and_pasimap\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498184_previous_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301967\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-GDB642-JOB1\nbamboo_planKey=JB-GDB642\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498184_branch_name=features/JAL-4489_cluster_pca_and_pasimap\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=features/JAL-4489_cluster_pca_and_pasimap\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	11-Nov-2024 15:21:20	444
build	11-Nov-2024 15:21:29	
build	11-Nov-2024 15:21:29	> Configure project :
build	11-Nov-2024 15:21:29	Using properties from file './utils/channels/default/channel_gradle.properties'
build	11-Nov-2024 15:21:29	JALVIEW_VERSION is set to '2.11.4.1'
build	11-Nov-2024 15:21:29	HEADLESS BUILD
build	11-Nov-2024 15:21:29	J2S ENABLED
build	11-Nov-2024 15:21:29	Using a LOCAL profile.
build	11-Nov-2024 15:21:30	eclipseDir exists
build	11-Nov-2024 15:21:33	
build	11-Nov-2024 15:21:33	> Task :cloverHtmlReport
build	11-Nov-2024 15:21:33	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	11-Nov-2024 15:21:34	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/clover'
build	11-Nov-2024 15:22:13	Done. Processed 116 packages in 39442ms (340ms per package).
build	11-Nov-2024 15:22:18	
build	11-Nov-2024 15:22:18	> Task :cloverXmlReport
build	11-Nov-2024 15:22:18	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	11-Nov-2024 15:22:19	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/clover/clover.xml'
build	11-Nov-2024 15:22:19	
build	11-Nov-2024 15:22:19	> Task :cloverReport
build	11-Nov-2024 15:22:19	
build	11-Nov-2024 15:22:19	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	11-Nov-2024 15:22:19	
build	11-Nov-2024 15:22:19	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	11-Nov-2024 15:22:19	
build	11-Nov-2024 15:22:19	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	11-Nov-2024 15:22:19	
build	11-Nov-2024 15:22:19	BUILD SUCCESSFUL in 59s
build	11-Nov-2024 15:22:19	2 actionable tasks: 2 executed
simple	11-Nov-2024 15:22:19	Finished task 'Clover Report' with result: Success
simple	11-Nov-2024 15:22:19	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	11-Nov-2024 15:22:19	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1...
simple	11-Nov-2024 15:22:19	Finished task 'TestNG Parser' with result: Success
simple	11-Nov-2024 15:22:19	Running post build plugin 'NCover Results Collector'
simple	11-Nov-2024 15:22:19	Running post build plugin 'Artifact Copier'
simple	11-Nov-2024 15:22:19	Publishing an artifact: Clover Report (System)
simple	11-Nov-2024 15:22:21	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.413 s
simple	11-Nov-2024 15:22:21	Publishing an artifact: TestNG report
error	11-Nov-2024 15:22:21	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/test does not exist.
simple	11-Nov-2024 15:22:21	The artifact hasn't been successfully published after 1.322 ms
simple	11-Nov-2024 15:22:21	Running post build plugin 'Artifactory Release Management Staging'
simple	11-Nov-2024 15:22:21	Running post build plugin 'Artifactory Build Info Copier'
simple	11-Nov-2024 15:22:21	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	11-Nov-2024 15:22:21	Running post build plugin 'npm Cache Cleanup'
simple	11-Nov-2024 15:22:21	Running post build plugin 'Clover Results Collector'
simple	11-Nov-2024 15:22:21	Running post build plugin 'Docker Container Cleanup'
simple	11-Nov-2024 15:22:21	Finalising the build...
simple	11-Nov-2024 15:22:21	Stopping timer.
simple	11-Nov-2024 15:22:21	Build JB-GDB642-JOB1-3 completed.
simple	11-Nov-2024 15:22:21	Running on server: post build plugin 'NCover Results Collector'
simple	11-Nov-2024 15:22:21	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	11-Nov-2024 15:22:21	Running on server: post build plugin 'Clover Delta Calculator'
simple	11-Nov-2024 15:22:21	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	11-Nov-2024 15:22:21	All post build plugins have finished
simple	11-Nov-2024 15:22:21	Generating build results summary...
simple	11-Nov-2024 15:22:21	Saving build results to disk...
simple	11-Nov-2024 15:22:21	Logging substituted variables...
simple	11-Nov-2024 15:22:21	Indexing build results...
simple	11-Nov-2024 15:22:21	Finished building JB-GDB642-JOB1-3.