simple	27-Nov-2025 17:07:34	Build Jalview Builds - Gradle Develop Build - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Clover and Tests #5 (JB-GDB729-JOB1-5) started building on agent Default Agent
simple	27-Nov-2025 17:07:34	
simple	27-Nov-2025 17:07:34	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1
simple	27-Nov-2025 17:07:34	Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Clover and Tests #5 (JB-GDB729-JOB1-5)
simple	27-Nov-2025 17:07:34	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	27-Nov-2025 17:07:34	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1
simple	27-Nov-2025 17:07:34	Updating source code to revision: acbb7d39481e53918a63f69cd008b4f6bbd7a588
simple	27-Nov-2025 17:07:34	Fetching 'refs/heads/bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	27-Nov-2025 17:07:35	Checking out revision acbb7d39481e53918a63f69cd008b4f6bbd7a588.
simple	27-Nov-2025 17:07:36	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	27-Nov-2025 17:07:36	 * [new branch]      patch/JAL-4601_stk_ss_annots_showhide -> origin/patch/JAL-4601_stk_ss_annots_showhide
simple	27-Nov-2025 17:07:36	Already on 'bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus'
simple	27-Nov-2025 17:07:36	Updated source code to revision: acbb7d39481e53918a63f69cd008b4f6bbd7a588
simple	27-Nov-2025 17:07:36	Finished task 'Checkout Default Repository' with result: Success
simple	27-Nov-2025 17:07:36	Running pre-build action: VCS Version Collector
simple	27-Nov-2025 17:07:36	Running pre-build action: Artifactory Release Staging
simple	27-Nov-2025 17:07:36	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	27-Nov-2025 17:07:36	Bamboo Artifactory Plugin version: 2.6.2
command	27-Nov-2025 17:07:36	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Clover and Tests #5 (JB-GDB729-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-GDB729-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_repository_46498601_name=Jalview Gitlab\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_repository_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB729-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-GDB729-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB729-JOB1\nbamboo_repository_46498601_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_shortPlanName=bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_planRepository_name=Jalview Gitlab\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-GDB729-JOB1-5\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - 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build	27-Nov-2025 17:07:36	444
build	27-Nov-2025 17:07:38	
build	27-Nov-2025 17:07:39	> Configure project :
build	27-Nov-2025 17:07:39	Using properties from file './utils/channels/default/channel_gradle.properties'
build	27-Nov-2025 17:07:39	JALVIEW_VERSION is set to '2.11.5.1'
build	27-Nov-2025 17:07:39	HEADLESS BUILD
build	27-Nov-2025 17:07:39	J2S ENABLED
build	27-Nov-2025 17:07:39	Using a LOCAL profile.
build	27-Nov-2025 17:07:39	eclipseDir exists
build	27-Nov-2025 17:07:40	
build	27-Nov-2025 17:07:40	> Task :clean
build	27-Nov-2025 17:07:40	> Task :cleanClover
build	27-Nov-2025 17:07:40	> Task :cleanTest UP-TO-DATE
build	27-Nov-2025 17:07:42	
build	27-Nov-2025 17:07:42	> Task :cloverInstrJava
build	27-Nov-2025 17:07:42	Clover: About to instrument 1107 files
build	27-Nov-2025 17:07:42	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	27-Nov-2025 17:07:42	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/clover/clover.db'.
build	27-Nov-2025 17:07:42	Processing files at 1.9 source level.
error	27-Nov-2025 17:07:47	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	27-Nov-2025 17:07:47	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	27-Nov-2025 17:07:47	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	27-Nov-2025 17:07:47	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	27-Nov-2025 17:07:47	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	27-Nov-2025 17:07:47	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	27-Nov-2025 17:07:47	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	27-Nov-2025 17:07:56	Clover all over. Instrumented 1107 files (112 packages).
build	27-Nov-2025 17:07:59	
build	27-Nov-2025 17:07:59	> Task :cloverInstrTests
build	27-Nov-2025 17:07:59	Clover: About to instrument test files
build	27-Nov-2025 17:07:59	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	27-Nov-2025 17:07:59	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/clover/clover.db'.
build	27-Nov-2025 17:07:59	Processing files at 1.9 source level.
build	27-Nov-2025 17:08:03	Clover all over. Instrumented 293 files (52 packages).
build	27-Nov-2025 17:08:03	1624 test methods detected.
build	27-Nov-2025 17:08:03	
build	27-Nov-2025 17:08:03	> Task :cloverInstr
build	27-Nov-2025 17:08:05	
build	27-Nov-2025 17:08:05	> Task :compileCloverJava
build	27-Nov-2025 17:08:05	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:08:05	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:05	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:05	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:05	Setting target compatibility to 11
error	27-Nov-2025 17:08:20	Note: Some input files use or override a deprecated API.
error	27-Nov-2025 17:08:20	Note: Recompile with -Xlint:deprecation for details.
error	27-Nov-2025 17:08:20	Note: Some input files use unchecked or unsafe operations.
error	27-Nov-2025 17:08:20	Note: Recompile with -Xlint:unchecked for details.
build	27-Nov-2025 17:08:27	
build	27-Nov-2025 17:08:27	> Task :processCloverResources NO-SOURCE
build	27-Nov-2025 17:08:27	> Task :cloverClasses
build	27-Nov-2025 17:08:28	> Task :copyHelp
build	27-Nov-2025 17:08:30	> Task :buildIndices
build	27-Nov-2025 17:08:30	> Task :copyResources
build	27-Nov-2025 17:08:30	> Task :copyChannelResources
build	27-Nov-2025 17:08:30	
build	27-Nov-2025 17:08:30	> Task :createBuildProperties
build	27-Nov-2025 17:08:30	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:08:30	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:30	
build	27-Nov-2025 17:08:30	> Task :buildResources
build	27-Nov-2025 17:08:30	> Task :copyDocs
build	27-Nov-2025 17:08:30	
build	27-Nov-2025 17:08:30	> Task :convertMdFiles
build	27-Nov-2025 17:08:30	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	27-Nov-2025 17:08:30	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	27-Nov-2025 17:08:30	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	27-Nov-2025 17:08:30	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/resources/doc_build/doc/building.html
build	27-Nov-2025 17:08:30	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	27-Nov-2025 17:08:30	
build	27-Nov-2025 17:08:30	> Task :releasesTemplates
build	27-Nov-2025 17:08:30	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:08:30	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:30	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:30	Stripping rc/test/etc for TEST
build	27-Nov-2025 17:08:30	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	27-Nov-2025 17:08:30	
build	27-Nov-2025 17:08:30	> Task :prepare
build	27-Nov-2025 17:08:32	
build	27-Nov-2025 17:08:32	> Task :compileJava
build	27-Nov-2025 17:08:32	Setting target compatibility to 11
error	27-Nov-2025 17:08:37	Note: Some input files use or override a deprecated API.
error	27-Nov-2025 17:08:37	Note: Recompile with -Xlint:deprecation for details.
error	27-Nov-2025 17:08:37	Note: Some input files use unchecked or unsafe operations.
error	27-Nov-2025 17:08:37	Note: Recompile with -Xlint:unchecked for details.
build	27-Nov-2025 17:08:41	
build	27-Nov-2025 17:08:41	> Task :compileTestJava
build	27-Nov-2025 17:08:41	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:08:41	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:41	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:41	Setting target compatibility to 11
error	27-Nov-2025 17:08:45	Note: Some input files use or override a deprecated API.
error	27-Nov-2025 17:08:45	Note: Recompile with -Xlint:deprecation for details.
error	27-Nov-2025 17:08:45	Note: Some input files use unchecked or unsafe operations.
error	27-Nov-2025 17:08:45	Note: Recompile with -Xlint:unchecked for details.
build	27-Nov-2025 17:08:47	
build	27-Nov-2025 17:08:47	> Task :processTestResources
build	27-Nov-2025 17:08:47	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:08:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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	27-Nov-2025 17:08:47	
build	27-Nov-2025 17:08:47	> Task :testClasses
build	27-Nov-2025 17:08:49	
build	27-Nov-2025 17:08:49	> Task :testTask0
build	27-Nov-2025 17:08:49	Running tests WITH clover
error	27-Nov-2025 17:08:51	WARNING: An illegal reflective access operation has occurred
error	27-Nov-2025 17:08:51	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	27-Nov-2025 17:08:51	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	27-Nov-2025 17:08:51	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	27-Nov-2025 17:08:51	WARNING: All illegal access operations will be denied in a future release
build	27-Nov-2025 17:13:35	
build	27-Nov-2025 17:13:35	> Task :testTask1
build	27-Nov-2025 17:13:35	Running tests WITH clover
error	27-Nov-2025 17:13:37	WARNING: An illegal reflective access operation has occurred
error	27-Nov-2025 17:13:37	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	27-Nov-2025 17:13:37	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	27-Nov-2025 17:13:37	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	27-Nov-2025 17:13:37	WARNING: All illegal access operations will be denied in a future release
build	27-Nov-2025 17:16:24	
build	27-Nov-2025 17:16:24	> Task :testTask2
build	27-Nov-2025 17:16:24	Running tests WITH clover
build	27-Nov-2025 17:16:29	
build	27-Nov-2025 17:16:29	> Task :testTask3
build	27-Nov-2025 17:16:29	Running tests WITH clover
error	27-Nov-2025 17:16:31	WARNING: An illegal reflective access operation has occurred
error	27-Nov-2025 17:16:31	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	27-Nov-2025 17:16:31	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	27-Nov-2025 17:16:31	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	27-Nov-2025 17:16:31	WARNING: All illegal access operations will be denied in a future release
build	27-Nov-2025 17:17:32	
build	27-Nov-2025 17:17:32	> Task :test NO-SOURCE
build	27-Nov-2025 17:17:32	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	27-Nov-2025 17:17:32	│jalview:testTask0 results: SUCCESS (1824 tests, 1824 successes, 0 failures, 0 skipped) in 4 minutes, 45.498 seconds   │
build	27-Nov-2025 17:17:32	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/tests/testTask0/index.html│
build	27-Nov-2025 17:17:32	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	27-Nov-2025 17:17:32	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 48.881 seconds       │
build	27-Nov-2025 17:17:32	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/tests/testTask1/index.html│
build	27-Nov-2025 17:17:32	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	27-Nov-2025 17:17:32	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.847 seconds                     │
build	27-Nov-2025 17:17:32	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/tests/testTask2/index.html│
build	27-Nov-2025 17:17:32	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	27-Nov-2025 17:17:32	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 6.005 seconds        │
build	27-Nov-2025 17:17:32	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/tests/testTask3/index.html│
build	27-Nov-2025 17:17:32	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	27-Nov-2025 17:17:32	│OVERALL: results: SUCCESS (1912 tests, 1912 successes, 0 failures, 0 skipped) in 7 minutes, 105.231 seconds           │
build	27-Nov-2025 17:17:32	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	27-Nov-2025 17:17:32	
build	27-Nov-2025 17:17:32	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	27-Nov-2025 17:17:32	
build	27-Nov-2025 17:17:32	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	27-Nov-2025 17:17:32	
build	27-Nov-2025 17:17:32	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	27-Nov-2025 17:17:32	
build	27-Nov-2025 17:17:32	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	27-Nov-2025 17:17:32	Please consult deprecation warnings for more details.
build	27-Nov-2025 17:17:32	
build	27-Nov-2025 17:17:32	BUILD SUCCESSFUL in 9m 55s
build	27-Nov-2025 17:17:32	21 actionable tasks: 20 executed, 1 up-to-date
simple	27-Nov-2025 17:17:33	Finished task 'Run tests with openclover under gradle' with result: Success
simple	27-Nov-2025 17:17:33	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	27-Nov-2025 17:17:33	Bamboo Artifactory Plugin version: 2.6.2
command	27-Nov-2025 17:17:33	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Clover and Tests #5 (JB-GDB729-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-GDB729-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_repository_46498601_name=Jalview Gitlab\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_repository_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB729-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-GDB729-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB729-JOB1\nbamboo_repository_46498601_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_shortPlanName=bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_planRepository_name=Jalview Gitlab\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-GDB729-JOB1-5\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_shortPlanKey=GDB729\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_buildTimeStamp=2025-11-27T17:07:33.881Z\nbamboo_repository_previous_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_repository_46498601_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_planRepository_previousRevision=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_repository_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_buildResultKey=JB-GDB729-JOB1-5\nbamboo_repository_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nSHLVL=1\nbamboo_repository_46498601_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\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=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_46498601_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_planRepository_branchDisplayName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\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_repository_46498601_previous_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_plan_storageTag=plan-46302773\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=https://gitlab.jalview.org/jalview/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-GDB729-JOB1\nbamboo_planKey=JB-GDB729\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498601_git_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	27-Nov-2025 17:17:33	444
build	27-Nov-2025 17:17:41	
build	27-Nov-2025 17:17:41	> Configure project :
build	27-Nov-2025 17:17:41	Using properties from file './utils/channels/default/channel_gradle.properties'
build	27-Nov-2025 17:17:41	JALVIEW_VERSION is set to '2.11.5.1'
build	27-Nov-2025 17:17:41	HEADLESS BUILD
build	27-Nov-2025 17:17:41	J2S ENABLED
build	27-Nov-2025 17:17:41	Using a LOCAL profile.
build	27-Nov-2025 17:17:43	eclipseDir exists
build	27-Nov-2025 17:17:45	
build	27-Nov-2025 17:17:45	> Task :cloverHtmlReport
build	27-Nov-2025 17:17:45	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	27-Nov-2025 17:17:47	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/clover'
build	27-Nov-2025 17:18:44	Done. Processed 116 packages in 57257ms (493ms per package).
build	27-Nov-2025 17:18:51	
build	27-Nov-2025 17:18:51	> Task :cloverXmlReport
build	27-Nov-2025 17:18:51	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	27-Nov-2025 17:18:54	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/clover/clover.xml'
build	27-Nov-2025 17:18:55	
build	27-Nov-2025 17:18:55	> Task :cloverReport
build	27-Nov-2025 17:18:55	
build	27-Nov-2025 17:18:55	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	27-Nov-2025 17:18:55	
build	27-Nov-2025 17:18:55	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	27-Nov-2025 17:18:55	
build	27-Nov-2025 17:18:55	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	27-Nov-2025 17:18:55	
build	27-Nov-2025 17:18:55	BUILD SUCCESSFUL in 1m 21s
build	27-Nov-2025 17:18:55	2 actionable tasks: 2 executed
simple	27-Nov-2025 17:18:55	Finished task 'Clover Report' with result: Success
simple	27-Nov-2025 17:18:55	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	27-Nov-2025 17:18:55	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1...
simple	27-Nov-2025 17:18:55	Finished task 'TestNG Parser' with result: Success
simple	27-Nov-2025 17:18:55	Running post build plugin 'NCover Results Collector'
simple	27-Nov-2025 17:18:55	Running post build plugin 'Artifact Copier'
simple	27-Nov-2025 17:18:55	Publishing an artifact: Clover Report (System)
simple	27-Nov-2025 17:19:02	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 6.654 s
simple	27-Nov-2025 17:19:02	Publishing an artifact: TestNG report
error	27-Nov-2025 17:19:02	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/tests/test does not exist.
simple	27-Nov-2025 17:19:02	The artifact hasn't been successfully published after 4.122 ms
simple	27-Nov-2025 17:19:02	Running post build plugin 'Artifactory Release Management Staging'
simple	27-Nov-2025 17:19:02	Running post build plugin 'Artifactory Build Info Copier'
simple	27-Nov-2025 17:19:02	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	27-Nov-2025 17:19:02	Running post build plugin 'npm Cache Cleanup'
simple	27-Nov-2025 17:19:02	Running post build plugin 'Clover Results Collector'
simple	27-Nov-2025 17:19:02	Running post build plugin 'Docker Container Cleanup'
simple	27-Nov-2025 17:19:02	Finalising the build...
simple	27-Nov-2025 17:19:02	Stopping timer.
simple	27-Nov-2025 17:19:02	Build JB-GDB729-JOB1-5 completed.
simple	27-Nov-2025 17:19:02	Running on server: post build plugin 'NCover Results Collector'
simple	27-Nov-2025 17:19:02	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	27-Nov-2025 17:19:02	Running on server: post build plugin 'Clover Delta Calculator'
simple	27-Nov-2025 17:19:02	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	27-Nov-2025 17:19:02	All post build plugins have finished
simple	27-Nov-2025 17:19:02	Generating build results summary...
simple	27-Nov-2025 17:19:04	Saving build results to disk...
simple	27-Nov-2025 17:19:04	Logging substituted variables...
simple	27-Nov-2025 17:19:04	Indexing build results...
simple	27-Nov-2025 17:19:04	Finished building JB-GDB729-JOB1-5.