simple	19-Jun-2026 07:23:12	Build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #2 (JB-GDB749-JOB1-2) started building on agent Default Agent
simple	19-Jun-2026 07:23:12	
simple	19-Jun-2026 07:23:12	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1
simple	19-Jun-2026 07:23:12	Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #2 (JB-GDB749-JOB1-2)
simple	19-Jun-2026 07:23:12	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	19-Jun-2026 07:23:12	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1
simple	19-Jun-2026 07:23:12	Updating source code to revision: 648892615bcaf223b2b6986392066ddbfcfb6745
simple	19-Jun-2026 07:23:12	Fetching 'refs/heads/patch/JAL-4410_multimers_from_3dbeacons' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	19-Jun-2026 07:23:12	Checking out revision 648892615bcaf223b2b6986392066ddbfcfb6745.
simple	19-Jun-2026 07:23:12	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	19-Jun-2026 07:23:12	   570cfd1..6488926  patch/JAL-4410_multimers_from_3dbeacons -> origin/patch/JAL-4410_multimers_from_3dbeacons
simple	19-Jun-2026 07:23:12	   1695a59..bb70b9d  epic/JAL-4320_JAL-4644_refactor_directory_structure -> origin/epic/JAL-4320_JAL-4644_refactor_directory_structure
simple	19-Jun-2026 07:23:12	 * [new branch]      epic/JAL-4320_JAL-4671_swingjs_gradle_plugin_for_jalviewjs -> origin/epic/JAL-4320_JAL-4671_swingjs_gradle_plugin_for_jalviewjs
simple	19-Jun-2026 07:23:12	 * [new branch]      feature/JAL-4478_multimer_pae_import -> origin/feature/JAL-4478_multimer_pae_import
simple	19-Jun-2026 07:23:12	 * [new branch]      patch/JAL-3848_slivka_java_client_update_06d3659 -> origin/patch/JAL-3848_slivka_java_client_update_06d3659
simple	19-Jun-2026 07:23:12	 * [new branch]      patch/JAL-4478_r212_initialpatch -> origin/patch/JAL-4478_r212_initialpatch
simple	19-Jun-2026 07:23:12	 * [new branch]      patch/JAL-4644_add_resources_for_testng -> origin/patch/JAL-4644_add_resources_for_testng
simple	19-Jun-2026 07:23:12	   0d6f149..6a7235f  patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts -> origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
simple	19-Jun-2026 07:23:12	 * [new branch]      patch/JAL-4672_for_2115_pdbe_query -> origin/patch/JAL-4672_for_2115_pdbe_query
simple	19-Jun-2026 07:23:12	 * [new branch]      spike/na_hack_JAL-4673 -> origin/spike/na_hack_JAL-4673
simple	19-Jun-2026 07:23:12	Already on 'patch/JAL-4410_multimers_from_3dbeacons'
simple	19-Jun-2026 07:23:12	Your branch is behind 'origin/patch/JAL-4410_multimers_from_3dbeacons' by 6 commits, and can be fast-forwarded.
simple	19-Jun-2026 07:23:12	  (use "git pull" to update your local branch)
simple	19-Jun-2026 07:23:13	HEAD is now at 6488926 JAL-4410 compressed PAE import tests (one failing) and refactor GZIP test/decompress FileParse methods to use with Platform.parseJSON
simple	19-Jun-2026 07:23:13	Updated source code to revision: 648892615bcaf223b2b6986392066ddbfcfb6745
simple	19-Jun-2026 07:23:13	Finished task 'Checkout Default Repository' with result: Success
simple	19-Jun-2026 07:23:13	Running pre-build action: VCS Version Collector
simple	19-Jun-2026 07:23:13	Running pre-build action: Artifactory Release Staging
simple	19-Jun-2026 07:23:13	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	19-Jun-2026 07:23:13	Bamboo Artifactory Plugin version: 2.6.2
command	19-Jun-2026 07:23:13	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #2 (JB-GDB749-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_revision_number=648892615bcaf223b2b6986392066ddbfcfb6745\nbamboo_repository_48169043_previous_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-2\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB749-JOB1\nbamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-2\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	19-Jun-2026 07:23:13	2414
build	19-Jun-2026 07:23:14	
build	19-Jun-2026 07:23:14	> Configure project :
build	19-Jun-2026 07:23:14	Using properties from file './utils/channels/default/channel_gradle.properties'
build	19-Jun-2026 07:23:14	JALVIEW_VERSION is set to '2.11.5.1'
build	19-Jun-2026 07:23:14	HEADLESS BUILD
build	19-Jun-2026 07:23:14	J2S ENABLED
build	19-Jun-2026 07:23:14	Using a LOCAL profile.
build	19-Jun-2026 07:23:14	eclipseDir exists
build	19-Jun-2026 07:23:15	
build	19-Jun-2026 07:23:15	> Task :clean
build	19-Jun-2026 07:23:15	> Task :cleanClover
build	19-Jun-2026 07:23:15	> Task :cleanTest UP-TO-DATE
build	19-Jun-2026 07:23:17	
build	19-Jun-2026 07:23:17	> Task :cloverInstrJava
build	19-Jun-2026 07:23:17	Clover: About to instrument 1110 files
build	19-Jun-2026 07:23:17	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Jun-2026 07:23:17	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'.
build	19-Jun-2026 07:23:17	Processing files at 1.9 source level.
error	19-Jun-2026 07:23:19	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	19-Jun-2026 07:23:19	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	19-Jun-2026 07:23:19	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	19-Jun-2026 07:23:19	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	19-Jun-2026 07:23:19	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	19-Jun-2026 07:23:19	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	19-Jun-2026 07:23:19	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	19-Jun-2026 07:23:25	Clover all over. Instrumented 1110 files (113 packages).
build	19-Jun-2026 07:23:27	
build	19-Jun-2026 07:23:27	> Task :cloverInstrTests
build	19-Jun-2026 07:23:27	Clover: About to instrument test files
build	19-Jun-2026 07:23:27	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Jun-2026 07:23:27	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'.
build	19-Jun-2026 07:23:27	Processing files at 1.9 source level.
build	19-Jun-2026 07:23:29	Clover all over. Instrumented 293 files (52 packages).
build	19-Jun-2026 07:23:29	1627 test methods detected.
build	19-Jun-2026 07:23:30	
build	19-Jun-2026 07:23:30	> Task :cloverInstr
build	19-Jun-2026 07:23:32	
build	19-Jun-2026 07:23:32	> Task :compileCloverJava
build	19-Jun-2026 07:23:32	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	19-Jun-2026 07:23:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:23:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:23:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:23:32	Setting target compatibility to 11
error	19-Jun-2026 07:23:43	Note: Some input files use or override a deprecated API.
error	19-Jun-2026 07:23:43	Note: Recompile with -Xlint:deprecation for details.
error	19-Jun-2026 07:23:43	Note: Some input files use unchecked or unsafe operations.
error	19-Jun-2026 07:23:43	Note: Recompile with -Xlint:unchecked for details.
build	19-Jun-2026 07:23:48	
build	19-Jun-2026 07:23:48	> Task :processCloverResources NO-SOURCE
build	19-Jun-2026 07:23:48	> Task :cloverClasses
build	19-Jun-2026 07:23:48	> Task :copyHelp
build	19-Jun-2026 07:23:49	> Task :buildIndices
build	19-Jun-2026 07:23:49	> Task :copyResources
build	19-Jun-2026 07:23:49	> Task :copyChannelResources
build	19-Jun-2026 07:23:49	
build	19-Jun-2026 07:23:49	> Task :createBuildProperties
build	19-Jun-2026 07:23:49	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	19-Jun-2026 07:23:49	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:23:49	
build	19-Jun-2026 07:23:49	> Task :buildResources
build	19-Jun-2026 07:23:49	> Task :copyDocs
build	19-Jun-2026 07:23:49	
build	19-Jun-2026 07:23:49	> Task :convertMdFiles
build	19-Jun-2026 07:23:49	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	19-Jun-2026 07:23:49	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	19-Jun-2026 07:23:49	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	19-Jun-2026 07:23:49	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/building.html
build	19-Jun-2026 07:23:49	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	19-Jun-2026 07:23:50	
build	19-Jun-2026 07:23:50	> Task :releasesTemplates
build	19-Jun-2026 07:23:50	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	19-Jun-2026 07:23:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:23:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:23:50	Stripping rc/test/etc for TEST
build	19-Jun-2026 07:23:50	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	19-Jun-2026 07:23:50	
build	19-Jun-2026 07:23:50	> Task :prepare
build	19-Jun-2026 07:23:52	
build	19-Jun-2026 07:23:52	> Task :compileJava
build	19-Jun-2026 07:23:52	Setting target compatibility to 11
error	19-Jun-2026 07:23:56	Note: Some input files use or override a deprecated API.
error	19-Jun-2026 07:23:56	Note: Recompile with -Xlint:deprecation for details.
error	19-Jun-2026 07:23:56	Note: Some input files use unchecked or unsafe operations.
error	19-Jun-2026 07:23:56	Note: Recompile with -Xlint:unchecked for details.
build	19-Jun-2026 07:23:58	
build	19-Jun-2026 07:23:58	> Task :compileTestJava
build	19-Jun-2026 07:23:58	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	19-Jun-2026 07:23:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:23:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:23:58	Setting target compatibility to 11
error	19-Jun-2026 07:24:02	Note: Some input files use or override a deprecated API.
error	19-Jun-2026 07:24:02	Note: Recompile with -Xlint:deprecation for details.
error	19-Jun-2026 07:24:02	Note: Some input files use unchecked or unsafe operations.
error	19-Jun-2026 07:24:02	Note: Recompile with -Xlint:unchecked for details.
build	19-Jun-2026 07:24:03	
build	19-Jun-2026 07:24:03	> Task :processTestResources
build	19-Jun-2026 07:24:03	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	19-Jun-2026 07:24:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:24:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:24:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:24:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:24:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:24:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:24:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:24:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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	19-Jun-2026 07:24:03	
build	19-Jun-2026 07:24:03	> Task :testClasses
build	19-Jun-2026 07:24:05	
build	19-Jun-2026 07:24:05	> Task :testTask0
build	19-Jun-2026 07:24:05	Running tests WITH clover
error	19-Jun-2026 07:24:07	WARNING: An illegal reflective access operation has occurred
error	19-Jun-2026 07:24:07	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	19-Jun-2026 07:24:07	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	19-Jun-2026 07:24:07	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	19-Jun-2026 07:24:07	WARNING: All illegal access operations will be denied in a future release
build	19-Jun-2026 07:24:21	
build	19-Jun-2026 07:24:21	Gradle suite > Gradle test > jalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructure[3](examples/AlphaFold/AF-Q5VSL9-F1-model_v4.pdb, examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_cmp.json) FAILED
build	19-Jun-2026 07:24:21	    java.lang.AssertionError: Exception importing paefile 'examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_cmp.json'
build	19-Jun-2026 07:24:21	        at org.testng.Assert.fail(Assert.java:83)
build	19-Jun-2026 07:24:21	        at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_1rvd1wm3rp7(EBIAlphaFoldTest.java:91)
build	19-Jun-2026 07:24:21	        at jalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructure(EBIAlphaFoldTest.java:62)
build	19-Jun-2026 07:24:21	
build	19-Jun-2026 07:24:21	        Caused by:
build	19-Jun-2026 07:24:21	        java.io.IOException: Stream Closed
build	19-Jun-2026 07:24:21	            at java.base/java.io.FileInputStream.readBytes(Native Method)
build	19-Jun-2026 07:24:21	            at java.base/java.io.FileInputStream.read(FileInputStream.java:279)
build	19-Jun-2026 07:24:21	            at java.base/java.io.BufferedInputStream.fill(BufferedInputStream.java:252)
build	19-Jun-2026 07:24:21	            at java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:292)
build	19-Jun-2026 07:24:21	            at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:351)
build	19-Jun-2026 07:24:21	            at java.base/java.io.FilterInputStream.read(FilterInputStream.java:107)
build	19-Jun-2026 07:24:21	            at jalview.util.Platform.isGzipStream(Platform.java:602)
build	19-Jun-2026 07:24:21	            at jalview.util.Platform.checkForGzipStream(Platform.java:644)
build	19-Jun-2026 07:24:21	            at jalview.util.Platform.parseJSON(Platform.java:534)
build	19-Jun-2026 07:24:21	            at jalview.ws.dbsources.EBIAlfaFold.parseJSONtoPAEContactMatrix(EBIAlfaFold.java:570)
build	19-Jun-2026 07:24:21	            at jalview.ws.dbsources.EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(EBIAlfaFold.java:605)
build	19-Jun-2026 07:24:21	            at jalview.ws.dbsources.EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(EBIAlfaFold.java:594)
build	19-Jun-2026 07:24:21	            at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_1rvd1wm3rp7(EBIAlphaFoldTest.java:85)
build	19-Jun-2026 07:24:21	            ... 1 more
error	19-Jun-2026 07:28:25	
error	19-Jun-2026 07:28:25	1838 tests completed, 1 failed
build	19-Jun-2026 07:28:25	There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask0/index.html
build	19-Jun-2026 07:28:27	
build	19-Jun-2026 07:28:27	> Task :testTask1
build	19-Jun-2026 07:28:27	Running tests WITH clover
error	19-Jun-2026 07:28:28	WARNING: An illegal reflective access operation has occurred
error	19-Jun-2026 07:28:28	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	19-Jun-2026 07:28:28	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	19-Jun-2026 07:28:28	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	19-Jun-2026 07:28:28	WARNING: All illegal access operations will be denied in a future release
build	19-Jun-2026 07:30:34	
build	19-Jun-2026 07:30:34	> Task :testTask2
build	19-Jun-2026 07:30:34	Running tests WITH clover
build	19-Jun-2026 07:30:37	
build	19-Jun-2026 07:30:37	> Task :testTask3
build	19-Jun-2026 07:30:37	Running tests WITH clover
error	19-Jun-2026 07:30:38	WARNING: An illegal reflective access operation has occurred
error	19-Jun-2026 07:30:38	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	19-Jun-2026 07:30:38	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	19-Jun-2026 07:30:38	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	19-Jun-2026 07:30:38	WARNING: All illegal access operations will be denied in a future release
build	19-Jun-2026 07:31:25	
build	19-Jun-2026 07:31:25	> Task :test NO-SOURCE
build	19-Jun-2026 07:31:25	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
error	19-Jun-2026 07:31:25	
error	19-Jun-2026 07:31:25	FAILURE: Build failed with an exception.
error	19-Jun-2026 07:31:25	
error	19-Jun-2026 07:31:25	* Where:
error	19-Jun-2026 07:31:25	Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build.gradle' line: 1967
error	19-Jun-2026 07:31:25	
error	19-Jun-2026 07:31:25	* What went wrong:
error	19-Jun-2026 07:31:25	Failed tests!
error	19-Jun-2026 07:31:25	
error	19-Jun-2026 07:31:25	* Try:
error	19-Jun-2026 07:31:25	> Run with --stacktrace option to get the stack trace.
error	19-Jun-2026 07:31:25	> Run with --info or --debug option to get more log output.
error	19-Jun-2026 07:31:25	> Run with --scan to get full insights.
error	19-Jun-2026 07:31:25	
error	19-Jun-2026 07:31:25	* Get more help at https://help.gradle.org
error	19-Jun-2026 07:31:25	
error	19-Jun-2026 07:31:25	BUILD FAILED in 8m 11s
build	19-Jun-2026 07:31:25	│jalview:testTask0 results: FAILURE (1838 tests, 1837 successes, 1 failures, 0 skipped) in 4 minutes, 22.132 seconds   │
build	19-Jun-2026 07:31:25	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask0/index.html│
build	19-Jun-2026 07:31:25	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Jun-2026 07:31:25	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 6.202 seconds        │
build	19-Jun-2026 07:31:25	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask1/index.html│
build	19-Jun-2026 07:31:25	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Jun-2026 07:31:25	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.220 seconds                     │
build	19-Jun-2026 07:31:25	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask2/index.html│
build	19-Jun-2026 07:31:25	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Jun-2026 07:31:25	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 49.447 seconds                  │
build	19-Jun-2026 07:31:25	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask3/index.html│
build	19-Jun-2026 07:31:25	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Jun-2026 07:31:25	│OVERALL: results: FAILURE (1926 tests, 1925 successes, 1 failures, 0 skipped) in 6 minutes, 81.001 seconds            │
build	19-Jun-2026 07:31:25	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	19-Jun-2026 07:31:25	
build	19-Jun-2026 07:31:25	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	19-Jun-2026 07:31:25	
build	19-Jun-2026 07:31:25	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	19-Jun-2026 07:31:25	
build	19-Jun-2026 07:31:25	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	19-Jun-2026 07:31:25	
build	19-Jun-2026 07:31:25	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	19-Jun-2026 07:31:25	Please consult deprecation warnings for more details.
build	19-Jun-2026 07:31:25	21 actionable tasks: 20 executed, 1 up-to-date
simple	19-Jun-2026 07:31:25	
simple	19-Jun-2026 07:31:25	Failing task since return code of [/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test] was 1 while expected 0
simple	19-Jun-2026 07:31:25	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	19-Jun-2026 07:31:25	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	19-Jun-2026 07:31:25	Bamboo Artifactory Plugin version: 2.6.2
command	19-Jun-2026 07:31:25	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #2 (JB-GDB749-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_revision_number=648892615bcaf223b2b6986392066ddbfcfb6745\nbamboo_repository_48169043_previous_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-2\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB749-JOB1\nbamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-2\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons\nbamboo_shortPlanKey=GDB749\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=648892615bcaf223b2b6986392066ddbfcfb6745\nbamboo_buildTimeStamp=2026-06-19T07:23:12.149+01:00\nbamboo_repository_previous_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_repository_48169043_name=Jalview Gitlab\nbamboo_planRepository_previousRevision=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_repository_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildResultKey=JB-GDB749-JOB1-2\nbamboo_repository_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=648892615bcaf223b2b6986392066ddbfcfb6745\nSHLVL=1\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/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=true\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_48169043_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=570cfd128c945bc7593ad75c31b9761ff81f5fee\nbamboo_planRepository_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4410_multimers_from_3dbeacons\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_48169043_revision_number=648892615bcaf223b2b6986392066ddbfcfb6745\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_repository_48169043_git_username=\nbamboo_plan_storageTag=plan-47972517\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=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-GDB749-JOB1\nbamboo_planKey=JB-GDB749\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4410_multimers_from_3dbeacons\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	19-Jun-2026 07:31:25	2414
build	19-Jun-2026 07:31:30	
build	19-Jun-2026 07:31:30	> Configure project :
build	19-Jun-2026 07:31:30	Using properties from file './utils/channels/default/channel_gradle.properties'
build	19-Jun-2026 07:31:31	JALVIEW_VERSION is set to '2.11.5.1'
build	19-Jun-2026 07:31:31	HEADLESS BUILD
build	19-Jun-2026 07:31:31	J2S ENABLED
build	19-Jun-2026 07:31:31	Using a LOCAL profile.
build	19-Jun-2026 07:31:32	eclipseDir exists
build	19-Jun-2026 07:31:34	
build	19-Jun-2026 07:31:34	> Task :cloverHtmlReport
build	19-Jun-2026 07:31:34	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Jun-2026 07:31:35	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/clover'
build	19-Jun-2026 07:32:22	Done. Processed 117 packages in 46593ms (398ms per package).
build	19-Jun-2026 07:32:27	
build	19-Jun-2026 07:32:27	> Task :cloverXmlReport
build	19-Jun-2026 07:32:27	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Jun-2026 07:32:29	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/clover/clover.xml'
build	19-Jun-2026 07:32:29	
build	19-Jun-2026 07:32:29	> Task :cloverReport
build	19-Jun-2026 07:32:29	
build	19-Jun-2026 07:32:29	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	19-Jun-2026 07:32:29	
build	19-Jun-2026 07:32:29	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	19-Jun-2026 07:32:29	
build	19-Jun-2026 07:32:29	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	19-Jun-2026 07:32:29	
build	19-Jun-2026 07:32:29	BUILD SUCCESSFUL in 1m 3s
build	19-Jun-2026 07:32:29	2 actionable tasks: 2 executed
simple	19-Jun-2026 07:32:29	Finished task 'Clover Report' with result: Success
simple	19-Jun-2026 07:32:29	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	19-Jun-2026 07:32:29	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1...
simple	19-Jun-2026 07:32:29	Failing task since 1 failing test cases were found.
simple	19-Jun-2026 07:32:29	Finished task 'TestNG Parser' with result: Failed
simple	19-Jun-2026 07:32:29	Running post build plugin 'NCover Results Collector'
simple	19-Jun-2026 07:32:29	Running post build plugin 'Artifact Copier'
simple	19-Jun-2026 07:32:29	Publishing an artifact: Clover Report (System)
simple	19-Jun-2026 07:32:31	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.181 s
simple	19-Jun-2026 07:32:31	Publishing an artifact: TestNG report
error	19-Jun-2026 07:32:31	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/test does not exist.
simple	19-Jun-2026 07:32:31	The artifact hasn't been successfully published after 3.907 ms
simple	19-Jun-2026 07:32:31	Running post build plugin 'Artifactory Release Management Staging'
simple	19-Jun-2026 07:32:31	Running post build plugin 'Artifactory Build Info Copier'
simple	19-Jun-2026 07:32:31	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	19-Jun-2026 07:32:31	Running post build plugin 'npm Cache Cleanup'
simple	19-Jun-2026 07:32:31	Running post build plugin 'Clover Results Collector'
simple	19-Jun-2026 07:32:31	Running post build plugin 'Docker Container Cleanup'
simple	19-Jun-2026 07:32:31	Finalising the build...
simple	19-Jun-2026 07:32:31	Stopping timer.
simple	19-Jun-2026 07:32:31	Build JB-GDB749-JOB1-2 completed.
simple	19-Jun-2026 07:32:31	Running on server: post build plugin 'NCover Results Collector'
simple	19-Jun-2026 07:32:31	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	19-Jun-2026 07:32:31	Running on server: post build plugin 'Clover Delta Calculator'
simple	19-Jun-2026 07:32:31	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	19-Jun-2026 07:32:31	All post build plugins have finished
simple	19-Jun-2026 07:32:31	Generating build results summary...
simple	19-Jun-2026 07:32:32	Saving build results to disk...
simple	19-Jun-2026 07:32:32	Logging substituted variables...
simple	19-Jun-2026 07:32:32	Indexing build results...
simple	19-Jun-2026 07:32:32	Finished building JB-GDB749-JOB1-2.