simple	05-Jan-2026 03:03:22	Build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6) started building on agent Default Agent
simple	05-Jan-2026 03:03:22	
simple	05-Jan-2026 03:03:22	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1
simple	05-Jan-2026 03:03:22	Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6)
simple	05-Jan-2026 03:03:22	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	05-Jan-2026 03:03:22	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1
simple	05-Jan-2026 03:03:22	Updating source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5
simple	05-Jan-2026 03:03:22	Fetching 'refs/heads/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	05-Jan-2026 03:03:23	Checking out revision b6ff7e553d3ba8b32e1d2650df7860706b2a37d5.
simple	05-Jan-2026 03:03:23	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	05-Jan-2026 03:03:23	   5857fe7..b6ff7e5  bug/JAL-4107_jalviewjs_fixes_on_2_12_branch -> origin/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch
simple	05-Jan-2026 03:03:23	Already on 'bug/JAL-4107_jalviewjs_fixes_on_2_12_branch'
simple	05-Jan-2026 03:03:23	Your branch is behind 'origin/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' by 1 commit, and can be fast-forwarded.
simple	05-Jan-2026 03:03:23	  (use "git pull" to update your local branch)
simple	05-Jan-2026 03:03:23	HEAD is now at b6ff7e5 JAL-4107 reinstate Console output of DESKTOP CREATED so jalviewjsHeadlessTest passes
simple	05-Jan-2026 03:03:23	Updated source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5
simple	05-Jan-2026 03:03:23	Finished task 'Checkout Default Repository' with result: Success
simple	05-Jan-2026 03:03:23	Running pre-build action: VCS Version Collector
simple	05-Jan-2026 03:03:23	Running pre-build action: Artifactory Release Staging
simple	05-Jan-2026 03:03:23	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	05-Jan-2026 03:03:23	Bamboo Artifactory Plugin version: 2.6.2
command	05-Jan-2026 03:03:23	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6)'\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-GDB734-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-JOB1-6\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-GDB734-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB734-JOB1\nbamboo_repository_46498616_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498616_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=6\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-GDB734-JOB1-6\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	05-Jan-2026 03:03:23	2414
build	05-Jan-2026 03:03:24	
build	05-Jan-2026 03:03:24	> Configure project :
build	05-Jan-2026 03:03:24	Using properties from file './utils/channels/default/channel_gradle.properties'
build	05-Jan-2026 03:03:24	JALVIEW_VERSION is set to '2.12.0'
build	05-Jan-2026 03:03:24	HEADLESS BUILD
build	05-Jan-2026 03:03:24	J2S ENABLED
build	05-Jan-2026 03:03:24	Using a LOCAL profile.
build	05-Jan-2026 03:03:24	eclipseDir exists
build	05-Jan-2026 03:03:25	
build	05-Jan-2026 03:03:25	> Task :clean
build	05-Jan-2026 03:03:25	> Task :cleanClover
build	05-Jan-2026 03:03:25	> Task :cleanTest UP-TO-DATE
build	05-Jan-2026 03:03:27	
build	05-Jan-2026 03:03:27	> Task :cloverInstrJava
build	05-Jan-2026 03:03:27	Clover: About to instrument 1253 files
build	05-Jan-2026 03:03:27	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	05-Jan-2026 03:03:27	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'.
build	05-Jan-2026 03:03:27	Processing files at 1.9 source level.
error	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:30	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	05-Jan-2026 03:03:36	Clover all over. Instrumented 1253 files (133 packages).
build	05-Jan-2026 03:03:38	
build	05-Jan-2026 03:03:38	> Task :cloverInstrTests
build	05-Jan-2026 03:03:38	Clover: About to instrument test files
build	05-Jan-2026 03:03:38	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	05-Jan-2026 03:03:38	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'.
build	05-Jan-2026 03:03:38	Processing files at 1.9 source level.
build	05-Jan-2026 03:03:40	Clover all over. Instrumented 315 files (58 packages).
build	05-Jan-2026 03:03:40	1770 test methods detected.
build	05-Jan-2026 03:03:41	
build	05-Jan-2026 03:03:41	> Task :cloverInstr
build	05-Jan-2026 03:03:43	
build	05-Jan-2026 03:03:43	> Task :compileCloverJava
build	05-Jan-2026 03:03:43	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	05-Jan-2026 03:03:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:03:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:03:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:03:43	Setting target compatibility to 11
error	05-Jan-2026 03:03:56	Note: Some input files use or override a deprecated API.
error	05-Jan-2026 03:03:56	Note: Recompile with -Xlint:deprecation for details.
error	05-Jan-2026 03:03:56	Note: Some input files use unchecked or unsafe operations.
error	05-Jan-2026 03:03:56	Note: Recompile with -Xlint:unchecked for details.
build	05-Jan-2026 03:04:01	
build	05-Jan-2026 03:04:01	> Task :processCloverResources NO-SOURCE
build	05-Jan-2026 03:04:01	> Task :cloverClasses
build	05-Jan-2026 03:04:01	> Task :copyHelp
build	05-Jan-2026 03:04:02	> Task :buildIndices
build	05-Jan-2026 03:04:02	> Task :copyResources
build	05-Jan-2026 03:04:02	> Task :copyChannelResources
build	05-Jan-2026 03:04:02	
build	05-Jan-2026 03:04:02	> Task :createBuildProperties
build	05-Jan-2026 03:04:02	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	05-Jan-2026 03:04:02	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:04:02	
build	05-Jan-2026 03:04:02	> Task :buildResources
build	05-Jan-2026 03:04:02	> Task :copyDocs
build	05-Jan-2026 03:04:02	
build	05-Jan-2026 03:04:02	> Task :convertMdFiles
build	05-Jan-2026 03:04:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	05-Jan-2026 03:04:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	05-Jan-2026 03:04:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	05-Jan-2026 03:04:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
build	05-Jan-2026 03:04:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/building.html
build	05-Jan-2026 03:04:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/addingWebClient.html
build	05-Jan-2026 03:04:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	05-Jan-2026 03:04:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
build	05-Jan-2026 03:04:03	
build	05-Jan-2026 03:04:03	> Task :releasesTemplates
build	05-Jan-2026 03:04:03	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	05-Jan-2026 03:04:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:04:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:04:03	Stripping rc/test/etc for TEST
build	05-Jan-2026 03:04:03	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	05-Jan-2026 03:04:03	
build	05-Jan-2026 03:04:03	> Task :prepare
build	05-Jan-2026 03:04:05	
build	05-Jan-2026 03:04:05	> Task :compileJava
build	05-Jan-2026 03:04:05	Setting target compatibility to 11
error	05-Jan-2026 03:04:09	Note: Some input files use or override a deprecated API.
error	05-Jan-2026 03:04:09	Note: Recompile with -Xlint:deprecation for details.
error	05-Jan-2026 03:04:09	Note: Some input files use unchecked or unsafe operations.
error	05-Jan-2026 03:04:09	Note: Recompile with -Xlint:unchecked for details.
build	05-Jan-2026 03:04:12	
build	05-Jan-2026 03:04:12	> Task :compileTestJava
build	05-Jan-2026 03:04:12	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	05-Jan-2026 03:04:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:04:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:04:12	Setting target compatibility to 11
error	05-Jan-2026 03:04:16	Note: Some input files use or override a deprecated API.
error	05-Jan-2026 03:04:16	Note: Recompile with -Xlint:deprecation for details.
error	05-Jan-2026 03:04:16	Note: Some input files use unchecked or unsafe operations.
error	05-Jan-2026 03:04:16	Note: Recompile with -Xlint:unchecked for details.
build	05-Jan-2026 03:04:18	
build	05-Jan-2026 03:04:18	> Task :processTestResources
build	05-Jan-2026 03:04:18	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	05-Jan-2026 03:04:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:04:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:04:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:04:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:04:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:04:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:04:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:04:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 03:04:18	
build	05-Jan-2026 03:04:18	> Task :testClasses
build	05-Jan-2026 03:04:20	
build	05-Jan-2026 03:04:20	> Task :testTask0
build	05-Jan-2026 03:04:20	Running tests WITH clover
error	05-Jan-2026 03:04:21	WARNING: An illegal reflective access operation has occurred
error	05-Jan-2026 03:04:21	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	05-Jan-2026 03:04:21	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	05-Jan-2026 03:04:21	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	05-Jan-2026 03:04:21	WARNING: All illegal access operations will be denied in a future release
build	05-Jan-2026 03:05:09	
build	05-Jan-2026 03:05:09	Gradle suite > Gradle test > jalview.bin.CommandLineOperations > testHeadlessModeOutputOperations[7](headless -open examples/uniref50.fa,  -html, test/jalview/bin/test_uniref50_out.html, true, 4096, 15000, null) FAILED
build	05-Jan-2026 03:05:09	    java.lang.AssertionError: Didn't create an output -html file.[headless -open examples/uniref50.fa] expected [true] but found [false]
build	05-Jan-2026 03:05:09	        at org.testng.Assert.fail(Assert.java:110)
build	05-Jan-2026 03:05:09	        at org.testng.Assert.failNotEquals(Assert.java:1413)
build	05-Jan-2026 03:05:09	        at org.testng.Assert.assertTrue(Assert.java:56)
build	05-Jan-2026 03:05:09	        at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:343)
build	05-Jan-2026 03:09:04	There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask0/index.html
error	05-Jan-2026 03:09:04	
error	05-Jan-2026 03:09:04	2102 tests completed, 1 failed
build	05-Jan-2026 03:09:06	
build	05-Jan-2026 03:09:06	> Task :testTask1
build	05-Jan-2026 03:09:06	Running tests WITH clover
error	05-Jan-2026 03:09:07	WARNING: An illegal reflective access operation has occurred
error	05-Jan-2026 03:09:07	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	05-Jan-2026 03:09:07	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	05-Jan-2026 03:09:07	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	05-Jan-2026 03:09:07	WARNING: All illegal access operations will be denied in a future release
build	05-Jan-2026 03:11:09	
build	05-Jan-2026 03:11:09	> Task :testTask2
build	05-Jan-2026 03:11:09	Running tests WITH clover
error	05-Jan-2026 03:11:10	WARNING: An illegal reflective access operation has occurred
error	05-Jan-2026 03:11:10	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	05-Jan-2026 03:11:10	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	05-Jan-2026 03:11:10	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	05-Jan-2026 03:11:10	WARNING: All illegal access operations will be denied in a future release
build	05-Jan-2026 03:11:14	
build	05-Jan-2026 03:11:14	> Task :testTask3
build	05-Jan-2026 03:11:14	Running tests WITH clover
error	05-Jan-2026 03:11:15	WARNING: An illegal reflective access operation has occurred
error	05-Jan-2026 03:11:15	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	05-Jan-2026 03:11:15	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	05-Jan-2026 03:11:15	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	05-Jan-2026 03:11:15	WARNING: All illegal access operations will be denied in a future release
build	05-Jan-2026 03:11:33	
build	05-Jan-2026 03:11:33	> Task :test NO-SOURCE
build	05-Jan-2026 03:11:33	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	05-Jan-2026 03:11:33	│jalview:testTask0 results: FAILURE (2102 tests, 2101 successes, 1 failures, 0 skipped) in 4 minutes, 46.257 seconds   │
build	05-Jan-2026 03:11:33	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask0/index.html│
build	05-Jan-2026 03:11:33	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	05-Jan-2026 03:11:33	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 2.841 seconds        │
build	05-Jan-2026 03:11:33	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask1/index.html│
build	05-Jan-2026 03:11:33	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	05-Jan-2026 03:11:33	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.432 seconds                     │
build	05-Jan-2026 03:11:33	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask2/index.html│
build	05-Jan-2026 03:11:33	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	05-Jan-2026 03:11:33	│jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 20.783 seconds                  │
build	05-Jan-2026 03:11:33	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask3/index.html│
build	05-Jan-2026 03:11:33	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	05-Jan-2026 03:11:33	│OVERALL: results: FAILURE (2179 tests, 2177 successes, 1 failures, 1 skipped) in 6 minutes, 74.313 seconds            │
build	05-Jan-2026 03:11:33	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	05-Jan-2026 03:11:33	
build	05-Jan-2026 03:11:33	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	05-Jan-2026 03:11:33	
build	05-Jan-2026 03:11:33	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	05-Jan-2026 03:11:33	
build	05-Jan-2026 03:11:33	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	05-Jan-2026 03:11:33	
build	05-Jan-2026 03:11:33	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	05-Jan-2026 03:11:33	Please consult deprecation warnings for more details.
error	05-Jan-2026 03:11:33	
error	05-Jan-2026 03:11:33	FAILURE: Build failed with an exception.
error	05-Jan-2026 03:11:33	
error	05-Jan-2026 03:11:33	* Where:
error	05-Jan-2026 03:11:33	Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build.gradle' line: 1964
error	05-Jan-2026 03:11:33	
error	05-Jan-2026 03:11:33	* What went wrong:
error	05-Jan-2026 03:11:33	Failed tests!
error	05-Jan-2026 03:11:33	
error	05-Jan-2026 03:11:33	* Try:
error	05-Jan-2026 03:11:33	> Run with --stacktrace option to get the stack trace.
error	05-Jan-2026 03:11:33	> Run with --info or --debug option to get more log output.
error	05-Jan-2026 03:11:33	> Run with --scan to get full insights.
error	05-Jan-2026 03:11:33	
error	05-Jan-2026 03:11:33	* Get more help at https://help.gradle.org
error	05-Jan-2026 03:11:33	
error	05-Jan-2026 03:11:33	BUILD FAILED in 8m 9s
build	05-Jan-2026 03:11:33	21 actionable tasks: 20 executed, 1 up-to-date
simple	05-Jan-2026 03:11:33	
simple	05-Jan-2026 03:11:33	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	05-Jan-2026 03:11:33	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	05-Jan-2026 03:11:33	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	05-Jan-2026 03:11:33	Bamboo Artifactory Plugin version: 2.6.2
command	05-Jan-2026 03:11:33	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6)'\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-GDB734-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-JOB1-6\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-GDB734-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB734-JOB1\nbamboo_repository_46498616_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498616_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=6\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-GDB734-JOB1-6\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-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_shortPlanKey=GDB734\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_buildTimeStamp=2026-01-05T03:03:22.820Z\nbamboo_repository_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_planRepository_previousRevision=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GDB734-JOB1-6\nbamboo_repository_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\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/\nbamboo_repository_46498616_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\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=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_planRepository_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302801\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-GDB734-JOB1\nbamboo_planKey=JB-GDB734\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498616_git_username=\nbamboo_repository_46498616_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_repository_46498616_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_46498616_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	05-Jan-2026 03:11:33	2414
build	05-Jan-2026 03:11:38	
build	05-Jan-2026 03:11:38	> Configure project :
build	05-Jan-2026 03:11:38	Using properties from file './utils/channels/default/channel_gradle.properties'
build	05-Jan-2026 03:11:38	JALVIEW_VERSION is set to '2.12.0'
build	05-Jan-2026 03:11:38	HEADLESS BUILD
build	05-Jan-2026 03:11:38	J2S ENABLED
build	05-Jan-2026 03:11:39	Using a LOCAL profile.
build	05-Jan-2026 03:11:39	eclipseDir exists
build	05-Jan-2026 03:11:42	
build	05-Jan-2026 03:11:42	> Task :cloverHtmlReport
build	05-Jan-2026 03:11:42	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	05-Jan-2026 03:11:43	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover'
error	05-Jan-2026 03:12:31	ERROR: Invalid Java source found or Clover failed to parse it: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/src/jalview/analysis/AlignmentUtils.java
build	05-Jan-2026 03:12:37	Done. Processed 137 packages in 53579ms (391ms per package).
build	05-Jan-2026 03:12:42	
build	05-Jan-2026 03:12:42	> Task :cloverXmlReport
build	05-Jan-2026 03:12:42	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	05-Jan-2026 03:12:42	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover/clover.xml'
build	05-Jan-2026 03:12:43	
build	05-Jan-2026 03:12:43	> Task :cloverReport
build	05-Jan-2026 03:12:43	
build	05-Jan-2026 03:12:43	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	05-Jan-2026 03:12:43	
build	05-Jan-2026 03:12:43	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	05-Jan-2026 03:12:43	
build	05-Jan-2026 03:12:43	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	05-Jan-2026 03:12:43	
build	05-Jan-2026 03:12:43	BUILD SUCCESSFUL in 1m 9s
build	05-Jan-2026 03:12:43	2 actionable tasks: 2 executed
simple	05-Jan-2026 03:12:43	Finished task 'Clover Report' with result: Success
simple	05-Jan-2026 03:12:43	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	05-Jan-2026 03:12:43	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1...
simple	05-Jan-2026 03:12:43	Failing task since 1 failing test cases were found.
simple	05-Jan-2026 03:12:43	Finished task 'TestNG Parser' with result: Failed
simple	05-Jan-2026 03:12:43	Running post build plugin 'NCover Results Collector'
simple	05-Jan-2026 03:12:43	Running post build plugin 'Artifact Copier'
simple	05-Jan-2026 03:12:43	Publishing an artifact: Clover Report (System)
simple	05-Jan-2026 03:12:45	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.048 s
simple	05-Jan-2026 03:12:45	Publishing an artifact: TestNG report
error	05-Jan-2026 03:12:45	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/test does not exist.
simple	05-Jan-2026 03:12:45	The artifact hasn't been successfully published after 80.75 μs
simple	05-Jan-2026 03:12:45	Running post build plugin 'Artifactory Release Management Staging'
simple	05-Jan-2026 03:12:45	Running post build plugin 'Artifactory Build Info Copier'
simple	05-Jan-2026 03:12:45	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	05-Jan-2026 03:12:45	Running post build plugin 'npm Cache Cleanup'
simple	05-Jan-2026 03:12:45	Running post build plugin 'Clover Results Collector'
simple	05-Jan-2026 03:12:45	Running post build plugin 'Docker Container Cleanup'
simple	05-Jan-2026 03:12:45	Finalising the build...
simple	05-Jan-2026 03:12:45	Stopping timer.
simple	05-Jan-2026 03:12:45	Build JB-GDB734-JOB1-6 completed.
simple	05-Jan-2026 03:12:45	Running on server: post build plugin 'NCover Results Collector'
simple	05-Jan-2026 03:12:45	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	05-Jan-2026 03:12:45	Running on server: post build plugin 'Clover Delta Calculator'
simple	05-Jan-2026 03:12:45	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	05-Jan-2026 03:12:45	All post build plugins have finished
simple	05-Jan-2026 03:12:45	Generating build results summary...
simple	05-Jan-2026 03:12:45	Saving build results to disk...
simple	05-Jan-2026 03:12:45	Logging substituted variables...
simple	05-Jan-2026 03:12:45	Indexing build results...
simple	05-Jan-2026 03:12:45	Finished building JB-GDB734-JOB1-6.
simple	05-Jan-2026 05:00:18	Build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6) started building on agent Default Agent
simple	05-Jan-2026 05:00:18	
simple	05-Jan-2026 05:00:18	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1
simple	05-Jan-2026 05:00:18	Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6)
simple	05-Jan-2026 05:00:18	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	05-Jan-2026 05:00:18	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1
simple	05-Jan-2026 05:00:18	Updating source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5
simple	05-Jan-2026 05:00:18	Fetching 'refs/heads/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	05-Jan-2026 05:00:18	Checking out revision b6ff7e553d3ba8b32e1d2650df7860706b2a37d5.
simple	05-Jan-2026 05:00:18	Already on 'bug/JAL-4107_jalviewjs_fixes_on_2_12_branch'
simple	05-Jan-2026 05:00:18	Updated source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5
simple	05-Jan-2026 05:00:18	Finished task 'Checkout Default Repository' with result: Success
simple	05-Jan-2026 05:00:18	Running pre-build action: VCS Version Collector
simple	05-Jan-2026 05:00:18	Running pre-build action: Artifactory Release Staging
simple	05-Jan-2026 05:00:18	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	05-Jan-2026 05:00:18	Bamboo Artifactory Plugin version: 2.6.2
command	05-Jan-2026 05:00:18	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6)'\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-GDB734-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_CLOVER_CLASSES=1607\nbamboo_buildKey=JB-GDB734-JOB1\nbamboo_CLOVER_COVERED_CONDITIONALS=16926\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-GDB734-JOB1-6\nbamboo_CLOVER_STATEMENTS=121136\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_CLOVER_NCLOC=290874\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_planRepository_previousRevision=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_CLOVER_CONDITIONALS=45046\nbamboo_repository_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_46498616_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_CLOVER_PACKAGES=135\nbamboo_planRepository_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\n_=/usr/bin/java\nbamboo_CLOVER_COVERAGE_DELTA=-0.1\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\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\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_ManualBuildTriggerReason_userName=jprocter\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_planKey=JB-GDB734\nbamboo_planRepository_username=\nbamboo_repository_46498616_git_username=\nbamboo_repository_46498616_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_planRepository_1_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_CLOVER_ELEMENTS=184000\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-JOB1-6\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_CLOVER_BUILD_COVERAGE=40.8\nbamboo_CLOVER_METHODS=17818\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_CLOVER_COVERED_STATEMENTS=50445\nbamboo_repository_46498616_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498616_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=6\nSHELL=/bin/bash\nbamboo_ManualBuildTriggerReason_stageName=Default Stage\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_shortPlanKey=GDB734\nbamboo_shortJobKey=JOB1\nbamboo_buildTimeStamp=2026-01-05T05:00:18.274Z\nbamboo_repository_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_CLOVER_COVERED_METHODS=7764\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GDB734-JOB1-6\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests\nbamboo_planRepository_1_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_4=/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\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\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\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=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_planRepository_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_plan_storageTag=plan-46302801\nbamboo_CLOVER_LOC=460432\nbamboo_CLOVER_FILES=1270\nUSER=bamboo\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_CLOVER_COVERED_ELEMENTS=75135\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1\nbamboo_RerunBuildTriggerReason_noOfRetries=1\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498616_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_repository_46498616_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	05-Jan-2026 05:00:18	2414
build	05-Jan-2026 05:00:20	
build	05-Jan-2026 05:00:20	> Configure project :
build	05-Jan-2026 05:00:20	Using properties from file './utils/channels/default/channel_gradle.properties'
build	05-Jan-2026 05:00:20	JALVIEW_VERSION is set to '2.12.0'
build	05-Jan-2026 05:00:20	HEADLESS BUILD
build	05-Jan-2026 05:00:20	J2S ENABLED
build	05-Jan-2026 05:00:20	Using a LOCAL profile.
build	05-Jan-2026 05:00:20	eclipseDir exists
build	05-Jan-2026 05:00:21	
build	05-Jan-2026 05:00:21	> Task :clean
build	05-Jan-2026 05:00:21	> Task :cleanClover
build	05-Jan-2026 05:00:21	> Task :cleanTest UP-TO-DATE
build	05-Jan-2026 05:00:23	
build	05-Jan-2026 05:00:23	> Task :cloverInstrJava
build	05-Jan-2026 05:00:23	Clover: About to instrument 1253 files
build	05-Jan-2026 05:00:23	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	05-Jan-2026 05:00:23	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'.
build	05-Jan-2026 05:00:23	Processing files at 1.9 source level.
error	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:25	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	05-Jan-2026 05:00:26	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	05-Jan-2026 05:00:26	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	05-Jan-2026 05:00:26	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	05-Jan-2026 05:00:26	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	05-Jan-2026 05:00:26	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	05-Jan-2026 05:00:26	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	05-Jan-2026 05:00:26	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	05-Jan-2026 05:00:26	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	05-Jan-2026 05:00:26	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	05-Jan-2026 05:00:26	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	05-Jan-2026 05:00:26	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	05-Jan-2026 05:00:26	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	05-Jan-2026 05:00:31	Clover all over. Instrumented 1253 files (133 packages).
build	05-Jan-2026 05:00:33	
build	05-Jan-2026 05:00:33	> Task :cloverInstrTests
build	05-Jan-2026 05:00:33	Clover: About to instrument test files
build	05-Jan-2026 05:00:33	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	05-Jan-2026 05:00:33	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'.
build	05-Jan-2026 05:00:33	Processing files at 1.9 source level.
build	05-Jan-2026 05:00:36	Clover all over. Instrumented 315 files (58 packages).
build	05-Jan-2026 05:00:36	1770 test methods detected.
build	05-Jan-2026 05:00:36	
build	05-Jan-2026 05:00:36	> Task :cloverInstr
build	05-Jan-2026 05:00:38	
build	05-Jan-2026 05:00:38	> Task :compileCloverJava
build	05-Jan-2026 05:00:38	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	05-Jan-2026 05:00:38	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:00:38	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:00:38	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:00:38	Setting target compatibility to 11
error	05-Jan-2026 05:00:51	Note: Some input files use or override a deprecated API.
error	05-Jan-2026 05:00:51	Note: Recompile with -Xlint:deprecation for details.
error	05-Jan-2026 05:00:51	Note: Some input files use unchecked or unsafe operations.
error	05-Jan-2026 05:00:51	Note: Recompile with -Xlint:unchecked for details.
build	05-Jan-2026 05:00:57	
build	05-Jan-2026 05:00:57	> Task :processCloverResources NO-SOURCE
build	05-Jan-2026 05:00:57	> Task :cloverClasses
build	05-Jan-2026 05:00:57	> Task :copyHelp
build	05-Jan-2026 05:00:58	> Task :buildIndices
build	05-Jan-2026 05:00:58	> Task :copyResources
build	05-Jan-2026 05:00:58	> Task :copyChannelResources
build	05-Jan-2026 05:00:58	
build	05-Jan-2026 05:00:58	> Task :createBuildProperties
build	05-Jan-2026 05:00:58	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	05-Jan-2026 05:00:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:00:58	
build	05-Jan-2026 05:00:58	> Task :buildResources
build	05-Jan-2026 05:00:58	> Task :copyDocs
build	05-Jan-2026 05:00:58	
build	05-Jan-2026 05:00:58	> Task :convertMdFiles
build	05-Jan-2026 05:00:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	05-Jan-2026 05:00:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	05-Jan-2026 05:00:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	05-Jan-2026 05:00:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
build	05-Jan-2026 05:00:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/building.html
build	05-Jan-2026 05:00:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/addingWebClient.html
build	05-Jan-2026 05:00:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	05-Jan-2026 05:00:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
build	05-Jan-2026 05:00:59	
build	05-Jan-2026 05:00:59	> Task :releasesTemplates
build	05-Jan-2026 05:00:59	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	05-Jan-2026 05:00:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:00:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:00:59	Stripping rc/test/etc for TEST
build	05-Jan-2026 05:00:59	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	05-Jan-2026 05:00:59	
build	05-Jan-2026 05:00:59	> Task :prepare
build	05-Jan-2026 05:01:01	
build	05-Jan-2026 05:01:01	> Task :compileJava
build	05-Jan-2026 05:01:01	Setting target compatibility to 11
error	05-Jan-2026 05:01:05	Note: Some input files use or override a deprecated API.
error	05-Jan-2026 05:01:05	Note: Recompile with -Xlint:deprecation for details.
error	05-Jan-2026 05:01:05	Note: Some input files use unchecked or unsafe operations.
error	05-Jan-2026 05:01:05	Note: Recompile with -Xlint:unchecked for details.
build	05-Jan-2026 05:01:08	
build	05-Jan-2026 05:01:08	> Task :compileTestJava
build	05-Jan-2026 05:01:08	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	05-Jan-2026 05:01:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:01:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:01:08	Setting target compatibility to 11
error	05-Jan-2026 05:01:13	Note: Some input files use or override a deprecated API.
error	05-Jan-2026 05:01:13	Note: Recompile with -Xlint:deprecation for details.
error	05-Jan-2026 05:01:13	Note: Some input files use unchecked or unsafe operations.
error	05-Jan-2026 05:01:13	Note: Recompile with -Xlint:unchecked for details.
build	05-Jan-2026 05:01:14	
build	05-Jan-2026 05:01:14	> Task :processTestResources
build	05-Jan-2026 05:01:14	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	05-Jan-2026 05:01:14	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:01:14	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:01:14	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:01:14	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:01:14	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:01:14	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:01:14	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:01:14	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	05-Jan-2026 05:01:14	
build	05-Jan-2026 05:01:14	> Task :testClasses
build	05-Jan-2026 05:01:16	
build	05-Jan-2026 05:01:16	> Task :testTask0
build	05-Jan-2026 05:01:16	Running tests WITH clover
error	05-Jan-2026 05:01:17	WARNING: An illegal reflective access operation has occurred
error	05-Jan-2026 05:01:17	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	05-Jan-2026 05:01:17	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	05-Jan-2026 05:01:17	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	05-Jan-2026 05:01:17	WARNING: All illegal access operations will be denied in a future release
build	05-Jan-2026 05:02:06	
build	05-Jan-2026 05:02:06	Gradle suite > Gradle test > jalview.bin.CommandLineOperations > testHeadlessModeOutputOperations[7](headless -open examples/uniref50.fa,  -html, test/jalview/bin/test_uniref50_out.html, true, 4096, 15000, null) FAILED
build	05-Jan-2026 05:02:06	    java.lang.AssertionError: Didn't create an output -html file.[headless -open examples/uniref50.fa] expected [true] but found [false]
build	05-Jan-2026 05:02:06	        at org.testng.Assert.fail(Assert.java:110)
build	05-Jan-2026 05:02:06	        at org.testng.Assert.failNotEquals(Assert.java:1413)
build	05-Jan-2026 05:02:06	        at org.testng.Assert.assertTrue(Assert.java:56)
build	05-Jan-2026 05:02:06	        at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:343)
build	05-Jan-2026 05:03:46	
build	05-Jan-2026 05:03:46	Gradle suite > Gradle test > jalview.project.Jalview2xmlTests > noDuplicatePdbMappingsMade FAILED
build	05-Jan-2026 05:03:46	    java.lang.AssertionError: Expected only two mappings for 1A70 expected [2] but found [0]
build	05-Jan-2026 05:03:46	        at org.testng.Assert.fail(Assert.java:110)
build	05-Jan-2026 05:03:46	        at org.testng.Assert.failNotEquals(Assert.java:1413)
build	05-Jan-2026 05:03:46	        at org.testng.Assert.assertEqualsImpl(Assert.java:149)
build	05-Jan-2026 05:03:46	        at org.testng.Assert.assertEquals(Assert.java:131)
build	05-Jan-2026 05:03:46	        at org.testng.Assert.assertEquals(Assert.java:1240)
build	05-Jan-2026 05:03:46	        at jalview.project.Jalview2xmlTests.__CLR4_4_11umpz94jwy(Jalview2xmlTests.java:355)
build	05-Jan-2026 05:03:46	        at jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade(Jalview2xmlTests.java:331)
error	05-Jan-2026 05:05:39	
error	05-Jan-2026 05:05:39	2102 tests completed, 2 failed
build	05-Jan-2026 05:05:39	There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask0/index.html
build	05-Jan-2026 05:05:41	
build	05-Jan-2026 05:05:41	> Task :testTask1
build	05-Jan-2026 05:05:41	Running tests WITH clover
error	05-Jan-2026 05:05:42	WARNING: An illegal reflective access operation has occurred
error	05-Jan-2026 05:05:42	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	05-Jan-2026 05:05:42	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	05-Jan-2026 05:05:42	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	05-Jan-2026 05:05:42	WARNING: All illegal access operations will be denied in a future release
command	05-Jan-2026 05:05:45	Request to stop 'JB-GDB734-JOB1-6' received from jprocter
simple	05-Jan-2026 05:05:45	Exception executing command "/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test Interrupted while waiting for process to finishcom.atlassian.utils.process.ProcessException: Interrupted while waiting for process to finish
simple	05-Jan-2026 05:05:45	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 143 while expected 0
simple	05-Jan-2026 05:05:45	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	05-Jan-2026 05:05:45	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	05-Jan-2026 05:05:45	Bamboo Artifactory Plugin version: 2.6.2
command	05-Jan-2026 05:05:45	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6)'\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-GDB734-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_CLOVER_CLASSES=1607\nbamboo_buildKey=JB-GDB734-JOB1\nbamboo_CLOVER_COVERED_CONDITIONALS=16926\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-GDB734-JOB1-6\nbamboo_CLOVER_STATEMENTS=121136\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_CLOVER_NCLOC=290874\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_planRepository_previousRevision=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_CLOVER_CONDITIONALS=45046\nbamboo_repository_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_46498616_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_CLOVER_PACKAGES=135\nbamboo_planRepository_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\n_=/usr/bin/java\nbamboo_CLOVER_COVERAGE_DELTA=-0.1\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\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\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_ManualBuildTriggerReason_userName=jprocter\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_planKey=JB-GDB734\nbamboo_planRepository_username=\nbamboo_repository_46498616_git_username=\nbamboo_repository_46498616_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_planRepository_1_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_CLOVER_ELEMENTS=184000\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-JOB1-6\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_CLOVER_BUILD_COVERAGE=40.8\nbamboo_CLOVER_METHODS=17818\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_CLOVER_COVERED_STATEMENTS=50445\nbamboo_repository_46498616_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498616_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=6\nSHELL=/bin/bash\nbamboo_ManualBuildTriggerReason_stageName=Default Stage\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_shortPlanKey=GDB734\nbamboo_shortJobKey=JOB1\nbamboo_buildTimeStamp=2026-01-05T05:00:18.274Z\nbamboo_repository_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_CLOVER_COVERED_METHODS=7764\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GDB734-JOB1-6\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests\nbamboo_planRepository_1_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_4=/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\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\nLANG=en_GB.UTF-8\nbamboo_buildFailed=true\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_planRepository_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_plan_storageTag=plan-46302801\nbamboo_CLOVER_LOC=460432\nbamboo_CLOVER_FILES=1270\nUSER=bamboo\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_CLOVER_COVERED_ELEMENTS=75135\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1\nbamboo_RerunBuildTriggerReason_noOfRetries=1\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498616_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_repository_46498616_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	05-Jan-2026 05:05:45	2414
build	05-Jan-2026 05:05:52	
build	05-Jan-2026 05:05:52	> Configure project :
build	05-Jan-2026 05:05:52	Using properties from file './utils/channels/default/channel_gradle.properties'
build	05-Jan-2026 05:05:52	JALVIEW_VERSION is set to '2.12.0'
build	05-Jan-2026 05:05:52	HEADLESS BUILD
build	05-Jan-2026 05:05:52	J2S ENABLED
build	05-Jan-2026 05:05:52	Using a LOCAL profile.
build	05-Jan-2026 05:05:53	eclipseDir exists
build	05-Jan-2026 05:05:55	
build	05-Jan-2026 05:05:55	> Task :cloverHtmlReport
build	05-Jan-2026 05:05:55	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	05-Jan-2026 05:06:00	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover'
error	05-Jan-2026 05:06:07	ERROR: Invalid Java source found or Clover failed to parse it: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/src/jalview/gui/AlignFrame.java
error	05-Jan-2026 05:06:46	Build JB-GDB734-JOB1-6 had to be cancelled: agent had been requested to stop the build but sent no response
build	05-Jan-2026 05:06:56	Done. Processed 137 packages in 56180ms (410ms per package).
build	05-Jan-2026 05:07:06	
build	05-Jan-2026 05:07:06	> Task :cloverXmlReport
build	05-Jan-2026 05:07:06	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	05-Jan-2026 05:07:13	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover/clover.xml'
build	05-Jan-2026 05:07:14	
build	05-Jan-2026 05:07:14	> Task :cloverReport
build	05-Jan-2026 05:07:14	
build	05-Jan-2026 05:07:14	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	05-Jan-2026 05:07:14	
build	05-Jan-2026 05:07:14	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	05-Jan-2026 05:07:14	
build	05-Jan-2026 05:07:14	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	05-Jan-2026 05:07:14	
build	05-Jan-2026 05:07:14	BUILD SUCCESSFUL in 1m 28s
build	05-Jan-2026 05:07:14	2 actionable tasks: 2 executed
simple	05-Jan-2026 05:07:14	Finished task 'Clover Report' with result: Success
simple	05-Jan-2026 05:07:14	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	05-Jan-2026 05:07:14	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1...
simple	05-Jan-2026 05:07:14	Failing task since 2 failing test cases were found.
simple	05-Jan-2026 05:07:14	Finished task 'TestNG Parser' with result: Failed
simple	05-Jan-2026 05:07:14	Running post build plugin 'NCover Results Collector'
simple	05-Jan-2026 05:07:14	Running post build plugin 'Artifact Copier'
simple	05-Jan-2026 05:07:16	Running post build plugin 'Artifactory Release Management Staging'
simple	05-Jan-2026 05:07:16	Running post build plugin 'Artifactory Build Info Copier'
simple	05-Jan-2026 05:07:16	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	05-Jan-2026 05:07:16	Running post build plugin 'npm Cache Cleanup'
simple	05-Jan-2026 05:07:16	Running post build plugin 'Clover Results Collector'
simple	05-Jan-2026 05:07:16	Running post build plugin 'Docker Container Cleanup'
simple	05-Jan-2026 05:07:16	Finalising the build...
simple	05-Jan-2026 05:07:16	Stopping timer.
simple	05-Jan-2026 05:07:16	Build JB-GDB734-JOB1-6 completed.
simple	05-Jan-2026 05:07:14	Publishing an artifact: Clover Report (System)
simple	05-Jan-2026 05:07:16	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.102 s
simple	05-Jan-2026 05:07:16	Publishing an artifact: TestNG report
error	05-Jan-2026 05:07:16	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/test does not exist.
simple	05-Jan-2026 05:07:16	The artifact hasn't been successfully published after 88.60 μs