simple	07-Jan-2026 02:48:48	Build Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests #3 (JB-GDB738-JOB1-3) started building on agent Default Agent
simple	07-Jan-2026 02:48:48	
simple	07-Jan-2026 02:48:48	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1
simple	07-Jan-2026 02:48:48	Executing build Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests #3 (JB-GDB738-JOB1-3)
simple	07-Jan-2026 02:48:48	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	07-Jan-2026 02:48:48	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1
simple	07-Jan-2026 02:48:48	Updating source code to revision: 89c895478e2de885c6475780e1191e8b19fe1dff
simple	07-Jan-2026 02:48:48	Fetching 'refs/heads/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	07-Jan-2026 02:48:49	Checking out revision 89c895478e2de885c6475780e1191e8b19fe1dff.
simple	07-Jan-2026 02:48:49	Already on 'feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp'
simple	07-Jan-2026 02:48:49	Updated source code to revision: 89c895478e2de885c6475780e1191e8b19fe1dff
simple	07-Jan-2026 02:48:49	Finished task 'Checkout Default Repository' with result: Success
simple	07-Jan-2026 02:48:49	Running pre-build action: VCS Version Collector
simple	07-Jan-2026 02:48:49	Running pre-build action: Artifactory Release Staging
simple	07-Jan-2026 02:48:49	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	07-Jan-2026 02:48:49	Bamboo Artifactory Plugin version: 2.6.2
command	07-Jan-2026 02:48:49	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests #3 (JB-GDB738-JOB1-3)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_repository_revision_number=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB738-JOB1-3\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-GDB738-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB738-JOB1\nbamboo_shortPlanName=feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_repository_48168979_name=Jalview Gitlab\nbamboo_buildNumber=3\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB738-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_shortPlanKey=GDB738\nbamboo_shortJobKey=JOB1\nbamboo_repository_48168979_git_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_buildTimeStamp=2026-01-07T02:48:48.608Z\nbamboo_repository_previous_revision_number=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_planRepository_previousRevision=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_repository_48168979_branch_name=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_repository_git_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_buildResultKey=JB-GDB738-JOB1-3\nbamboo_repository_branch_name=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - 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build	07-Jan-2026 02:48:49	2414
build	07-Jan-2026 02:48:50	
build	07-Jan-2026 02:48:50	> Configure project :
build	07-Jan-2026 02:48:50	Using properties from file './utils/channels/default/channel_gradle.properties'
build	07-Jan-2026 02:48:50	JALVIEW_VERSION is set to '2.12.0'
build	07-Jan-2026 02:48:50	HEADLESS BUILD
build	07-Jan-2026 02:48:50	J2S ENABLED
build	07-Jan-2026 02:48:50	Using a LOCAL profile.
build	07-Jan-2026 02:48:50	eclipseDir exists
build	07-Jan-2026 02:48:50	
build	07-Jan-2026 02:48:50	> Task :clean
build	07-Jan-2026 02:48:50	> Task :cleanClover
build	07-Jan-2026 02:48:50	> Task :cleanTest UP-TO-DATE
build	07-Jan-2026 02:48:52	
build	07-Jan-2026 02:48:52	> Task :cloverInstrJava
build	07-Jan-2026 02:48:52	Clover: About to instrument 1255 files
build	07-Jan-2026 02:48:52	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	07-Jan-2026 02:48:52	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover.db'.
build	07-Jan-2026 02:48:52	Processing files at 1.9 source level.
error	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:48:55	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	07-Jan-2026 02:49:01	Clover all over. Instrumented 1255 files (133 packages).
build	07-Jan-2026 02:49:03	
build	07-Jan-2026 02:49:03	> Task :cloverInstrTests
build	07-Jan-2026 02:49:03	Clover: About to instrument test files
build	07-Jan-2026 02:49:03	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	07-Jan-2026 02:49:03	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover.db'.
build	07-Jan-2026 02:49:03	Processing files at 1.9 source level.
build	07-Jan-2026 02:49:05	Clover all over. Instrumented 316 files (58 packages).
build	07-Jan-2026 02:49:05	1774 test methods detected.
build	07-Jan-2026 02:49:05	
build	07-Jan-2026 02:49:05	> Task :cloverInstr
build	07-Jan-2026 02:49:07	
build	07-Jan-2026 02:49:07	> Task :compileCloverJava
build	07-Jan-2026 02:49:07	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	07-Jan-2026 02:49:07	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:07	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:07	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:07	Setting target compatibility to 11
error	07-Jan-2026 02:49:19	Note: Some input files use or override a deprecated API.
error	07-Jan-2026 02:49:19	Note: Recompile with -Xlint:deprecation for details.
error	07-Jan-2026 02:49:19	Note: Some input files use unchecked or unsafe operations.
error	07-Jan-2026 02:49:19	Note: Recompile with -Xlint:unchecked for details.
build	07-Jan-2026 02:49:24	
build	07-Jan-2026 02:49:24	> Task :processCloverResources NO-SOURCE
build	07-Jan-2026 02:49:24	> Task :cloverClasses
build	07-Jan-2026 02:49:24	> Task :copyHelp
build	07-Jan-2026 02:49:25	> Task :buildIndices
build	07-Jan-2026 02:49:25	> Task :copyResources
build	07-Jan-2026 02:49:25	> Task :copyChannelResources
build	07-Jan-2026 02:49:25	
build	07-Jan-2026 02:49:25	> Task :createBuildProperties
build	07-Jan-2026 02:49:25	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	07-Jan-2026 02:49:25	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:25	
build	07-Jan-2026 02:49:25	> Task :buildResources
build	07-Jan-2026 02:49:25	> Task :copyDocs
build	07-Jan-2026 02:49:25	
build	07-Jan-2026 02:49:25	> Task :convertMdFiles
build	07-Jan-2026 02:49:25	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	07-Jan-2026 02:49:25	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	07-Jan-2026 02:49:25	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	07-Jan-2026 02:49:25	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
build	07-Jan-2026 02:49:25	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/building.html
build	07-Jan-2026 02:49:25	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/addingWebClient.html
build	07-Jan-2026 02:49:25	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	07-Jan-2026 02:49:25	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
build	07-Jan-2026 02:49:26	
build	07-Jan-2026 02:49:26	> Task :releasesTemplates
build	07-Jan-2026 02:49:26	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	07-Jan-2026 02:49:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:26	Stripping rc/test/etc for TEST
build	07-Jan-2026 02:49:26	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	07-Jan-2026 02:49:26	
build	07-Jan-2026 02:49:26	> Task :prepare
build	07-Jan-2026 02:49:28	
build	07-Jan-2026 02:49:28	> Task :compileJava
build	07-Jan-2026 02:49:28	Setting target compatibility to 11
error	07-Jan-2026 02:49:32	Note: Some input files use or override a deprecated API.
error	07-Jan-2026 02:49:32	Note: Recompile with -Xlint:deprecation for details.
error	07-Jan-2026 02:49:32	Note: Some input files use unchecked or unsafe operations.
error	07-Jan-2026 02:49:32	Note: Recompile with -Xlint:unchecked for details.
build	07-Jan-2026 02:49:35	
build	07-Jan-2026 02:49:35	> Task :compileTestJava
build	07-Jan-2026 02:49:35	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	07-Jan-2026 02:49:35	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:35	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:35	Setting target compatibility to 11
error	07-Jan-2026 02:49:39	Note: Some input files use or override a deprecated API.
error	07-Jan-2026 02:49:39	Note: Recompile with -Xlint:deprecation for details.
error	07-Jan-2026 02:49:39	Note: Some input files use unchecked or unsafe operations.
error	07-Jan-2026 02:49:39	Note: Recompile with -Xlint:unchecked for details.
build	07-Jan-2026 02:49:40	
build	07-Jan-2026 02:49:40	> Task :processTestResources
build	07-Jan-2026 02:49:40	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	07-Jan-2026 02:49:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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	07-Jan-2026 02:49:40	
build	07-Jan-2026 02:49:40	> Task :testClasses
build	07-Jan-2026 02:49:42	
build	07-Jan-2026 02:49:42	> Task :testTask0
build	07-Jan-2026 02:49:42	Running tests WITH clover
error	07-Jan-2026 02:49:43	WARNING: An illegal reflective access operation has occurred
error	07-Jan-2026 02:49:43	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	07-Jan-2026 02:49:43	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	07-Jan-2026 02:49:43	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	07-Jan-2026 02:49:43	WARNING: All illegal access operations will be denied in a future release
build	07-Jan-2026 02:52:09	[148.377s][warning][gc,alloc] AWT-EventQueue-0: Retried waiting for GCLocker too often allocating 135080516 words
build	07-Jan-2026 02:54:20	
build	07-Jan-2026 02:54:20	> Task :testTask1
build	07-Jan-2026 02:54:20	Running tests WITH clover
error	07-Jan-2026 02:54:21	WARNING: An illegal reflective access operation has occurred
error	07-Jan-2026 02:54:21	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	07-Jan-2026 02:54:21	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	07-Jan-2026 02:54:21	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	07-Jan-2026 02:54:21	WARNING: All illegal access operations will be denied in a future release
build	07-Jan-2026 02:56:21	
build	07-Jan-2026 02:56:21	> Task :testTask2
build	07-Jan-2026 02:56:21	Running tests WITH clover
error	07-Jan-2026 02:56:22	WARNING: An illegal reflective access operation has occurred
error	07-Jan-2026 02:56:22	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	07-Jan-2026 02:56:22	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	07-Jan-2026 02:56:22	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	07-Jan-2026 02:56:22	WARNING: All illegal access operations will be denied in a future release
build	07-Jan-2026 02:56:26	
build	07-Jan-2026 02:56:26	> Task :testTask3
build	07-Jan-2026 02:56:26	Running tests WITH clover
error	07-Jan-2026 02:56:27	WARNING: An illegal reflective access operation has occurred
error	07-Jan-2026 02:56:27	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	07-Jan-2026 02:56:27	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	07-Jan-2026 02:56:27	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	07-Jan-2026 02:56:27	WARNING: All illegal access operations will be denied in a future release
build	07-Jan-2026 02:56:44	
build	07-Jan-2026 02:56:44	> Task :test NO-SOURCE
build	07-Jan-2026 02:56:44	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	07-Jan-2026 02:56:44	│jalview:testTask0 results: SUCCESS (2107 tests, 2107 successes, 0 failures, 0 skipped) in 4 minutes, 37.769 seconds   │
build	07-Jan-2026 02:56:44	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/testTask0/index.html│
build	07-Jan-2026 02:56:44	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	07-Jan-2026 02:56:44	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 0.858 seconds        │
build	07-Jan-2026 02:56:44	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/testTask1/index.html│
build	07-Jan-2026 02:56:44	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	07-Jan-2026 02:56:44	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.675 seconds                     │
build	07-Jan-2026 02:56:44	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/testTask2/index.html│
build	07-Jan-2026 02:56:44	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	07-Jan-2026 02:56:44	│jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 19.714 seconds                  │
build	07-Jan-2026 02:56:44	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/testTask3/index.html│
build	07-Jan-2026 02:56:44	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	07-Jan-2026 02:56:44	│OVERALL: results: SUCCESS (2184 tests, 2183 successes, 0 failures, 1 skipped) in 6 minutes, 63.016 seconds            │
build	07-Jan-2026 02:56:44	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	07-Jan-2026 02:56:44	
build	07-Jan-2026 02:56:44	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	07-Jan-2026 02:56:44	
build	07-Jan-2026 02:56:44	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	07-Jan-2026 02:56:44	
build	07-Jan-2026 02:56:44	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	07-Jan-2026 02:56:44	
build	07-Jan-2026 02:56:44	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	07-Jan-2026 02:56:44	Please consult deprecation warnings for more details.
build	07-Jan-2026 02:56:44	
build	07-Jan-2026 02:56:44	BUILD SUCCESSFUL in 7m 55s
build	07-Jan-2026 02:56:44	21 actionable tasks: 20 executed, 1 up-to-date
simple	07-Jan-2026 02:56:44	Finished task 'Run tests with openclover under gradle' with result: Success
simple	07-Jan-2026 02:56:44	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	07-Jan-2026 02:56:44	Bamboo Artifactory Plugin version: 2.6.2
command	07-Jan-2026 02:56:44	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests #3 (JB-GDB738-JOB1-3)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_repository_revision_number=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB738-JOB1-3\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-GDB738-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB738-JOB1\nbamboo_shortPlanName=feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_repository_48168979_name=Jalview Gitlab\nbamboo_buildNumber=3\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB738-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_shortPlanKey=GDB738\nbamboo_shortJobKey=JOB1\nbamboo_repository_48168979_git_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_buildTimeStamp=2026-01-07T02:48:48.608Z\nbamboo_repository_previous_revision_number=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_planRepository_previousRevision=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_repository_48168979_branch_name=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_repository_git_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_buildResultKey=JB-GDB738-JOB1-3\nbamboo_repository_branch_name=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=89c895478e2de885c6475780e1191e8b19fe1dff\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_dependenciesDisabled=false\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_repository_48168979_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_48168979_git_username=\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_planRepository_branchDisplayName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_repository_48168979_previous_revision_number=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_48168979_revision_number=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-47972389\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_ManualBuildTriggerReason_userName=jprocter\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1\nbamboo_planKey=JB-GDB738\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	07-Jan-2026 02:56:44	2414
build	07-Jan-2026 02:56:49	
build	07-Jan-2026 02:56:49	> Configure project :
build	07-Jan-2026 02:56:49	Using properties from file './utils/channels/default/channel_gradle.properties'
build	07-Jan-2026 02:56:49	JALVIEW_VERSION is set to '2.12.0'
build	07-Jan-2026 02:56:49	HEADLESS BUILD
build	07-Jan-2026 02:56:49	J2S ENABLED
build	07-Jan-2026 02:56:49	Using a LOCAL profile.
build	07-Jan-2026 02:56:50	eclipseDir exists
build	07-Jan-2026 02:56:52	
build	07-Jan-2026 02:56:52	> Task :cloverHtmlReport
build	07-Jan-2026 02:56:52	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	07-Jan-2026 02:56:53	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/clover'
error	07-Jan-2026 02:57:37	ERROR: Invalid Java source found or Clover failed to parse it: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/src/jalview/schemes/ResidueProperties.java
build	07-Jan-2026 02:57:43	Done. Processed 137 packages in 49260ms (359ms per package).
build	07-Jan-2026 02:57:48	
build	07-Jan-2026 02:57:48	> Task :cloverXmlReport
build	07-Jan-2026 02:57:48	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	07-Jan-2026 02:57:49	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/clover/clover.xml'
build	07-Jan-2026 02:57:49	
build	07-Jan-2026 02:57:49	> Task :cloverReport
build	07-Jan-2026 02:57:49	
build	07-Jan-2026 02:57:49	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	07-Jan-2026 02:57:49	
build	07-Jan-2026 02:57:49	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	07-Jan-2026 02:57:49	
build	07-Jan-2026 02:57:49	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	07-Jan-2026 02:57:49	
build	07-Jan-2026 02:57:49	BUILD SUCCESSFUL in 1m 4s
build	07-Jan-2026 02:57:49	2 actionable tasks: 2 executed
simple	07-Jan-2026 02:57:49	Finished task 'Clover Report' with result: Success
simple	07-Jan-2026 02:57:49	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	07-Jan-2026 02:57:49	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1...
simple	07-Jan-2026 02:57:49	Finished task 'TestNG Parser' with result: Success
simple	07-Jan-2026 02:57:49	Running post build plugin 'NCover Results Collector'
simple	07-Jan-2026 02:57:49	Running post build plugin 'Artifact Copier'
simple	07-Jan-2026 02:57:49	Publishing an artifact: Clover Report (System)
simple	07-Jan-2026 02:57:51	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.940 s
simple	07-Jan-2026 02:57:51	Publishing an artifact: TestNG report
error	07-Jan-2026 02:57:51	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/test does not exist.
simple	07-Jan-2026 02:57:51	The artifact hasn't been successfully published after 1.379 ms
simple	07-Jan-2026 02:57:51	Running post build plugin 'Artifactory Release Management Staging'
simple	07-Jan-2026 02:57:51	Running post build plugin 'Artifactory Build Info Copier'
simple	07-Jan-2026 02:57:51	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	07-Jan-2026 02:57:51	Running post build plugin 'npm Cache Cleanup'
simple	07-Jan-2026 02:57:51	Running post build plugin 'Clover Results Collector'
simple	07-Jan-2026 02:57:51	Running post build plugin 'Docker Container Cleanup'
simple	07-Jan-2026 02:57:51	Finalising the build...
simple	07-Jan-2026 02:57:51	Stopping timer.
simple	07-Jan-2026 02:57:51	Build JB-GDB738-JOB1-3 completed.
simple	07-Jan-2026 02:57:51	Running on server: post build plugin 'NCover Results Collector'
simple	07-Jan-2026 02:57:51	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	07-Jan-2026 02:57:51	Running on server: post build plugin 'Clover Delta Calculator'
simple	07-Jan-2026 02:57:51	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	07-Jan-2026 02:57:51	All post build plugins have finished
simple	07-Jan-2026 02:57:51	Generating build results summary...
simple	07-Jan-2026 02:57:51	Saving build results to disk...
simple	07-Jan-2026 02:57:51	Logging substituted variables...
simple	07-Jan-2026 02:57:51	Indexing build results...
simple	07-Jan-2026 02:57:51	Finished building JB-GDB738-JOB1-3.