simple	06-Jan-2026 03:20:51	Build Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests #6 (JB-GDB732-JOB1-6) started building on agent Default Agent
simple	06-Jan-2026 03:20:51	
simple	06-Jan-2026 03:20:51	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1
simple	06-Jan-2026 03:20:51	Executing build Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests #6 (JB-GDB732-JOB1-6)
simple	06-Jan-2026 03:20:51	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	06-Jan-2026 03:20:51	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1
simple	06-Jan-2026 03:20:51	Updating source code to revision: 1f2ba28869776942e4726500e9264371cd278e90
simple	06-Jan-2026 03:20:51	Fetching 'refs/heads/development/Release_2_12_Branch' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	06-Jan-2026 03:20:52	Checking out revision 1f2ba28869776942e4726500e9264371cd278e90.
simple	06-Jan-2026 03:20:52	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	06-Jan-2026 03:20:52	   ba2177b..1f2ba28  development/Release_2_12_Branch -> origin/development/Release_2_12_Branch
simple	06-Jan-2026 03:20:52	Already on 'development/Release_2_12_Branch'
simple	06-Jan-2026 03:20:52	Your branch is behind 'origin/development/Release_2_12_Branch' by 1 commit, and can be fast-forwarded.
simple	06-Jan-2026 03:20:52	  (use "git pull" to update your local branch)
simple	06-Jan-2026 03:20:52	HEAD is now at 1f2ba28 JAL-4107 JAL-4640 fix broken getInstance and patched out ops on local Hmmer preference widgets not initialised in JalviewJS
simple	06-Jan-2026 03:20:52	Updated source code to revision: 1f2ba28869776942e4726500e9264371cd278e90
simple	06-Jan-2026 03:20:52	Finished task 'Checkout Default Repository' with result: Success
simple	06-Jan-2026 03:20:52	Running pre-build action: VCS Version Collector
simple	06-Jan-2026 03:20:52	Running pre-build action: Artifactory Release Staging
simple	06-Jan-2026 03:20:52	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	06-Jan-2026 03:20:52	Bamboo Artifactory Plugin version: 2.6.2
command	06-Jan-2026 03:20:52	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests #6 (JB-GDB732-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-GDB732-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_12_Branch\nbamboo_repository_46498611_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=development/Release_2_12_Branch\nbamboo_repository_revision_number=1f2ba28869776942e4726500e9264371cd278e90\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB732-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-GDB732-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB732-JOB1\nbamboo_shortPlanName=development-Release_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-GDB732-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 - development-Release_2_12_Branch\nbamboo_shortPlanKey=GDB732\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1f2ba28869776942e4726500e9264371cd278e90\nbamboo_buildTimeStamp=2026-01-06T03:18:22.644Z\nbamboo_repository_previous_revision_number=ba2177bba3a1e2417aec91f5283bcd923c650917\nbamboo_planRepository_previousRevision=ba2177bba3a1e2417aec91f5283bcd923c650917\nbamboo_repository_git_branch=development/Release_2_12_Branch\nbamboo_buildResultKey=JB-GDB732-JOB1-6\nbamboo_repository_branch_name=development/Release_2_12_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=1f2ba28869776942e4726500e9264371cd278e90\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498611_revision_number=1f2ba28869776942e4726500e9264371cd278e90\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46498611_git_branch=development/Release_2_12_Branch\nbamboo_planRepository_branch=development/Release_2_12_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_repository_46498611_git_username=\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=ba2177bba3a1e2417aec91f5283bcd923c650917\nbamboo_repository_46498611_name=Jalview Gitlab\nbamboo_repository_46498611_previous_revision_number=ba2177bba3a1e2417aec91f5283bcd923c650917\nbamboo_planRepository_branchDisplayName=development/Release_2_12_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=development/Release_2_12_Branch\nbamboo_repository_46498611_branch_name=development/Release_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-46302793\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-GDB732-JOB1\nbamboo_planKey=JB-GDB732\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=development/Release_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	06-Jan-2026 03:20:52	2414
build	06-Jan-2026 03:20:53	
build	06-Jan-2026 03:20:53	> Configure project :
build	06-Jan-2026 03:20:53	Using properties from file './utils/channels/default/channel_gradle.properties'
build	06-Jan-2026 03:20:53	JALVIEW_VERSION is set to '2.12.0'
build	06-Jan-2026 03:20:53	HEADLESS BUILD
build	06-Jan-2026 03:20:53	J2S ENABLED
build	06-Jan-2026 03:20:53	Using a LOCAL profile.
build	06-Jan-2026 03:20:53	eclipseDir exists
build	06-Jan-2026 03:20:54	
build	06-Jan-2026 03:20:54	> Task :clean
build	06-Jan-2026 03:20:54	> Task :cleanClover
build	06-Jan-2026 03:20:54	> Task :cleanTest UP-TO-DATE
build	06-Jan-2026 03:20:56	
build	06-Jan-2026 03:20:56	> Task :cloverInstrJava
build	06-Jan-2026 03:20:56	Clover: About to instrument 1253 files
build	06-Jan-2026 03:20:56	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	06-Jan-2026 03:20:56	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover.db'.
build	06-Jan-2026 03:20:56	Processing files at 1.9 source level.
error	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:58	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:20:59	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	06-Jan-2026 03:21:05	Clover all over. Instrumented 1253 files (133 packages).
build	06-Jan-2026 03:21:07	
build	06-Jan-2026 03:21:07	> Task :cloverInstrTests
build	06-Jan-2026 03:21:07	Clover: About to instrument test files
build	06-Jan-2026 03:21:07	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	06-Jan-2026 03:21:07	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover.db'.
build	06-Jan-2026 03:21:07	Processing files at 1.9 source level.
build	06-Jan-2026 03:21:09	Clover all over. Instrumented 315 files (58 packages).
build	06-Jan-2026 03:21:09	1770 test methods detected.
build	06-Jan-2026 03:21:10	
build	06-Jan-2026 03:21:10	> Task :cloverInstr
build	06-Jan-2026 03:21:12	
build	06-Jan-2026 03:21:12	> Task :compileCloverJava
build	06-Jan-2026 03:21:12	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	06-Jan-2026 03:21:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:12	Setting target compatibility to 11
error	06-Jan-2026 03:21:25	Note: Some input files use or override a deprecated API.
error	06-Jan-2026 03:21:25	Note: Recompile with -Xlint:deprecation for details.
error	06-Jan-2026 03:21:25	Note: Some input files use unchecked or unsafe operations.
error	06-Jan-2026 03:21:25	Note: Recompile with -Xlint:unchecked for details.
build	06-Jan-2026 03:21:30	
build	06-Jan-2026 03:21:30	> Task :processCloverResources NO-SOURCE
build	06-Jan-2026 03:21:30	> Task :cloverClasses
build	06-Jan-2026 03:21:30	> Task :copyHelp
build	06-Jan-2026 03:21:31	> Task :buildIndices
build	06-Jan-2026 03:21:31	> Task :copyResources
build	06-Jan-2026 03:21:31	> Task :copyChannelResources
build	06-Jan-2026 03:21:31	
build	06-Jan-2026 03:21:31	> Task :createBuildProperties
build	06-Jan-2026 03:21:31	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	06-Jan-2026 03:21:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:31	
build	06-Jan-2026 03:21:31	> Task :buildResources
build	06-Jan-2026 03:21:31	> Task :copyDocs
build	06-Jan-2026 03:21:31	
build	06-Jan-2026 03:21:31	> Task :convertMdFiles
build	06-Jan-2026 03:21:31	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	06-Jan-2026 03:21:31	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	06-Jan-2026 03:21:31	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	06-Jan-2026 03:21:31	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
build	06-Jan-2026 03:21:31	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/building.html
build	06-Jan-2026 03:21:31	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/addingWebClient.html
build	06-Jan-2026 03:21:31	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	06-Jan-2026 03:21:31	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
build	06-Jan-2026 03:21:32	
build	06-Jan-2026 03:21:32	> Task :releasesTemplates
build	06-Jan-2026 03:21:32	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	06-Jan-2026 03:21:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:32	Stripping rc/test/etc for TEST
build	06-Jan-2026 03:21:32	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	06-Jan-2026 03:21:32	
build	06-Jan-2026 03:21:32	> Task :prepare
build	06-Jan-2026 03:21:34	
build	06-Jan-2026 03:21:34	> Task :compileJava
build	06-Jan-2026 03:21:34	Setting target compatibility to 11
error	06-Jan-2026 03:21:38	Note: Some input files use or override a deprecated API.
error	06-Jan-2026 03:21:38	Note: Recompile with -Xlint:deprecation for details.
error	06-Jan-2026 03:21:38	Note: Some input files use unchecked or unsafe operations.
error	06-Jan-2026 03:21:38	Note: Recompile with -Xlint:unchecked for details.
build	06-Jan-2026 03:21:41	
build	06-Jan-2026 03:21:41	> Task :compileTestJava
build	06-Jan-2026 03:21:41	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	06-Jan-2026 03:21:41	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:41	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:41	Setting target compatibility to 11
error	06-Jan-2026 03:21:46	Note: Some input files use or override a deprecated API.
error	06-Jan-2026 03:21:46	Note: Recompile with -Xlint:deprecation for details.
error	06-Jan-2026 03:21:46	Note: Some input files use unchecked or unsafe operations.
error	06-Jan-2026 03:21:46	Note: Recompile with -Xlint:unchecked for details.
build	06-Jan-2026 03:21:47	
build	06-Jan-2026 03:21:47	> Task :processTestResources
build	06-Jan-2026 03:21:47	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	06-Jan-2026 03:21:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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	06-Jan-2026 03:21:47	
build	06-Jan-2026 03:21:47	> Task :testClasses
build	06-Jan-2026 03:21:49	
build	06-Jan-2026 03:21:49	> Task :testTask0
build	06-Jan-2026 03:21:49	Running tests WITH clover
error	06-Jan-2026 03:21:50	WARNING: An illegal reflective access operation has occurred
error	06-Jan-2026 03:21:50	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	06-Jan-2026 03:21:50	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	06-Jan-2026 03:21:50	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	06-Jan-2026 03:21:50	WARNING: All illegal access operations will be denied in a future release
build	06-Jan-2026 03:26:15	
build	06-Jan-2026 03:26:15	> Task :testTask1
build	06-Jan-2026 03:26:15	Running tests WITH clover
error	06-Jan-2026 03:26:16	WARNING: An illegal reflective access operation has occurred
error	06-Jan-2026 03:26:16	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	06-Jan-2026 03:26:16	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	06-Jan-2026 03:26:16	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	06-Jan-2026 03:26:16	WARNING: All illegal access operations will be denied in a future release
build	06-Jan-2026 03:28:22	
build	06-Jan-2026 03:28:22	> Task :testTask2
build	06-Jan-2026 03:28:22	Running tests WITH clover
error	06-Jan-2026 03:28:23	WARNING: An illegal reflective access operation has occurred
error	06-Jan-2026 03:28:23	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	06-Jan-2026 03:28:23	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	06-Jan-2026 03:28:23	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	06-Jan-2026 03:28:23	WARNING: All illegal access operations will be denied in a future release
build	06-Jan-2026 03:28:27	
build	06-Jan-2026 03:28:27	> Task :testTask3
build	06-Jan-2026 03:28:27	Running tests WITH clover
error	06-Jan-2026 03:28:28	WARNING: An illegal reflective access operation has occurred
error	06-Jan-2026 03:28:28	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	06-Jan-2026 03:28:28	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	06-Jan-2026 03:28:28	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	06-Jan-2026 03:28:28	WARNING: All illegal access operations will be denied in a future release
build	06-Jan-2026 03:28:45	
build	06-Jan-2026 03:28:45	> Task :test NO-SOURCE
build	06-Jan-2026 03:28:45	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	06-Jan-2026 03:28:45	│jalview:testTask0 results: SUCCESS (2103 tests, 2103 successes, 0 failures, 0 skipped) in 4 minutes, 26.147 seconds   │
build	06-Jan-2026 03:28:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/testTask0/index.html│
build	06-Jan-2026 03:28:45	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	06-Jan-2026 03:28:45	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 6.906 seconds        │
build	06-Jan-2026 03:28:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/testTask1/index.html│
build	06-Jan-2026 03:28:45	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	06-Jan-2026 03:28:45	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.655 seconds                     │
build	06-Jan-2026 03:28:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/testTask2/index.html│
build	06-Jan-2026 03:28:45	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	06-Jan-2026 03:28:45	│jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 20.008 seconds                  │
build	06-Jan-2026 03:28:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/testTask3/index.html│
build	06-Jan-2026 03:28:45	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	06-Jan-2026 03:28:45	│OVERALL: results: SUCCESS (2180 tests, 2179 successes, 0 failures, 1 skipped) in 6 minutes, 57.716 seconds            │
build	06-Jan-2026 03:28:45	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	06-Jan-2026 03:28:45	
build	06-Jan-2026 03:28:45	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	06-Jan-2026 03:28:45	
build	06-Jan-2026 03:28:45	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	06-Jan-2026 03:28:45	
build	06-Jan-2026 03:28:45	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	06-Jan-2026 03:28:45	
build	06-Jan-2026 03:28:45	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	06-Jan-2026 03:28:45	Please consult deprecation warnings for more details.
build	06-Jan-2026 03:28:45	
build	06-Jan-2026 03:28:45	BUILD SUCCESSFUL in 7m 52s
build	06-Jan-2026 03:28:45	21 actionable tasks: 20 executed, 1 up-to-date
simple	06-Jan-2026 03:28:45	Finished task 'Run tests with openclover under gradle' with result: Success
simple	06-Jan-2026 03:28:45	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	06-Jan-2026 03:28:45	Bamboo Artifactory Plugin version: 2.6.2
command	06-Jan-2026 03:28:45	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests #6 (JB-GDB732-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-GDB732-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_12_Branch\nbamboo_repository_46498611_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=development/Release_2_12_Branch\nbamboo_repository_revision_number=1f2ba28869776942e4726500e9264371cd278e90\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB732-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-GDB732-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB732-JOB1\nbamboo_shortPlanName=development-Release_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-GDB732-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 - development-Release_2_12_Branch\nbamboo_shortPlanKey=GDB732\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1f2ba28869776942e4726500e9264371cd278e90\nbamboo_buildTimeStamp=2026-01-06T03:18:22.644Z\nbamboo_repository_previous_revision_number=ba2177bba3a1e2417aec91f5283bcd923c650917\nbamboo_planRepository_previousRevision=ba2177bba3a1e2417aec91f5283bcd923c650917\nbamboo_repository_git_branch=development/Release_2_12_Branch\nbamboo_buildResultKey=JB-GDB732-JOB1-6\nbamboo_repository_branch_name=development/Release_2_12_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=1f2ba28869776942e4726500e9264371cd278e90\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498611_revision_number=1f2ba28869776942e4726500e9264371cd278e90\nbamboo_repository_name=Jalview Gitlab\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46498611_git_branch=development/Release_2_12_Branch\nbamboo_planRepository_branch=development/Release_2_12_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=false\nbamboo_repository_46498611_git_username=\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=ba2177bba3a1e2417aec91f5283bcd923c650917\nbamboo_repository_46498611_name=Jalview Gitlab\nbamboo_repository_46498611_previous_revision_number=ba2177bba3a1e2417aec91f5283bcd923c650917\nbamboo_planRepository_branchDisplayName=development/Release_2_12_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=development/Release_2_12_Branch\nbamboo_repository_46498611_branch_name=development/Release_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-46302793\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-GDB732-JOB1\nbamboo_planKey=JB-GDB732\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=development/Release_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	06-Jan-2026 03:28:45	2414
build	06-Jan-2026 03:28:51	
build	06-Jan-2026 03:28:51	> Configure project :
build	06-Jan-2026 03:28:51	Using properties from file './utils/channels/default/channel_gradle.properties'
build	06-Jan-2026 03:28:51	JALVIEW_VERSION is set to '2.12.0'
build	06-Jan-2026 03:28:51	HEADLESS BUILD
build	06-Jan-2026 03:28:51	J2S ENABLED
build	06-Jan-2026 03:28:51	Using a LOCAL profile.
build	06-Jan-2026 03:28:52	eclipseDir exists
build	06-Jan-2026 03:28:54	
build	06-Jan-2026 03:28:54	> Task :cloverHtmlReport
build	06-Jan-2026 03:28:54	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	06-Jan-2026 03:28:56	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/clover'
build	06-Jan-2026 03:29:48	Done. Processed 137 packages in 52674ms (384ms per package).
build	06-Jan-2026 03:29:54	
build	06-Jan-2026 03:29:54	> Task :cloverXmlReport
build	06-Jan-2026 03:29:54	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	06-Jan-2026 03:29:56	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/clover/clover.xml'
build	06-Jan-2026 03:29:56	
build	06-Jan-2026 03:29:56	> Task :cloverReport
build	06-Jan-2026 03:29:56	
build	06-Jan-2026 03:29:56	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	06-Jan-2026 03:29:56	
build	06-Jan-2026 03:29:56	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	06-Jan-2026 03:29:56	
build	06-Jan-2026 03:29:56	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	06-Jan-2026 03:29:56	
build	06-Jan-2026 03:29:56	BUILD SUCCESSFUL in 1m 10s
build	06-Jan-2026 03:29:56	2 actionable tasks: 2 executed
simple	06-Jan-2026 03:29:56	Finished task 'Clover Report' with result: Success
simple	06-Jan-2026 03:29:56	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	06-Jan-2026 03:29:56	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1...
simple	06-Jan-2026 03:29:56	Finished task 'TestNG Parser' with result: Success
simple	06-Jan-2026 03:29:56	Running post build plugin 'NCover Results Collector'
simple	06-Jan-2026 03:29:56	Running post build plugin 'Artifact Copier'
simple	06-Jan-2026 03:29:56	Publishing an artifact: Clover Report (System)
simple	06-Jan-2026 03:29:58	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.786 s
simple	06-Jan-2026 03:29:58	Publishing an artifact: TestNG report
error	06-Jan-2026 03:29:58	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/test does not exist.
simple	06-Jan-2026 03:29:58	The artifact hasn't been successfully published after 1.426 ms
simple	06-Jan-2026 03:29:58	Running post build plugin 'Artifactory Release Management Staging'
simple	06-Jan-2026 03:29:58	Running post build plugin 'Artifactory Build Info Copier'
simple	06-Jan-2026 03:29:58	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	06-Jan-2026 03:29:58	Running post build plugin 'npm Cache Cleanup'
simple	06-Jan-2026 03:29:58	Running post build plugin 'Clover Results Collector'
simple	06-Jan-2026 03:29:58	Running post build plugin 'Docker Container Cleanup'
simple	06-Jan-2026 03:29:58	Finalising the build...
simple	06-Jan-2026 03:29:58	Stopping timer.
simple	06-Jan-2026 03:29:58	Build JB-GDB732-JOB1-6 completed.
simple	06-Jan-2026 03:29:58	Running on server: post build plugin 'NCover Results Collector'
simple	06-Jan-2026 03:29:58	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	06-Jan-2026 03:29:58	Running on server: post build plugin 'Clover Delta Calculator'
simple	06-Jan-2026 03:29:58	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	06-Jan-2026 03:29:58	All post build plugins have finished
simple	06-Jan-2026 03:29:58	Generating build results summary...
simple	06-Jan-2026 03:29:58	Saving build results to disk...
simple	06-Jan-2026 03:29:58	Logging substituted variables...
simple	06-Jan-2026 03:29:58	Indexing build results...
simple	06-Jan-2026 03:29:58	Finished building JB-GDB732-JOB1-6.