simple	14-Jan-2026 14:33:13	Build Jalview Builds - Gradle Develop Build - task-JAL-4645_JAL-4320_add_gradle_wrapper - Clover and Tests #1 (JB-GDB742-JOB1-1) started building on agent Default Agent
simple	14-Jan-2026 14:33:13	
simple	14-Jan-2026 14:33:13	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1
simple	14-Jan-2026 14:33:13	Executing build Jalview Builds - Gradle Develop Build - task-JAL-4645_JAL-4320_add_gradle_wrapper - Clover and Tests #1 (JB-GDB742-JOB1-1)
simple	14-Jan-2026 14:33:13	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	14-Jan-2026 14:33:13	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1
simple	14-Jan-2026 14:33:13	Updating source code to revision: 116b049a0074ef137377d0d1cb7dfff537d28ab5
simple	14-Jan-2026 14:33:13	Fetching 'refs/heads/task/JAL-4645_JAL-4320_add_gradle_wrapper' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	14-Jan-2026 14:33:14	Checking out revision 116b049a0074ef137377d0d1cb7dfff537d28ab5.
simple	14-Jan-2026 14:33:14	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/.git'.
simple	14-Jan-2026 14:33:14	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1'...
simple	14-Jan-2026 14:33:14	done.
simple	14-Jan-2026 14:33:19	Switched to a new branch 'task/JAL-4645_JAL-4320_add_gradle_wrapper'
simple	14-Jan-2026 14:33:19	Branch task/JAL-4645_JAL-4320_add_gradle_wrapper set up to track remote branch task/JAL-4645_JAL-4320_add_gradle_wrapper from origin.
simple	14-Jan-2026 14:33:19	Updated source code to revision: 116b049a0074ef137377d0d1cb7dfff537d28ab5
simple	14-Jan-2026 14:33:19	Finished task 'Checkout Default Repository' with result: Success
simple	14-Jan-2026 14:33:19	Running pre-build action: VCS Version Collector
simple	14-Jan-2026 14:33:19	Running pre-build action: Artifactory Release Staging
simple	14-Jan-2026 14:33:19	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	14-Jan-2026 14:33:19	Bamboo Artifactory Plugin version: 2.6.2
command	14-Jan-2026 14:33:19	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - task-JAL-4645_JAL-4320_add_gradle_wrapper - Clover and Tests #1 (JB-GDB742-JOB1-1)'\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-GDB742-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_repository_48169001_revision_number=116b049a0074ef137377d0d1cb7dfff537d28ab5\nbamboo_repository_48169001_git_username=\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_repository_revision_number=116b049a0074ef137377d0d1cb7dfff537d28ab5\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB742-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_48169001_branch_name=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_repository_48169001_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB742-JOB1\nbamboo_shortPlanName=task-JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\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-GDB742-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - task-JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_shortPlanKey=GDB742\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=116b049a0074ef137377d0d1cb7dfff537d28ab5\nbamboo_buildTimeStamp=2026-01-14T14:33:13.868Z\nbamboo_repository_git_branch=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_buildResultKey=JB-GDB742-JOB1-1\nbamboo_repository_branch_name=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - task-JAL-4645_JAL-4320_add_gradle_wrapper - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=116b049a0074ef137377d0d1cb7dfff537d28ab5\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169001_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\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_planRepository_branch=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=task/JAL-4645_JAL-4320_add_gradle_wrapper\n_=/usr/bin/java\nbamboo_repository_48169001_git_branch=task/JAL-4645_JAL-4320_add_gradle_wrapper\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-47972433\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-GDB742-JOB1\nbamboo_planKey=JB-GDB742\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=task/JAL-4645_JAL-4320_add_gradle_wrapper\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	14-Jan-2026 14:33:19	2414
build	14-Jan-2026 14:33:20	
build	14-Jan-2026 14:33:20	> Configure project :
build	14-Jan-2026 14:33:20	Using properties from file './utils/channels/default/channel_gradle.properties'
build	14-Jan-2026 14:33:20	JALVIEW_VERSION is set to '2.12.0'
build	14-Jan-2026 14:33:20	HEADLESS BUILD
build	14-Jan-2026 14:33:20	J2S ENABLED
build	14-Jan-2026 14:33:20	Using a LOCAL profile.
build	14-Jan-2026 14:33:20	eclipseDir exists
build	14-Jan-2026 14:33:20	
build	14-Jan-2026 14:33:20	> Task :clean
build	14-Jan-2026 14:33:20	> Task :cleanClover
build	14-Jan-2026 14:33:20	> Task :cleanTest UP-TO-DATE
build	14-Jan-2026 14:33:22	
build	14-Jan-2026 14:33:22	> Task :cloverInstrJava
build	14-Jan-2026 14:33:22	Clover: About to instrument 1253 files
build	14-Jan-2026 14:33:23	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	14-Jan-2026 14:33:23	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/clover/clover.db'.
build	14-Jan-2026 14:33:23	Processing files at 1.9 source level.
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:26	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:27	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:27	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:27	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:27	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:27	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:27	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:27	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:27	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:27	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:27	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:27	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	14-Jan-2026 14:33:27	WARN: Trying to 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	14-Jan-2026 14:33:32	Clover all over. Instrumented 1253 files (133 packages).
build	14-Jan-2026 14:33:34	
build	14-Jan-2026 14:33:34	> Task :cloverInstrTests
build	14-Jan-2026 14:33:34	Clover: About to instrument test files
build	14-Jan-2026 14:33:34	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	14-Jan-2026 14:33:34	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/clover/clover.db'.
build	14-Jan-2026 14:33:34	Processing files at 1.9 source level.
build	14-Jan-2026 14:33:37	Clover all over. Instrumented 315 files (58 packages).
build	14-Jan-2026 14:33:37	1770 test methods detected.
build	14-Jan-2026 14:33:37	
build	14-Jan-2026 14:33:37	> Task :cloverInstr
build	14-Jan-2026 14:33:40	
build	14-Jan-2026 14:33:40	> Task :compileCloverJava
build	14-Jan-2026 14:33:40	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	14-Jan-2026 14:33:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:33:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:33:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:33:40	Setting target compatibility to 11
error	14-Jan-2026 14:33:54	Note: Some input files use or override a deprecated API.
error	14-Jan-2026 14:33:54	Note: Recompile with -Xlint:deprecation for details.
error	14-Jan-2026 14:33:54	Note: Some input files use unchecked or unsafe operations.
error	14-Jan-2026 14:33:54	Note: Recompile with -Xlint:unchecked for details.
build	14-Jan-2026 14:34:00	
build	14-Jan-2026 14:34:00	> Task :processCloverResources NO-SOURCE
build	14-Jan-2026 14:34:00	> Task :cloverClasses
build	14-Jan-2026 14:34:00	> Task :copyHelp
build	14-Jan-2026 14:34:01	> Task :buildIndices
build	14-Jan-2026 14:34:01	> Task :copyResources
build	14-Jan-2026 14:34:01	> Task :copyChannelResources
build	14-Jan-2026 14:34:01	
build	14-Jan-2026 14:34:01	> Task :createBuildProperties
build	14-Jan-2026 14:34:01	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	14-Jan-2026 14:34:01	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:34:01	
build	14-Jan-2026 14:34:01	> Task :buildResources
build	14-Jan-2026 14:34:01	> Task :copyDocs
build	14-Jan-2026 14:34:01	
build	14-Jan-2026 14:34:01	> Task :convertMdFiles
build	14-Jan-2026 14:34:01	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	14-Jan-2026 14:34:01	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	14-Jan-2026 14:34:01	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	14-Jan-2026 14:34:01	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
build	14-Jan-2026 14:34:01	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/resources/doc_build/doc/building.html
build	14-Jan-2026 14:34:01	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/resources/doc_build/doc/addingWebClient.html
build	14-Jan-2026 14:34:01	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	14-Jan-2026 14:34:01	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
build	14-Jan-2026 14:34:01	
build	14-Jan-2026 14:34:01	> Task :releasesTemplates
build	14-Jan-2026 14:34:01	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	14-Jan-2026 14:34:01	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:34:01	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:34:01	Stripping rc/test/etc for TEST
build	14-Jan-2026 14:34:01	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	14-Jan-2026 14:34:01	
build	14-Jan-2026 14:34:01	> Task :prepare
build	14-Jan-2026 14:34:03	
build	14-Jan-2026 14:34:03	> Task :compileJava
build	14-Jan-2026 14:34:03	Setting target compatibility to 11
error	14-Jan-2026 14:34:09	Note: Some input files use or override a deprecated API.
error	14-Jan-2026 14:34:09	Note: Recompile with -Xlint:deprecation for details.
error	14-Jan-2026 14:34:09	Note: Some input files use unchecked or unsafe operations.
error	14-Jan-2026 14:34:09	Note: Recompile with -Xlint:unchecked for details.
build	14-Jan-2026 14:34:12	
build	14-Jan-2026 14:34:12	> Task :compileTestJava
build	14-Jan-2026 14:34:12	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	14-Jan-2026 14:34:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:34:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:34:12	Setting target compatibility to 11
error	14-Jan-2026 14:34:17	Note: Some input files use or override a deprecated API.
error	14-Jan-2026 14:34:17	Note: Recompile with -Xlint:deprecation for details.
error	14-Jan-2026 14:34:17	Note: Some input files use unchecked or unsafe operations.
error	14-Jan-2026 14:34:17	Note: Recompile with -Xlint:unchecked for details.
build	14-Jan-2026 14:34:19	
build	14-Jan-2026 14:34:19	> Task :processTestResources
build	14-Jan-2026 14:34:19	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	14-Jan-2026 14:34:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:34:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:34:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:34:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:34:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:34:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:34:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-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	14-Jan-2026 14:34:19	
build	14-Jan-2026 14:34:19	> Task :testClasses
build	14-Jan-2026 14:34:21	
build	14-Jan-2026 14:34:21	> Task :testTask0
build	14-Jan-2026 14:34:21	Running tests WITH clover
error	14-Jan-2026 14:34:22	WARNING: An illegal reflective access operation has occurred
error	14-Jan-2026 14:34:22	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	14-Jan-2026 14:34:22	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	14-Jan-2026 14:34:22	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	14-Jan-2026 14:34:22	WARNING: All illegal access operations will be denied in a future release
build	14-Jan-2026 14:36:54	
build	14-Jan-2026 14:36:54	Gradle suite > Gradle test > jalview.project.Jalview2xmlTests > noDuplicatePdbMappingsMade FAILED
build	14-Jan-2026 14:36:54	    java.lang.AssertionError: Expected only two mappings for 1A70 expected [2] but found [0]
build	14-Jan-2026 14:36:54	        at org.testng.Assert.fail(Assert.java:110)
build	14-Jan-2026 14:36:54	        at org.testng.Assert.failNotEquals(Assert.java:1413)
build	14-Jan-2026 14:36:54	        at org.testng.Assert.assertEqualsImpl(Assert.java:149)
build	14-Jan-2026 14:36:54	        at org.testng.Assert.assertEquals(Assert.java:131)
build	14-Jan-2026 14:36:54	        at org.testng.Assert.assertEquals(Assert.java:1240)
build	14-Jan-2026 14:36:54	        at jalview.project.Jalview2xmlTests.__CLR4_4_11umpz94jy6(Jalview2xmlTests.java:355)
build	14-Jan-2026 14:36:54	        at jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade(Jalview2xmlTests.java:331)
error	14-Jan-2026 14:38:51	
error	14-Jan-2026 14:38:51	2103 tests completed, 1 failed
build	14-Jan-2026 14:38:51	There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/reports/tests/testTask0/index.html
build	14-Jan-2026 14:38:54	
build	14-Jan-2026 14:38:54	> Task :testTask1
build	14-Jan-2026 14:38:54	Running tests WITH clover
error	14-Jan-2026 14:38:55	WARNING: An illegal reflective access operation has occurred
error	14-Jan-2026 14:38:55	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	14-Jan-2026 14:38:55	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	14-Jan-2026 14:38:55	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	14-Jan-2026 14:38:55	WARNING: All illegal access operations will be denied in a future release
build	14-Jan-2026 14:41:01	
build	14-Jan-2026 14:41:01	> Task :testTask2
build	14-Jan-2026 14:41:01	Running tests WITH clover
error	14-Jan-2026 14:41:02	WARNING: An illegal reflective access operation has occurred
error	14-Jan-2026 14:41:02	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	14-Jan-2026 14:41:02	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	14-Jan-2026 14:41:02	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	14-Jan-2026 14:41:02	WARNING: All illegal access operations will be denied in a future release
build	14-Jan-2026 14:41:05	
build	14-Jan-2026 14:41:05	> Task :testTask3
build	14-Jan-2026 14:41:05	Running tests WITH clover
error	14-Jan-2026 14:41:07	WARNING: An illegal reflective access operation has occurred
error	14-Jan-2026 14:41:07	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	14-Jan-2026 14:41:07	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	14-Jan-2026 14:41:07	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	14-Jan-2026 14:41:07	WARNING: All illegal access operations will be denied in a future release
build	14-Jan-2026 14:41:24	
build	14-Jan-2026 14:41:24	> Task :test NO-SOURCE
build	14-Jan-2026 14:41:24	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	14-Jan-2026 14:41:24	│jalview:testTask0 results: FAILURE (2103 tests, 2102 successes, 1 failures, 0 skipped) in 4 minutes, 32.372 seconds   │
build	14-Jan-2026 14:41:24	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/reports/tests/testTask0/index.html│
build	14-Jan-2026 14:41:24	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	14-Jan-2026 14:41:24	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 7.024 seconds        │
error	14-Jan-2026 14:41:24	
error	14-Jan-2026 14:41:24	FAILURE: Build failed with an exception.
error	14-Jan-2026 14:41:24	
error	14-Jan-2026 14:41:24	* Where:
error	14-Jan-2026 14:41:24	Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build.gradle' line: 1964
error	14-Jan-2026 14:41:24	
error	14-Jan-2026 14:41:24	* What went wrong:
error	14-Jan-2026 14:41:24	Failed tests!
error	14-Jan-2026 14:41:24	
error	14-Jan-2026 14:41:24	* Try:
error	14-Jan-2026 14:41:24	> Run with --stacktrace option to get the stack trace.
error	14-Jan-2026 14:41:24	> Run with --info or --debug option to get more log output.
error	14-Jan-2026 14:41:24	> Run with --scan to get full insights.
error	14-Jan-2026 14:41:24	
error	14-Jan-2026 14:41:24	* Get more help at https://help.gradle.org
error	14-Jan-2026 14:41:24	
error	14-Jan-2026 14:41:24	BUILD FAILED in 8m 5s
build	14-Jan-2026 14:41:24	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/reports/tests/testTask1/index.html│
build	14-Jan-2026 14:41:24	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	14-Jan-2026 14:41:24	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.741 seconds                     │
build	14-Jan-2026 14:41:24	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/reports/tests/testTask2/index.html│
build	14-Jan-2026 14:41:24	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	14-Jan-2026 14:41:24	│jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 20.738 seconds                  │
build	14-Jan-2026 14:41:24	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/reports/tests/testTask3/index.html│
build	14-Jan-2026 14:41:24	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	14-Jan-2026 14:41:24	│OVERALL: results: FAILURE (2180 tests, 2178 successes, 1 failures, 1 skipped) in 6 minutes, 64.875 seconds            │
build	14-Jan-2026 14:41:24	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	14-Jan-2026 14:41:24	
build	14-Jan-2026 14:41:24	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	14-Jan-2026 14:41:24	
build	14-Jan-2026 14:41:24	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	14-Jan-2026 14:41:24	
build	14-Jan-2026 14:41:24	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	14-Jan-2026 14:41:24	
build	14-Jan-2026 14:41:24	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	14-Jan-2026 14:41:24	Please consult deprecation warnings for more details.
build	14-Jan-2026 14:41:24	21 actionable tasks: 20 executed, 1 up-to-date
simple	14-Jan-2026 14:41:25	
simple	14-Jan-2026 14:41:25	Failing task since return code of [/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test] was 1 while expected 0
simple	14-Jan-2026 14:41:25	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	14-Jan-2026 14:41:25	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	14-Jan-2026 14:41:25	Bamboo Artifactory Plugin version: 2.6.2
command	14-Jan-2026 14:41:25	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - task-JAL-4645_JAL-4320_add_gradle_wrapper - Clover and Tests #1 (JB-GDB742-JOB1-1)'\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-GDB742-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_repository_48169001_revision_number=116b049a0074ef137377d0d1cb7dfff537d28ab5\nbamboo_repository_48169001_git_username=\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_repository_revision_number=116b049a0074ef137377d0d1cb7dfff537d28ab5\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB742-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_48169001_branch_name=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_repository_48169001_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB742-JOB1\nbamboo_shortPlanName=task-JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\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-GDB742-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - task-JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_shortPlanKey=GDB742\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=116b049a0074ef137377d0d1cb7dfff537d28ab5\nbamboo_buildTimeStamp=2026-01-14T14:33:13.868Z\nbamboo_repository_git_branch=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_buildResultKey=JB-GDB742-JOB1-1\nbamboo_repository_branch_name=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - task-JAL-4645_JAL-4320_add_gradle_wrapper - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=116b049a0074ef137377d0d1cb7dfff537d28ab5\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169001_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_name=Jalview Gitlab\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=true\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=task/JAL-4645_JAL-4320_add_gradle_wrapper\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=task/JAL-4645_JAL-4320_add_gradle_wrapper\n_=/usr/bin/java\nbamboo_repository_48169001_git_branch=task/JAL-4645_JAL-4320_add_gradle_wrapper\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-47972433\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-GDB742-JOB1\nbamboo_planKey=JB-GDB742\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=task/JAL-4645_JAL-4320_add_gradle_wrapper\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	14-Jan-2026 14:41:25	2414
build	14-Jan-2026 14:41:30	
build	14-Jan-2026 14:41:30	> Configure project :
build	14-Jan-2026 14:41:30	Using properties from file './utils/channels/default/channel_gradle.properties'
build	14-Jan-2026 14:41:30	JALVIEW_VERSION is set to '2.12.0'
build	14-Jan-2026 14:41:30	HEADLESS BUILD
build	14-Jan-2026 14:41:30	J2S ENABLED
build	14-Jan-2026 14:41:30	Using a LOCAL profile.
build	14-Jan-2026 14:41:31	eclipseDir exists
build	14-Jan-2026 14:41:33	
build	14-Jan-2026 14:41:33	> Task :cloverHtmlReport
build	14-Jan-2026 14:41:33	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	14-Jan-2026 14:41:35	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/reports/clover'
build	14-Jan-2026 14:42:27	Done. Processed 137 packages in 52713ms (384ms per package).
build	14-Jan-2026 14:42:33	
build	14-Jan-2026 14:42:33	> Task :cloverXmlReport
build	14-Jan-2026 14:42:33	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	14-Jan-2026 14:42:34	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/reports/clover/clover.xml'
build	14-Jan-2026 14:42:34	
build	14-Jan-2026 14:42:34	> Task :cloverReport
build	14-Jan-2026 14:42:34	
build	14-Jan-2026 14:42:34	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	14-Jan-2026 14:42:34	
build	14-Jan-2026 14:42:34	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	14-Jan-2026 14:42:34	
build	14-Jan-2026 14:42:34	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	14-Jan-2026 14:42:34	
build	14-Jan-2026 14:42:34	BUILD SUCCESSFUL in 1m 9s
build	14-Jan-2026 14:42:34	2 actionable tasks: 2 executed
simple	14-Jan-2026 14:42:34	Finished task 'Clover Report' with result: Success
simple	14-Jan-2026 14:42:34	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	14-Jan-2026 14:42:34	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1...
simple	14-Jan-2026 14:42:34	Failing task since 1 failing test cases were found.
simple	14-Jan-2026 14:42:34	Finished task 'TestNG Parser' with result: Failed
simple	14-Jan-2026 14:42:34	Running post build plugin 'NCover Results Collector'
simple	14-Jan-2026 14:42:34	Running post build plugin 'Artifact Copier'
simple	14-Jan-2026 14:42:34	Publishing an artifact: Clover Report (System)
simple	14-Jan-2026 14:42:36	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.082 s
simple	14-Jan-2026 14:42:36	Publishing an artifact: TestNG report
error	14-Jan-2026 14:42:36	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB742-JOB1/build/reports/tests/test does not exist.
simple	14-Jan-2026 14:42:36	The artifact hasn't been successfully published after 1.483 ms
simple	14-Jan-2026 14:42:36	Running post build plugin 'Artifactory Release Management Staging'
simple	14-Jan-2026 14:42:36	Running post build plugin 'Artifactory Build Info Copier'
simple	14-Jan-2026 14:42:36	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	14-Jan-2026 14:42:36	Running post build plugin 'npm Cache Cleanup'
simple	14-Jan-2026 14:42:36	Running post build plugin 'Clover Results Collector'
simple	14-Jan-2026 14:42:36	Running post build plugin 'Docker Container Cleanup'
simple	14-Jan-2026 14:42:36	Finalising the build...
simple	14-Jan-2026 14:42:36	Stopping timer.
simple	14-Jan-2026 14:42:36	Build JB-GDB742-JOB1-1 completed.
simple	14-Jan-2026 14:42:36	Running on server: post build plugin 'NCover Results Collector'
simple	14-Jan-2026 14:42:36	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	14-Jan-2026 14:42:36	Running on server: post build plugin 'Clover Delta Calculator'
simple	14-Jan-2026 14:42:36	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	14-Jan-2026 14:42:36	All post build plugins have finished
simple	14-Jan-2026 14:42:36	Generating build results summary...
simple	14-Jan-2026 14:42:37	Saving build results to disk...
simple	14-Jan-2026 14:42:37	Logging substituted variables...
simple	14-Jan-2026 14:42:37	Indexing build results...
simple	14-Jan-2026 14:42:37	Finished building JB-GDB742-JOB1-1.