simple	10-Mar-2026 14:58:14	Build Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #1 (JB-GDB747-JOB1-1) started building on agent Default Agent
simple	10-Mar-2026 14:58:14	
simple	10-Mar-2026 14:58:14	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1
simple	10-Mar-2026 14:58:14	Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #1 (JB-GDB747-JOB1-1)
simple	10-Mar-2026 14:58:14	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	10-Mar-2026 14:58:14	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1
simple	10-Mar-2026 14:58:14	Updating source code to revision: 0d6f14957df15006b71decb225c4c15ca80eead6
simple	10-Mar-2026 14:58:14	Fetching 'refs/heads/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	10-Mar-2026 14:58:14	Checking out revision 0d6f14957df15006b71decb225c4c15ca80eead6.
simple	10-Mar-2026 14:58:14	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/.git'.
simple	10-Mar-2026 14:58:14	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1'...
simple	10-Mar-2026 14:58:14	done.
simple	10-Mar-2026 14:58:21	Branch patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts set up to track remote branch patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts from origin.
simple	10-Mar-2026 14:58:21	Switched to a new branch 'patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts'
simple	10-Mar-2026 14:58:21	Updated source code to revision: 0d6f14957df15006b71decb225c4c15ca80eead6
simple	10-Mar-2026 14:58:21	Finished task 'Checkout Default Repository' with result: Success
simple	10-Mar-2026 14:58:21	Running pre-build action: VCS Version Collector
simple	10-Mar-2026 14:58:21	Running pre-build action: Artifactory Release Staging
simple	10-Mar-2026 14:58:21	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	10-Mar-2026 14:58:21	Bamboo Artifactory Plugin version: 2.6.2
command	10-Mar-2026 14:58:21	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #1 (JB-GDB747-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-GDB747-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_repository_revision_number=0d6f14957df15006b71decb225c4c15ca80eead6\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB747-JOB1-1\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-GDB747-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB747-JOB1\nbamboo_shortPlanName=patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts\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-GDB747-JOB1-1\nbamboo_repository_48169034_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_shortPlanKey=GDB747\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=0d6f14957df15006b71decb225c4c15ca80eead6\nbamboo_buildTimeStamp=2026-03-10T14:58:14.165Z\nbamboo_repository_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_buildResultKey=JB-GDB747-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=0d6f14957df15006b71decb225c4c15ca80eead6\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169034_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_repository_48169034_branch_name=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\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=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_repository_48169034_name=Jalview Gitlab\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\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-47972499\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_repository_48169034_revision_number=0d6f14957df15006b71decb225c4c15ca80eead6\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-GDB747-JOB1\nbamboo_planKey=JB-GDB747\nbamboo_repository_48169034_git_username=\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	10-Mar-2026 14:58:21	2414
build	10-Mar-2026 14:58:22	Starting a Gradle Daemon (subsequent builds will be faster)
build	10-Mar-2026 14:58:28	
build	10-Mar-2026 14:58:28	> Configure project :
build	10-Mar-2026 14:58:28	Using properties from file './utils/channels/default/channel_gradle.properties'
build	10-Mar-2026 14:58:28	JALVIEW_VERSION is set to '2.12.0'
build	10-Mar-2026 14:58:28	HEADLESS BUILD
build	10-Mar-2026 14:58:28	J2S ENABLED
build	10-Mar-2026 14:58:29	Using a LOCAL profile.
build	10-Mar-2026 14:58:29	eclipseDir exists
build	10-Mar-2026 14:58:30	
build	10-Mar-2026 14:58:30	> Task :clean
build	10-Mar-2026 14:58:30	> Task :cleanClover
build	10-Mar-2026 14:58:30	> Task :cleanTest UP-TO-DATE
build	10-Mar-2026 14:58:32	
build	10-Mar-2026 14:58:32	> Task :cloverInstrJava
build	10-Mar-2026 14:58:32	Clover: About to instrument 1255 files
build	10-Mar-2026 14:58:32	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	10-Mar-2026 14:58:32	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover.db'.
build	10-Mar-2026 14:58:32	Processing files at 1.9 source level.
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:36	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:37	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	10-Mar-2026 14:58:37	WARN: Trying to 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	10-Mar-2026 14:58:42	Clover all over. Instrumented 1255 files (133 packages).
build	10-Mar-2026 14:58:45	
build	10-Mar-2026 14:58:45	> Task :cloverInstrTests
build	10-Mar-2026 14:58:45	Clover: About to instrument test files
build	10-Mar-2026 14:58:45	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	10-Mar-2026 14:58:45	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover.db'.
build	10-Mar-2026 14:58:45	Processing files at 1.9 source level.
build	10-Mar-2026 14:58:47	Clover all over. Instrumented 315 files (58 packages).
build	10-Mar-2026 14:58:47	1771 test methods detected.
build	10-Mar-2026 14:58:48	
build	10-Mar-2026 14:58:48	> Task :cloverInstr
build	10-Mar-2026 14:58:51	
build	10-Mar-2026 14:58:51	> Task :compileCloverJava
build	10-Mar-2026 14:58:51	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	10-Mar-2026 14:58:51	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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	10-Mar-2026 14:58:51	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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	10-Mar-2026 14:58:51	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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	10-Mar-2026 14:58:51	Setting target compatibility to 11
error	10-Mar-2026 14:58:56	/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-instr/jalview/gui/CalculationChooser.java:62: error: cannot find symbol
error	10-Mar-2026 14:58:56	import jalview.analysis.scoremodels.ValueAnnotationDistanceModel;
error	10-Mar-2026 14:58:56	                                   ^
error	10-Mar-2026 14:58:56	  symbol:   class ValueAnnotationDistanceModel
error	10-Mar-2026 14:58:56	  location: package jalview.analysis.scoremodels
error	10-Mar-2026 14:59:01	/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-instr/jalview/gui/CalculationChooser.java:744: error: cannot find symbol
error	10-Mar-2026 14:59:01	                      || sm.isSecondaryStructure() && ssPresent || sm instanceof ValueAnnotationDistanceModel))&&(__CLR4_4_11w671w67mmkqjcvr.R.iget(88621)!=0|true))||(__CLR4_4_11w671w67mmkqjcvr.R.iget(88622)==0&false)))
error	10-Mar-2026 14:59:01	                                                                                 ^
error	10-Mar-2026 14:59:01	  symbol:   class ValueAnnotationDistanceModel
error	10-Mar-2026 14:59:01	  location: class CalculationChooser
error	10-Mar-2026 14:59:08	/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-instr/jalview/analysis/scoremodels/ScoreModels.java:86: error: cannot find symbol
error	10-Mar-2026 14:59:08	    __CLR4_4_13hv23hv2mmkqjfj1.R.inc(163129);registerScoreModel(new ValueAnnotationDistanceModel());
error	10-Mar-2026 14:59:08	                                                                    ^
error	10-Mar-2026 14:59:08	  symbol:   class ValueAnnotationDistanceModel
error	10-Mar-2026 14:59:08	  location: class ScoreModels
build	10-Mar-2026 14:59:09	
build	10-Mar-2026 14:59:09	> Task :compileCloverJava FAILED
error	10-Mar-2026 14:59:09	Note: Some input files use or override a deprecated API.
error	10-Mar-2026 14:59:09	Note: Recompile with -Xlint:deprecation for details.
error	10-Mar-2026 14:59:09	Note: Some input files use unchecked or unsafe operations.
error	10-Mar-2026 14:59:09	Note: Recompile with -Xlint:unchecked for details.
error	10-Mar-2026 14:59:09	3 errors
error	10-Mar-2026 14:59:09	
error	10-Mar-2026 14:59:09	FAILURE: Build failed with an exception.
error	10-Mar-2026 14:59:09	
error	10-Mar-2026 14:59:09	* What went wrong:
error	10-Mar-2026 14:59:09	Execution failed for task ':compileCloverJava'.
error	10-Mar-2026 14:59:09	> Compilation failed; see the compiler error output for details.
error	10-Mar-2026 14:59:09	
error	10-Mar-2026 14:59:09	* Try:
error	10-Mar-2026 14:59:09	> Run with --stacktrace option to get the stack trace.
error	10-Mar-2026 14:59:09	> Run with --info or --debug option to get more log output.
error	10-Mar-2026 14:59:09	> Run with --scan to get full insights.
error	10-Mar-2026 14:59:09	
build	10-Mar-2026 14:59:09	
build	10-Mar-2026 14:59:09	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	10-Mar-2026 14:59:09	
build	10-Mar-2026 14:59:09	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	10-Mar-2026 14:59:09	
build	10-Mar-2026 14:59:09	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	10-Mar-2026 14:59:09	
build	10-Mar-2026 14:59:09	Execution optimizations have been disabled for 1 invalid unit(s) of work during this build to ensure correctness.
build	10-Mar-2026 14:59:09	Please consult deprecation warnings for more details.
build	10-Mar-2026 14:59:09	6 actionable tasks: 5 executed, 1 up-to-date
error	10-Mar-2026 14:59:09	* Get more help at https://help.gradle.org
error	10-Mar-2026 14:59:09	
error	10-Mar-2026 14:59:09	BUILD FAILED in 48s
simple	10-Mar-2026 14:59:10	
simple	10-Mar-2026 14:59:10	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	10-Mar-2026 14:59:10	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	10-Mar-2026 14:59:10	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	10-Mar-2026 14:59:10	Bamboo Artifactory Plugin version: 2.6.2
command	10-Mar-2026 14:59:10	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #1 (JB-GDB747-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-GDB747-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_repository_revision_number=0d6f14957df15006b71decb225c4c15ca80eead6\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB747-JOB1-1\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-GDB747-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB747-JOB1\nbamboo_shortPlanName=patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts\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-GDB747-JOB1-1\nbamboo_repository_48169034_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_shortPlanKey=GDB747\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=0d6f14957df15006b71decb225c4c15ca80eead6\nbamboo_buildTimeStamp=2026-03-10T14:58:14.165Z\nbamboo_repository_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_buildResultKey=JB-GDB747-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=0d6f14957df15006b71decb225c4c15ca80eead6\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169034_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_repository_48169034_branch_name=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\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=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_repository_48169034_name=Jalview Gitlab\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\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-47972499\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_repository_48169034_revision_number=0d6f14957df15006b71decb225c4c15ca80eead6\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-GDB747-JOB1\nbamboo_planKey=JB-GDB747\nbamboo_repository_48169034_git_username=\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	10-Mar-2026 14:59:10	2414
build	10-Mar-2026 14:59:15	
build	10-Mar-2026 14:59:15	> Configure project :
build	10-Mar-2026 14:59:15	Using properties from file './utils/channels/default/channel_gradle.properties'
build	10-Mar-2026 14:59:15	JALVIEW_VERSION is set to '2.12.0'
build	10-Mar-2026 14:59:15	HEADLESS BUILD
build	10-Mar-2026 14:59:15	J2S ENABLED
build	10-Mar-2026 14:59:15	Using a LOCAL profile.
build	10-Mar-2026 14:59:16	eclipseDir exists
build	10-Mar-2026 14:59:18	
build	10-Mar-2026 14:59:18	> Task :cloverHtmlReport
build	10-Mar-2026 14:59:18	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	10-Mar-2026 14:59:18	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/clover'
build	10-Mar-2026 14:59:28	Done. Processed 137 packages in 11278ms (82ms per package).
build	10-Mar-2026 14:59:32	
build	10-Mar-2026 14:59:32	> Task :cloverXmlReport
build	10-Mar-2026 14:59:32	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	10-Mar-2026 14:59:32	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/clover/clover.xml'
build	10-Mar-2026 14:59:32	
build	10-Mar-2026 14:59:32	> Task :cloverReport
build	10-Mar-2026 14:59:32	
build	10-Mar-2026 14:59:32	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	10-Mar-2026 14:59:32	
build	10-Mar-2026 14:59:32	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	10-Mar-2026 14:59:32	
build	10-Mar-2026 14:59:32	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	10-Mar-2026 14:59:32	
build	10-Mar-2026 14:59:32	BUILD SUCCESSFUL in 22s
build	10-Mar-2026 14:59:32	2 actionable tasks: 2 executed
simple	10-Mar-2026 14:59:32	Finished task 'Clover Report' with result: Success
simple	10-Mar-2026 14:59:32	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	10-Mar-2026 14:59:32	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1...
simple	10-Mar-2026 14:59:32	Failing task since test cases were expected but none were found.
simple	10-Mar-2026 14:59:32	Finished task 'TestNG Parser' with result: Failed
simple	10-Mar-2026 14:59:32	Running post build plugin 'NCover Results Collector'
simple	10-Mar-2026 14:59:32	Running post build plugin 'Artifact Copier'
simple	10-Mar-2026 14:59:32	Publishing an artifact: Clover Report (System)
simple	10-Mar-2026 14:59:33	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.158 s
simple	10-Mar-2026 14:59:33	Publishing an artifact: TestNG report
error	10-Mar-2026 14:59:33	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/tests/test does not exist.
simple	10-Mar-2026 14:59:33	The artifact hasn't been successfully published after 2.274 ms
simple	10-Mar-2026 14:59:33	Running post build plugin 'Artifactory Release Management Staging'
simple	10-Mar-2026 14:59:33	Running post build plugin 'Artifactory Build Info Copier'
simple	10-Mar-2026 14:59:33	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	10-Mar-2026 14:59:33	Running post build plugin 'npm Cache Cleanup'
simple	10-Mar-2026 14:59:33	Running post build plugin 'Clover Results Collector'
simple	10-Mar-2026 14:59:33	Running post build plugin 'Docker Container Cleanup'
simple	10-Mar-2026 14:59:33	Finalising the build...
simple	10-Mar-2026 14:59:33	Stopping timer.
simple	10-Mar-2026 14:59:33	Build JB-GDB747-JOB1-1 completed.
simple	10-Mar-2026 14:59:33	Running on server: post build plugin 'NCover Results Collector'
simple	10-Mar-2026 14:59:33	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	10-Mar-2026 14:59:33	Running on server: post build plugin 'Clover Delta Calculator'
simple	10-Mar-2026 14:59:33	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	10-Mar-2026 14:59:33	All post build plugins have finished
simple	10-Mar-2026 14:59:33	Generating build results summary...
simple	10-Mar-2026 14:59:33	Saving build results to disk...
simple	10-Mar-2026 14:59:33	Logging substituted variables...
simple	10-Mar-2026 14:59:33	Indexing build results...
simple	10-Mar-2026 14:59:33	Finished building JB-GDB747-JOB1-1.