simple	19-Feb-2026 11:15:20	Build Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests #4 (JB-GDB744-JOB1-4) started building on agent Default Agent
simple	19-Feb-2026 11:15:20	
simple	19-Feb-2026 11:15:20	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1
simple	19-Feb-2026 11:15:20	Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests #4 (JB-GDB744-JOB1-4)
simple	19-Feb-2026 11:15:20	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	19-Feb-2026 11:15:20	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1
simple	19-Feb-2026 11:15:20	Updating source code to revision: 944aa492571e8adede487266d9a4a7143a7cc0df
simple	19-Feb-2026 11:15:20	Fetching 'refs/heads/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	19-Feb-2026 11:15:20	Checking out revision 944aa492571e8adede487266d9a4a7143a7cc0df.
simple	19-Feb-2026 11:15:21	Already on 'bug/JAL-4624_JAL-4623_Mul_SS_in_PCA'
simple	19-Feb-2026 11:15:21	Updated source code to revision: 944aa492571e8adede487266d9a4a7143a7cc0df
simple	19-Feb-2026 11:15:21	Finished task 'Checkout Default Repository' with result: Success
simple	19-Feb-2026 11:15:21	Running pre-build action: VCS Version Collector
simple	19-Feb-2026 11:15:21	Running pre-build action: Artifactory Release Staging
simple	19-Feb-2026 11:15:21	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	19-Feb-2026 11:15:21	Bamboo Artifactory Plugin version: 2.6.2
command	19-Feb-2026 11:15:21	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests #4 (JB-GDB744-JOB1-4)'\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-GDB744-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_repository_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB744-JOB1-4\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-GDB744-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB744-JOB1\nbamboo_shortPlanName=bug-JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=4\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-GDB744-JOB1-4\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_shortPlanKey=GDB744\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_buildTimeStamp=2026-02-19T11:15:20.537Z\nbamboo_repository_previous_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_planRepository_previousRevision=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_repository_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildResultKey=JB-GDB744-JOB1-4\nbamboo_repository_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests\nbamboo_repository_48169013_git_username=\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_48169013_name=Jalview Gitlab\nbamboo_planRepository_1_revision=944aa492571e8adede487266d9a4a7143a7cc0df\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169013_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_48169013_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_dependenciesDisabled=false\nbamboo_repository_48169013_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\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_48169013_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_planRepository_branchDisplayName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\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-47972457\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_ManualBuildTriggerReason_userName=reniacorreya\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169013_previous_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\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-GDB744-JOB1\nbamboo_planKey=JB-GDB744\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	19-Feb-2026 11:15:21	2414
build	19-Feb-2026 11:15:22	
build	19-Feb-2026 11:15:22	> Configure project :
build	19-Feb-2026 11:15:22	Using properties from file './utils/channels/default/channel_gradle.properties'
build	19-Feb-2026 11:15:22	JALVIEW_VERSION is set to '2.12.0'
build	19-Feb-2026 11:15:22	HEADLESS BUILD
build	19-Feb-2026 11:15:22	J2S ENABLED
build	19-Feb-2026 11:15:22	Using a LOCAL profile.
build	19-Feb-2026 11:15:22	eclipseDir exists
build	19-Feb-2026 11:15:23	
build	19-Feb-2026 11:15:23	> Task :clean
build	19-Feb-2026 11:15:23	> Task :cleanClover
build	19-Feb-2026 11:15:23	> Task :cleanTest UP-TO-DATE
build	19-Feb-2026 11:15:25	
build	19-Feb-2026 11:15:25	> Task :cloverInstrJava
build	19-Feb-2026 11:15:25	Clover: About to instrument 1255 files
build	19-Feb-2026 11:15:25	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Feb-2026 11:15:25	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover.db'.
build	19-Feb-2026 11:15:25	Processing files at 1.9 source level.
error	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:27	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	19-Feb-2026 11:15:28	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	19-Feb-2026 11:15:28	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	19-Feb-2026 11:15:28	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	19-Feb-2026 11:15:28	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	19-Feb-2026 11:15:28	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	19-Feb-2026 11:15:28	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	19-Feb-2026 11:15:28	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	19-Feb-2026 11:15:28	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	19-Feb-2026 11:15:28	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	19-Feb-2026 11:15:28	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	19-Feb-2026 11:15:28	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	19-Feb-2026 11:15:28	WARN: Trying to 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	19-Feb-2026 11:15:34	Clover all over. Instrumented 1255 files (133 packages).
build	19-Feb-2026 11:15:36	
build	19-Feb-2026 11:15:36	> Task :cloverInstrTests
build	19-Feb-2026 11:15:36	Clover: About to instrument test files
build	19-Feb-2026 11:15:36	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Feb-2026 11:15:36	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover.db'.
build	19-Feb-2026 11:15:36	Processing files at 1.9 source level.
build	19-Feb-2026 11:15:38	Clover all over. Instrumented 315 files (58 packages).
build	19-Feb-2026 11:15:38	1771 test methods detected.
build	19-Feb-2026 11:15:38	
build	19-Feb-2026 11:15:38	> Task :cloverInstr
build	19-Feb-2026 11:15:40	
build	19-Feb-2026 11:15:40	> Task :compileCloverJava
build	19-Feb-2026 11:15:40	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	19-Feb-2026 11:15:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:15:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:15:40	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:15:40	Setting target compatibility to 11
error	19-Feb-2026 11:15:55	Note: Some input files use or override a deprecated API.
error	19-Feb-2026 11:15:55	Note: Recompile with -Xlint:deprecation for details.
error	19-Feb-2026 11:15:55	Note: Some input files use unchecked or unsafe operations.
error	19-Feb-2026 11:15:55	Note: Recompile with -Xlint:unchecked for details.
build	19-Feb-2026 11:16:01	
build	19-Feb-2026 11:16:01	> Task :processCloverResources NO-SOURCE
build	19-Feb-2026 11:16:01	> Task :cloverClasses
build	19-Feb-2026 11:16:01	> Task :copyHelp
build	19-Feb-2026 11:16:02	> Task :buildIndices
build	19-Feb-2026 11:16:02	> Task :copyResources
build	19-Feb-2026 11:16:02	> Task :copyChannelResources
build	19-Feb-2026 11:16:02	
build	19-Feb-2026 11:16:02	> Task :createBuildProperties
build	19-Feb-2026 11:16:02	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	19-Feb-2026 11:16:02	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:16:02	
build	19-Feb-2026 11:16:02	> Task :buildResources
build	19-Feb-2026 11:16:02	> Task :copyDocs
build	19-Feb-2026 11:16:02	
build	19-Feb-2026 11:16:02	> Task :convertMdFiles
build	19-Feb-2026 11:16:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	19-Feb-2026 11:16:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	19-Feb-2026 11:16:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	19-Feb-2026 11:16:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
build	19-Feb-2026 11:16:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/building.html
build	19-Feb-2026 11:16:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/addingWebClient.html
build	19-Feb-2026 11:16:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	19-Feb-2026 11:16:02	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
build	19-Feb-2026 11:16:03	
build	19-Feb-2026 11:16:03	> Task :releasesTemplates
build	19-Feb-2026 11:16:03	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	19-Feb-2026 11:16:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:16:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:16:03	Stripping rc/test/etc for TEST
build	19-Feb-2026 11:16:03	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	19-Feb-2026 11:16:03	
build	19-Feb-2026 11:16:03	> Task :prepare
build	19-Feb-2026 11:16:05	
build	19-Feb-2026 11:16:05	> Task :compileJava
build	19-Feb-2026 11:16:05	Setting target compatibility to 11
error	19-Feb-2026 11:16:10	Note: Some input files use or override a deprecated API.
error	19-Feb-2026 11:16:10	Note: Recompile with -Xlint:deprecation for details.
error	19-Feb-2026 11:16:10	Note: Some input files use unchecked or unsafe operations.
error	19-Feb-2026 11:16:10	Note: Recompile with -Xlint:unchecked for details.
build	19-Feb-2026 11:16:12	
build	19-Feb-2026 11:16:12	> Task :compileTestJava
build	19-Feb-2026 11:16:12	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	19-Feb-2026 11:16:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:16:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:16:12	Setting target compatibility to 11
error	19-Feb-2026 11:16:18	Note: Some input files use or override a deprecated API.
error	19-Feb-2026 11:16:18	Note: Recompile with -Xlint:deprecation for details.
error	19-Feb-2026 11:16:18	Note: Some input files use unchecked or unsafe operations.
error	19-Feb-2026 11:16:18	Note: Recompile with -Xlint:unchecked for details.
build	19-Feb-2026 11:16:19	
build	19-Feb-2026 11:16:19	> Task :processTestResources
build	19-Feb-2026 11:16:19	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	19-Feb-2026 11:16:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:16:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:16:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:16:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:16:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:16:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:16:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:16:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-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	19-Feb-2026 11:16:19	
build	19-Feb-2026 11:16:19	> Task :testClasses
build	19-Feb-2026 11:16:21	
build	19-Feb-2026 11:16:21	> Task :testTask0
build	19-Feb-2026 11:16:21	Running tests WITH clover
error	19-Feb-2026 11:16:23	WARNING: An illegal reflective access operation has occurred
error	19-Feb-2026 11:16:23	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	19-Feb-2026 11:16:23	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	19-Feb-2026 11:16:23	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	19-Feb-2026 11:16:23	WARNING: All illegal access operations will be denied in a future release
build	19-Feb-2026 11:21:08	
build	19-Feb-2026 11:21:08	> Task :testTask1
build	19-Feb-2026 11:21:08	Running tests WITH clover
error	19-Feb-2026 11:21:09	WARNING: An illegal reflective access operation has occurred
error	19-Feb-2026 11:21:09	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	19-Feb-2026 11:21:09	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	19-Feb-2026 11:21:09	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	19-Feb-2026 11:21:09	WARNING: All illegal access operations will be denied in a future release
build	19-Feb-2026 11:23:20	
build	19-Feb-2026 11:23:20	> Task :testTask2
build	19-Feb-2026 11:23:20	Running tests WITH clover
error	19-Feb-2026 11:23:22	WARNING: An illegal reflective access operation has occurred
error	19-Feb-2026 11:23:22	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	19-Feb-2026 11:23:22	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	19-Feb-2026 11:23:22	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	19-Feb-2026 11:23:22	WARNING: All illegal access operations will be denied in a future release
build	19-Feb-2026 11:23:25	
build	19-Feb-2026 11:23:25	> Task :testTask3
build	19-Feb-2026 11:23:25	Running tests WITH clover
error	19-Feb-2026 11:23:27	WARNING: An illegal reflective access operation has occurred
error	19-Feb-2026 11:23:27	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	19-Feb-2026 11:23:27	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	19-Feb-2026 11:23:27	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	19-Feb-2026 11:23:27	WARNING: All illegal access operations will be denied in a future release
build	19-Feb-2026 11:23:45	
build	19-Feb-2026 11:23:45	> Task :test NO-SOURCE
build	19-Feb-2026 11:23:45	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	19-Feb-2026 11:23:45	│jalview:testTask0 results: SUCCESS (2104 tests, 2104 successes, 0 failures, 0 skipped) in 4 minutes, 45.908 seconds   │
build	19-Feb-2026 11:23:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/testTask0/index.html│
build	19-Feb-2026 11:23:45	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Feb-2026 11:23:45	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 12.548 seconds       │
build	19-Feb-2026 11:23:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/testTask1/index.html│
build	19-Feb-2026 11:23:45	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Feb-2026 11:23:45	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 5.062 seconds                     │
build	19-Feb-2026 11:23:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/testTask2/index.html│
build	19-Feb-2026 11:23:45	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Feb-2026 11:23:45	│jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 21.219 seconds                  │
build	19-Feb-2026 11:23:45	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/testTask3/index.html│
build	19-Feb-2026 11:23:45	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Feb-2026 11:23:45	│OVERALL: results: SUCCESS (2181 tests, 2180 successes, 0 failures, 1 skipped) in 6 minutes, 84.737 seconds            │
build	19-Feb-2026 11:23:45	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	19-Feb-2026 11:23:45	
build	19-Feb-2026 11:23:45	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	19-Feb-2026 11:23:45	
build	19-Feb-2026 11:23:45	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	19-Feb-2026 11:23:45	
build	19-Feb-2026 11:23:45	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	19-Feb-2026 11:23:45	
build	19-Feb-2026 11:23:45	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	19-Feb-2026 11:23:45	Please consult deprecation warnings for more details.
build	19-Feb-2026 11:23:45	
build	19-Feb-2026 11:23:45	BUILD SUCCESSFUL in 8m 23s
build	19-Feb-2026 11:23:45	21 actionable tasks: 20 executed, 1 up-to-date
simple	19-Feb-2026 11:23:45	Finished task 'Run tests with openclover under gradle' with result: Success
simple	19-Feb-2026 11:23:45	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	19-Feb-2026 11:23:45	Bamboo Artifactory Plugin version: 2.6.2
command	19-Feb-2026 11:23:45	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests #4 (JB-GDB744-JOB1-4)'\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-GDB744-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_repository_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB744-JOB1-4\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-GDB744-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB744-JOB1\nbamboo_shortPlanName=bug-JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=4\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-GDB744-JOB1-4\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_shortPlanKey=GDB744\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_buildTimeStamp=2026-02-19T11:15:20.537Z\nbamboo_repository_previous_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_planRepository_previousRevision=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_repository_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildResultKey=JB-GDB744-JOB1-4\nbamboo_repository_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests\nbamboo_repository_48169013_git_username=\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_48169013_name=Jalview Gitlab\nbamboo_planRepository_1_revision=944aa492571e8adede487266d9a4a7143a7cc0df\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169013_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_repository_name=Jalview Gitlab\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_48169013_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_dependenciesDisabled=false\nbamboo_repository_48169013_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\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_48169013_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_planRepository_branchDisplayName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\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-47972457\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_ManualBuildTriggerReason_userName=reniacorreya\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169013_previous_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\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-GDB744-JOB1\nbamboo_planKey=JB-GDB744\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	19-Feb-2026 11:23:45	2414
build	19-Feb-2026 11:23:50	
build	19-Feb-2026 11:23:50	> Configure project :
build	19-Feb-2026 11:23:50	Using properties from file './utils/channels/default/channel_gradle.properties'
build	19-Feb-2026 11:23:51	JALVIEW_VERSION is set to '2.12.0'
build	19-Feb-2026 11:23:51	HEADLESS BUILD
build	19-Feb-2026 11:23:51	J2S ENABLED
build	19-Feb-2026 11:23:51	Using a LOCAL profile.
build	19-Feb-2026 11:23:52	eclipseDir exists
build	19-Feb-2026 11:23:54	
build	19-Feb-2026 11:23:54	> Task :cloverHtmlReport
build	19-Feb-2026 11:23:54	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Feb-2026 11:23:55	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/clover'
build	19-Feb-2026 11:24:49	Done. Processed 137 packages in 53498ms (390ms per package).
build	19-Feb-2026 11:24:55	
build	19-Feb-2026 11:24:55	> Task :cloverXmlReport
build	19-Feb-2026 11:24:55	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Feb-2026 11:24:55	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/clover/clover.xml'
build	19-Feb-2026 11:24:56	
build	19-Feb-2026 11:24:56	> Task :cloverReport
build	19-Feb-2026 11:24:56	
build	19-Feb-2026 11:24:56	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	19-Feb-2026 11:24:56	
build	19-Feb-2026 11:24:56	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	19-Feb-2026 11:24:56	
build	19-Feb-2026 11:24:56	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	19-Feb-2026 11:24:56	
build	19-Feb-2026 11:24:56	BUILD SUCCESSFUL in 1m 10s
build	19-Feb-2026 11:24:56	2 actionable tasks: 2 executed
simple	19-Feb-2026 11:24:56	Finished task 'Clover Report' with result: Success
simple	19-Feb-2026 11:24:56	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	19-Feb-2026 11:24:56	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1...
simple	19-Feb-2026 11:24:56	Finished task 'TestNG Parser' with result: Success
simple	19-Feb-2026 11:24:56	Running post build plugin 'NCover Results Collector'
simple	19-Feb-2026 11:24:56	Running post build plugin 'Artifact Copier'
simple	19-Feb-2026 11:24:56	Publishing an artifact: Clover Report (System)
simple	19-Feb-2026 11:24:58	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.865 s
simple	19-Feb-2026 11:24:58	Publishing an artifact: TestNG report
error	19-Feb-2026 11:24:58	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/test does not exist.
simple	19-Feb-2026 11:24:58	The artifact hasn't been successfully published after 2.368 ms
simple	19-Feb-2026 11:24:58	Running post build plugin 'Artifactory Release Management Staging'
simple	19-Feb-2026 11:24:58	Running post build plugin 'Artifactory Build Info Copier'
simple	19-Feb-2026 11:24:58	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	19-Feb-2026 11:24:58	Running post build plugin 'npm Cache Cleanup'
simple	19-Feb-2026 11:24:58	Running post build plugin 'Clover Results Collector'
simple	19-Feb-2026 11:24:58	Running post build plugin 'Docker Container Cleanup'
simple	19-Feb-2026 11:24:58	Finalising the build...
simple	19-Feb-2026 11:24:58	Stopping timer.
simple	19-Feb-2026 11:24:58	Build JB-GDB744-JOB1-4 completed.
simple	19-Feb-2026 11:24:58	Running on server: post build plugin 'NCover Results Collector'
simple	19-Feb-2026 11:24:58	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	19-Feb-2026 11:24:58	Running on server: post build plugin 'Clover Delta Calculator'
simple	19-Feb-2026 11:24:58	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	19-Feb-2026 11:24:58	All post build plugins have finished
simple	19-Feb-2026 11:24:58	Generating build results summary...
simple	19-Feb-2026 11:24:58	Saving build results to disk...
simple	19-Feb-2026 11:24:58	Logging substituted variables...
simple	19-Feb-2026 11:24:58	Indexing build results...
simple	19-Feb-2026 11:24:58	Finished building JB-GDB744-JOB1-4.