simple	04-Feb-2026 17:46:23	Build Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests #2 (JB-GDB744-JOB1-2) started building on agent Default Agent
simple	04-Feb-2026 17:46:23	
simple	04-Feb-2026 17:46:23	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1
simple	04-Feb-2026 17:46:23	Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests #2 (JB-GDB744-JOB1-2)
simple	04-Feb-2026 17:46:23	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	04-Feb-2026 17:46:23	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1
simple	04-Feb-2026 17:46:23	Updating source code to revision: dbbef339de0089e00e1a460dd6f099e671ff9382
simple	04-Feb-2026 17:46:23	Fetching 'refs/heads/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	04-Feb-2026 17:46:23	Checking out revision dbbef339de0089e00e1a460dd6f099e671ff9382.
simple	04-Feb-2026 17:46:24	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	04-Feb-2026 17:46:24	   205fb76..dbbef33  bug/JAL-4624_JAL-4623_Mul_SS_in_PCA -> origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA
simple	04-Feb-2026 17:46:24	   b0aa69e..c709dd6  epic/JAL-3907_jalview_running_under_java_17 -> origin/epic/JAL-3907_jalview_running_under_java_17
simple	04-Feb-2026 17:46:24	 * [new branch]      epic/JAL-4320_gradle_upgrade_to_gradle9 -> origin/epic/JAL-4320_gradle_upgrade_to_gradle9
simple	04-Feb-2026 17:46:25	Already on 'bug/JAL-4624_JAL-4623_Mul_SS_in_PCA'
simple	04-Feb-2026 17:46:25	Your branch is behind 'origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA' by 2 commits, and can be fast-forwarded.
simple	04-Feb-2026 17:46:25	  (use "git pull" to update your local branch)
simple	04-Feb-2026 17:46:25	HEAD is now at dbbef33 JAL-4623 Exclude seq without annotation for analysis
simple	04-Feb-2026 17:46:25	Updated source code to revision: dbbef339de0089e00e1a460dd6f099e671ff9382
simple	04-Feb-2026 17:46:25	Finished task 'Checkout Default Repository' with result: Success
simple	04-Feb-2026 17:46:25	Running pre-build action: VCS Version Collector
simple	04-Feb-2026 17:46:25	Running pre-build action: Artifactory Release Staging
simple	04-Feb-2026 17:46:25	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	04-Feb-2026 17:46:25	Bamboo Artifactory Plugin version: 2.6.2
command	04-Feb-2026 17:46:25	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests #2 (JB-GDB744-JOB1-2)'\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=dbbef339de0089e00e1a460dd6f099e671ff9382\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB744-JOB1-2\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=2\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-JOB1-2\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=dbbef339de0089e00e1a460dd6f099e671ff9382\nbamboo_buildTimeStamp=2026-02-04T17:46:23.604Z\nbamboo_repository_previous_revision_number=205fb769b67a07590580f2d3b6f0e36cfa3ddeec\nbamboo_planRepository_previousRevision=205fb769b67a07590580f2d3b6f0e36cfa3ddeec\nbamboo_repository_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildResultKey=JB-GDB744-JOB1-2\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=dbbef339de0089e00e1a460dd6f099e671ff9382\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169013_revision_number=dbbef339de0089e00e1a460dd6f099e671ff9382\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_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=205fb769b67a07590580f2d3b6f0e36cfa3ddeec\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_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169013_previous_revision_number=205fb769b67a07590580f2d3b6f0e36cfa3ddeec\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	04-Feb-2026 17:46:25	2414
build	04-Feb-2026 17:46:26	Starting a Gradle Daemon (subsequent builds will be faster)
build	04-Feb-2026 17:46:36	
build	04-Feb-2026 17:46:36	> Configure project :
build	04-Feb-2026 17:46:36	Using properties from file './utils/channels/default/channel_gradle.properties'
build	04-Feb-2026 17:46:36	JALVIEW_VERSION is set to '2.12.0'
build	04-Feb-2026 17:46:36	HEADLESS BUILD
build	04-Feb-2026 17:46:36	J2S ENABLED
build	04-Feb-2026 17:46:37	Using a LOCAL profile.
build	04-Feb-2026 17:46:38	eclipseDir exists
build	04-Feb-2026 17:46:39	
build	04-Feb-2026 17:46:39	> Task :clean
build	04-Feb-2026 17:46:39	> Task :cleanClover
build	04-Feb-2026 17:46:39	> Task :cleanTest UP-TO-DATE
build	04-Feb-2026 17:46:41	
build	04-Feb-2026 17:46:41	> Task :cloverInstrJava
build	04-Feb-2026 17:46:41	Clover: About to instrument 1255 files
build	04-Feb-2026 17:46:41	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	04-Feb-2026 17:46:41	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover.db'.
build	04-Feb-2026 17:46:41	Processing files at 1.9 source level.
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	04-Feb-2026 17:46:44	WARN: Trying to 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	04-Feb-2026 17:46:50	Clover all over. Instrumented 1255 files (133 packages).
build	04-Feb-2026 17:46:53	
build	04-Feb-2026 17:46:53	> Task :cloverInstrTests
build	04-Feb-2026 17:46:53	Clover: About to instrument test files
build	04-Feb-2026 17:46:53	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	04-Feb-2026 17:46:53	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/clover/clover.db'.
build	04-Feb-2026 17:46:53	Processing files at 1.9 source level.
build	04-Feb-2026 17:46:55	Clover all over. Instrumented 315 files (58 packages).
build	04-Feb-2026 17:46:55	1770 test methods detected.
build	04-Feb-2026 17:46:56	
build	04-Feb-2026 17:46:56	> Task :cloverInstr
build	04-Feb-2026 17:46:58	
build	04-Feb-2026 17:46:58	> Task :compileCloverJava
build	04-Feb-2026 17:46:58	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	04-Feb-2026 17:46:58	  - 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	04-Feb-2026 17:46:58	  - 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	04-Feb-2026 17:46:58	  - 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	04-Feb-2026 17:46:58	Setting target compatibility to 11
error	04-Feb-2026 17:47:22	Note: Some input files use or override a deprecated API.
error	04-Feb-2026 17:47:22	Note: Recompile with -Xlint:deprecation for details.
error	04-Feb-2026 17:47:22	Note: Some input files use unchecked or unsafe operations.
error	04-Feb-2026 17:47:22	Note: Recompile with -Xlint:unchecked for details.
build	04-Feb-2026 17:47:30	
build	04-Feb-2026 17:47:30	> Task :processCloverResources NO-SOURCE
build	04-Feb-2026 17:47:30	> Task :cloverClasses
build	04-Feb-2026 17:47:30	> Task :copyHelp
build	04-Feb-2026 17:47:31	> Task :buildIndices
build	04-Feb-2026 17:47:31	> Task :copyResources
build	04-Feb-2026 17:47:31	> Task :copyChannelResources
build	04-Feb-2026 17:47:31	
build	04-Feb-2026 17:47:31	> Task :createBuildProperties
build	04-Feb-2026 17:47:31	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	04-Feb-2026 17:47:31	  - 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	04-Feb-2026 17:47:31	
build	04-Feb-2026 17:47:31	> Task :buildResources
build	04-Feb-2026 17:47:32	> Task :copyDocs
build	04-Feb-2026 17:47:32	
build	04-Feb-2026 17:47:32	> Task :convertMdFiles
build	04-Feb-2026 17:47:32	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	04-Feb-2026 17:47:32	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	04-Feb-2026 17:47:32	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	04-Feb-2026 17:47:32	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
build	04-Feb-2026 17:47:32	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/building.html
build	04-Feb-2026 17:47:32	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/addingWebClient.html
build	04-Feb-2026 17:47:32	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	04-Feb-2026 17:47:32	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
build	04-Feb-2026 17:47:32	
build	04-Feb-2026 17:47:32	> Task :releasesTemplates
build	04-Feb-2026 17:47:32	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	04-Feb-2026 17:47:32	  - 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	04-Feb-2026 17:47:32	  - 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	04-Feb-2026 17:47:32	Stripping rc/test/etc for TEST
build	04-Feb-2026 17:47:32	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	04-Feb-2026 17:47:32	
build	04-Feb-2026 17:47:32	> Task :prepare
build	04-Feb-2026 17:47:34	
build	04-Feb-2026 17:47:34	> Task :compileJava
build	04-Feb-2026 17:47:34	Setting target compatibility to 11
error	04-Feb-2026 17:47:41	Note: Some input files use or override a deprecated API.
error	04-Feb-2026 17:47:41	Note: Recompile with -Xlint:deprecation for details.
error	04-Feb-2026 17:47:41	Note: Some input files use unchecked or unsafe operations.
error	04-Feb-2026 17:47:41	Note: Recompile with -Xlint:unchecked for details.
build	04-Feb-2026 17:47:45	
build	04-Feb-2026 17:47:45	> Task :compileTestJava
build	04-Feb-2026 17:47:45	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	04-Feb-2026 17:47:45	  - 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	04-Feb-2026 17:47:45	  - 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	04-Feb-2026 17:47:45	Setting target compatibility to 11
error	04-Feb-2026 17:47:52	Note: Some input files use or override a deprecated API.
error	04-Feb-2026 17:47:52	Note: Recompile with -Xlint:deprecation for details.
error	04-Feb-2026 17:47:52	Note: Some input files use unchecked or unsafe operations.
error	04-Feb-2026 17:47:52	Note: Recompile with -Xlint:unchecked for details.
build	04-Feb-2026 17:47:53	
build	04-Feb-2026 17:47:53	> Task :processTestResources
build	04-Feb-2026 17:47:53	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	04-Feb-2026 17:47:53	  - 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	04-Feb-2026 17:47:53	  - 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	04-Feb-2026 17:47:53	  - 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	04-Feb-2026 17:47:53	  - 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	04-Feb-2026 17:47:53	  - 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	04-Feb-2026 17:47:53	  - 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	04-Feb-2026 17:47:53	  - 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	04-Feb-2026 17:47:53	  - 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	04-Feb-2026 17:47:53	
build	04-Feb-2026 17:47:53	> Task :testClasses
build	04-Feb-2026 17:47:55	
build	04-Feb-2026 17:47:55	> Task :testTask0
build	04-Feb-2026 17:47:55	Running tests WITH clover
error	04-Feb-2026 17:47:57	WARNING: An illegal reflective access operation has occurred
error	04-Feb-2026 17:47:57	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	04-Feb-2026 17:47:57	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	04-Feb-2026 17:47:57	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	04-Feb-2026 17:47:57	WARNING: All illegal access operations will be denied in a future release
build	04-Feb-2026 17:50:23	[149.914s][warning][gc,alloc] AWT-EventQueue-0: Retried waiting for GCLocker too often allocating 135080516 words
build	04-Feb-2026 17:52:49	
build	04-Feb-2026 17:52:49	> Task :testTask1
build	04-Feb-2026 17:52:49	Running tests WITH clover
error	04-Feb-2026 17:52:51	WARNING: An illegal reflective access operation has occurred
error	04-Feb-2026 17:52:51	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	04-Feb-2026 17:52:51	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	04-Feb-2026 17:52:51	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	04-Feb-2026 17:52:51	WARNING: All illegal access operations will be denied in a future release
build	04-Feb-2026 17:55:03	
build	04-Feb-2026 17:55:03	> Task :testTask2
build	04-Feb-2026 17:55:03	Running tests WITH clover
error	04-Feb-2026 17:55:05	WARNING: An illegal reflective access operation has occurred
error	04-Feb-2026 17:55:05	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	04-Feb-2026 17:55:05	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	04-Feb-2026 17:55:05	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	04-Feb-2026 17:55:05	WARNING: All illegal access operations will be denied in a future release
build	04-Feb-2026 17:55:09	
build	04-Feb-2026 17:55:09	> Task :testTask3
build	04-Feb-2026 17:55:09	Running tests WITH clover
error	04-Feb-2026 17:55:11	WARNING: An illegal reflective access operation has occurred
error	04-Feb-2026 17:55:11	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	04-Feb-2026 17:55:11	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	04-Feb-2026 17:55:11	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	04-Feb-2026 17:55:11	WARNING: All illegal access operations will be denied in a future release
build	04-Feb-2026 17:55:30	
build	04-Feb-2026 17:55:30	> Task :test NO-SOURCE
build	04-Feb-2026 17:55:31	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	04-Feb-2026 17:55:31	│jalview:testTask0 results: SUCCESS (2103 tests, 2103 successes, 0 failures, 0 skipped) in 4 minutes, 52.913 seconds   │
build	04-Feb-2026 17:55:31	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/testTask0/index.html│
build	04-Feb-2026 17:55:31	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	04-Feb-2026 17:55:31	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 14.132 seconds       │
build	04-Feb-2026 17:55:31	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/testTask1/index.html│
build	04-Feb-2026 17:55:31	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	04-Feb-2026 17:55:31	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 6.085 seconds                     │
build	04-Feb-2026 17:55:31	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/testTask2/index.html│
build	04-Feb-2026 17:55:31	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	04-Feb-2026 17:55:31	│jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 22.975 seconds                  │
build	04-Feb-2026 17:55:31	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/tests/testTask3/index.html│
build	04-Feb-2026 17:55:31	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	04-Feb-2026 17:55:31	│OVERALL: results: SUCCESS (2180 tests, 2179 successes, 0 failures, 1 skipped) in 6 minutes, 96.105 seconds            │
build	04-Feb-2026 17:55:31	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	04-Feb-2026 17:55:31	
build	04-Feb-2026 17:55:31	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	04-Feb-2026 17:55:31	
build	04-Feb-2026 17:55:31	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	04-Feb-2026 17:55:31	
build	04-Feb-2026 17:55:31	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	04-Feb-2026 17:55:31	
build	04-Feb-2026 17:55:31	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	04-Feb-2026 17:55:31	Please consult deprecation warnings for more details.
build	04-Feb-2026 17:55:31	
build	04-Feb-2026 17:55:31	BUILD SUCCESSFUL in 9m 5s
build	04-Feb-2026 17:55:31	21 actionable tasks: 20 executed, 1 up-to-date
simple	04-Feb-2026 17:55:31	Finished task 'Run tests with openclover under gradle' with result: Success
simple	04-Feb-2026 17:55:31	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	04-Feb-2026 17:55:31	Bamboo Artifactory Plugin version: 2.6.2
command	04-Feb-2026 17:55:31	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Clover and Tests #2 (JB-GDB744-JOB1-2)'\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=dbbef339de0089e00e1a460dd6f099e671ff9382\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB744-JOB1-2\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=2\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-JOB1-2\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=dbbef339de0089e00e1a460dd6f099e671ff9382\nbamboo_buildTimeStamp=2026-02-04T17:46:23.604Z\nbamboo_repository_previous_revision_number=205fb769b67a07590580f2d3b6f0e36cfa3ddeec\nbamboo_planRepository_previousRevision=205fb769b67a07590580f2d3b6f0e36cfa3ddeec\nbamboo_repository_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildResultKey=JB-GDB744-JOB1-2\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=dbbef339de0089e00e1a460dd6f099e671ff9382\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169013_revision_number=dbbef339de0089e00e1a460dd6f099e671ff9382\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_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=205fb769b67a07590580f2d3b6f0e36cfa3ddeec\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_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169013_previous_revision_number=205fb769b67a07590580f2d3b6f0e36cfa3ddeec\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	04-Feb-2026 17:55:31	2414
build	04-Feb-2026 17:55:37	
build	04-Feb-2026 17:55:37	> Configure project :
build	04-Feb-2026 17:55:37	Using properties from file './utils/channels/default/channel_gradle.properties'
build	04-Feb-2026 17:55:37	JALVIEW_VERSION is set to '2.12.0'
build	04-Feb-2026 17:55:37	HEADLESS BUILD
build	04-Feb-2026 17:55:37	J2S ENABLED
build	04-Feb-2026 17:55:38	Using a LOCAL profile.
build	04-Feb-2026 17:55:38	eclipseDir exists
build	04-Feb-2026 17:55:41	
build	04-Feb-2026 17:55:41	> Task :cloverHtmlReport
build	04-Feb-2026 17:55:41	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	04-Feb-2026 17:55:43	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/clover'
error	04-Feb-2026 17:56:18	ERROR: Invalid Java source found or Clover failed to parse it: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/src/jalview/bin/Jalview.java
build	04-Feb-2026 17:56:37	Done. Processed 137 packages in 54437ms (397ms per package).
build	04-Feb-2026 17:56:42	
build	04-Feb-2026 17:56:42	> Task :cloverXmlReport
build	04-Feb-2026 17:56:42	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	04-Feb-2026 17:56:43	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1/build/reports/clover/clover.xml'
build	04-Feb-2026 17:56:44	
build	04-Feb-2026 17:56:44	> Task :cloverReport
build	04-Feb-2026 17:56:44	
build	04-Feb-2026 17:56:44	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	04-Feb-2026 17:56:44	
build	04-Feb-2026 17:56:44	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	04-Feb-2026 17:56:44	
build	04-Feb-2026 17:56:44	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	04-Feb-2026 17:56:44	
build	04-Feb-2026 17:56:44	BUILD SUCCESSFUL in 1m 12s
build	04-Feb-2026 17:56:44	2 actionable tasks: 2 executed
simple	04-Feb-2026 17:56:44	Finished task 'Clover Report' with result: Success
simple	04-Feb-2026 17:56:44	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	04-Feb-2026 17:56:44	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB744-JOB1...
simple	04-Feb-2026 17:56:44	Finished task 'TestNG Parser' with result: Success
simple	04-Feb-2026 17:56:44	Running post build plugin 'NCover Results Collector'
simple	04-Feb-2026 17:56:44	Running post build plugin 'Artifact Copier'
simple	04-Feb-2026 17:56:44	Publishing an artifact: Clover Report (System)
simple	04-Feb-2026 17:56:46	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.843 s
simple	04-Feb-2026 17:56:46	Publishing an artifact: TestNG report
error	04-Feb-2026 17:56:46	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	04-Feb-2026 17:56:46	The artifact hasn't been successfully published after 3.301 ms
simple	04-Feb-2026 17:56:46	Running post build plugin 'Artifactory Release Management Staging'
simple	04-Feb-2026 17:56:46	Running post build plugin 'Artifactory Build Info Copier'
simple	04-Feb-2026 17:56:46	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	04-Feb-2026 17:56:46	Running post build plugin 'npm Cache Cleanup'
simple	04-Feb-2026 17:56:46	Running post build plugin 'Clover Results Collector'
simple	04-Feb-2026 17:56:46	Running post build plugin 'Docker Container Cleanup'
simple	04-Feb-2026 17:56:46	Finalising the build...
simple	04-Feb-2026 17:56:46	Stopping timer.
simple	04-Feb-2026 17:56:46	Build JB-GDB744-JOB1-2 completed.
simple	04-Feb-2026 17:56:46	Running on server: post build plugin 'NCover Results Collector'
simple	04-Feb-2026 17:56:46	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	04-Feb-2026 17:56:46	Running on server: post build plugin 'Clover Delta Calculator'
simple	04-Feb-2026 17:56:46	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	04-Feb-2026 17:56:46	All post build plugins have finished
simple	04-Feb-2026 17:56:46	Generating build results summary...
simple	04-Feb-2026 17:56:46	Saving build results to disk...
simple	04-Feb-2026 17:56:46	Logging substituted variables...
simple	04-Feb-2026 17:56:47	Indexing build results...
simple	04-Feb-2026 17:56:47	Finished building JB-GDB744-JOB1-2.