simple 07-Jan-2026 02:39:23 Build Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests #2 (JB-GDB738-JOB1-2) started building on agent Default Agent simple 07-Jan-2026 02:39:23 simple 07-Jan-2026 02:39:23 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1 simple 07-Jan-2026 02:39:23 Executing build Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests #2 (JB-GDB738-JOB1-2) simple 07-Jan-2026 02:39:23 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 07-Jan-2026 02:39:23 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1 simple 07-Jan-2026 02:39:23 Updating source code to revision: 89c895478e2de885c6475780e1191e8b19fe1dff simple 07-Jan-2026 02:39:23 Fetching 'refs/heads/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 07-Jan-2026 02:39:23 Checking out revision 89c895478e2de885c6475780e1191e8b19fe1dff. simple 07-Jan-2026 02:39:23 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 07-Jan-2026 02:39:23 6c41459..89c8954 feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp -> origin/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp simple 07-Jan-2026 02:39:25 Already on 'feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp' simple 07-Jan-2026 02:39:25 Your branch is behind 'origin/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp' by 1 commit, and can be fast-forwarded. simple 07-Jan-2026 02:39:25 (use "git pull" to update your local branch) simple 07-Jan-2026 02:39:25 HEAD is now at 89c8954 JAL-4637 rearrange testShowOrDontShowOccupancy to more directly test positive cases simple 07-Jan-2026 02:39:25 Updated source code to revision: 89c895478e2de885c6475780e1191e8b19fe1dff simple 07-Jan-2026 02:39:25 Finished task 'Checkout Default Repository' with result: Success simple 07-Jan-2026 02:39:25 Running pre-build action: VCS Version Collector simple 07-Jan-2026 02:39:25 Running pre-build action: Artifactory Release Staging simple 07-Jan-2026 02:39:25 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 07-Jan-2026 02:39:25 Bamboo Artifactory Plugin version: 2.6.2 command 07-Jan-2026 02:39:25 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests #2 (JB-GDB738-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-GDB738-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_repository_revision_number=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB738-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-GDB738-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB738-JOB1\nbamboo_shortPlanName=feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_repository_48168979_name=Jalview Gitlab\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-GDB738-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 - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_shortPlanKey=GDB738\nbamboo_shortJobKey=JOB1\nbamboo_repository_48168979_git_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_buildTimeStamp=2026-01-07T02:39:23.550Z\nbamboo_repository_previous_revision_number=6c414592dabe553216b6c62e1a28208e99dd8186\nbamboo_planRepository_previousRevision=6c414592dabe553216b6c62e1a28208e99dd8186\nbamboo_repository_48168979_branch_name=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_repository_git_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_buildResultKey=JB-GDB738-JOB1-2\nbamboo_repository_branch_name=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=89c895478e2de885c6475780e1191e8b19fe1dff\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_repository_48168979_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_48168979_git_username=\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=6c414592dabe553216b6c62e1a28208e99dd8186\nbamboo_planRepository_branchDisplayName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_repository_48168979_previous_revision_number=6c414592dabe553216b6c62e1a28208e99dd8186\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_48168979_revision_number=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-47972389\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1\nbamboo_planKey=JB-GDB738\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 07-Jan-2026 02:39:25 2414 build 07-Jan-2026 02:39:26 build 07-Jan-2026 02:39:26 > Configure project : build 07-Jan-2026 02:39:26 Using properties from file './utils/channels/default/channel_gradle.properties' build 07-Jan-2026 02:39:26 JALVIEW_VERSION is set to '2.12.0' build 07-Jan-2026 02:39:26 HEADLESS BUILD build 07-Jan-2026 02:39:26 J2S ENABLED build 07-Jan-2026 02:39:26 Using a LOCAL profile. build 07-Jan-2026 02:39:26 eclipseDir exists build 07-Jan-2026 02:39:27 build 07-Jan-2026 02:39:27 > Task :clean build 07-Jan-2026 02:39:27 > Task :cleanClover build 07-Jan-2026 02:39:27 > Task :cleanTest UP-TO-DATE build 07-Jan-2026 02:39:29 build 07-Jan-2026 02:39:29 > Task :cloverInstrJava build 07-Jan-2026 02:39:29 Clover: About to instrument 1255 files build 07-Jan-2026 02:39:29 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 07-Jan-2026 02:39:29 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover.db'. build 07-Jan-2026 02:39:29 Processing files at 1.9 source level. error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:31 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:32 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:32 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:32 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:32 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:32 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:32 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:32 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:32 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:32 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:32 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:32 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 07-Jan-2026 02:39:32 WARN: Trying to 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 07-Jan-2026 02:39:36 Clover all over. Instrumented 1255 files (133 packages). build 07-Jan-2026 02:39:39 build 07-Jan-2026 02:39:39 > Task :cloverInstrTests build 07-Jan-2026 02:39:39 Clover: About to instrument test files build 07-Jan-2026 02:39:39 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 07-Jan-2026 02:39:39 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover.db'. build 07-Jan-2026 02:39:39 Processing files at 1.9 source level. build 07-Jan-2026 02:39:41 Clover all over. Instrumented 316 files (58 packages). build 07-Jan-2026 02:39:41 1774 test methods detected. build 07-Jan-2026 02:39:41 build 07-Jan-2026 02:39:41 > Task :cloverInstr build 07-Jan-2026 02:39:43 build 07-Jan-2026 02:39:43 > Task :compileCloverJava build 07-Jan-2026 02:39:43 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 07-Jan-2026 02:39:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:39:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:39:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:39:43 Setting target compatibility to 11 error 07-Jan-2026 02:39:55 Note: Some input files use or override a deprecated API. error 07-Jan-2026 02:39:55 Note: Recompile with -Xlint:deprecation for details. error 07-Jan-2026 02:39:55 Note: Some input files use unchecked or unsafe operations. error 07-Jan-2026 02:39:55 Note: Recompile with -Xlint:unchecked for details. build 07-Jan-2026 02:40:00 build 07-Jan-2026 02:40:00 > Task :processCloverResources NO-SOURCE build 07-Jan-2026 02:40:00 > Task :cloverClasses build 07-Jan-2026 02:40:00 > Task :copyHelp build 07-Jan-2026 02:40:01 > Task :buildIndices build 07-Jan-2026 02:40:02 > Task :copyResources build 07-Jan-2026 02:40:02 > Task :copyChannelResources build 07-Jan-2026 02:40:02 build 07-Jan-2026 02:40:02 > Task :createBuildProperties build 07-Jan-2026 02:40:02 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 07-Jan-2026 02:40:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:40:02 build 07-Jan-2026 02:40:02 > Task :buildResources build 07-Jan-2026 02:40:02 > Task :copyDocs build 07-Jan-2026 02:40:02 build 07-Jan-2026 02:40:02 > Task :convertMdFiles build 07-Jan-2026 02:40:02 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 07-Jan-2026 02:40:02 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/releaseprocess.html build 07-Jan-2026 02:40:02 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 07-Jan-2026 02:40:02 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/JalviewJS-API.html build 07-Jan-2026 02:40:02 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/building.html build 07-Jan-2026 02:40:02 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/addingWebClient.html build 07-Jan-2026 02:40:02 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/jalview-projects.html build 07-Jan-2026 02:40:02 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html build 07-Jan-2026 02:40:02 build 07-Jan-2026 02:40:02 > Task :releasesTemplates build 07-Jan-2026 02:40:02 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 07-Jan-2026 02:40:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:40:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:40:02 Stripping rc/test/etc for TEST build 07-Jan-2026 02:40:02 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 07-Jan-2026 02:40:02 build 07-Jan-2026 02:40:02 > Task :prepare build 07-Jan-2026 02:40:04 build 07-Jan-2026 02:40:04 > Task :compileJava build 07-Jan-2026 02:40:04 Setting target compatibility to 11 error 07-Jan-2026 02:40:09 Note: Some input files use or override a deprecated API. error 07-Jan-2026 02:40:09 Note: Recompile with -Xlint:deprecation for details. error 07-Jan-2026 02:40:09 Note: Some input files use unchecked or unsafe operations. error 07-Jan-2026 02:40:09 Note: Recompile with -Xlint:unchecked for details. build 07-Jan-2026 02:40:11 build 07-Jan-2026 02:40:11 > Task :compileTestJava build 07-Jan-2026 02:40:11 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 07-Jan-2026 02:40:11 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:40:11 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:40:11 Setting target compatibility to 11 error 07-Jan-2026 02:40:16 Note: Some input files use or override a deprecated API. error 07-Jan-2026 02:40:16 Note: Recompile with -Xlint:deprecation for details. error 07-Jan-2026 02:40:16 Note: Some input files use unchecked or unsafe operations. error 07-Jan-2026 02:40:16 Note: Recompile with -Xlint:unchecked for details. build 07-Jan-2026 02:40:17 build 07-Jan-2026 02:40:17 > Task :processTestResources build 07-Jan-2026 02:40:17 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 07-Jan-2026 02:40:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:40:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:40:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:40:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:40:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:40:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:40:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:40:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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 07-Jan-2026 02:40:17 build 07-Jan-2026 02:40:17 > Task :testClasses build 07-Jan-2026 02:40:19 build 07-Jan-2026 02:40:19 > Task :testTask0 build 07-Jan-2026 02:40:19 Running tests WITH clover error 07-Jan-2026 02:40:20 WARNING: An illegal reflective access operation has occurred error 07-Jan-2026 02:40:20 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 07-Jan-2026 02:40:20 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 07-Jan-2026 02:40:20 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 07-Jan-2026 02:40:20 WARNING: All illegal access operations will be denied in a future release build 07-Jan-2026 02:41:53 build 07-Jan-2026 02:41:53 Gradle suite > Gradle test > jalview.gui.AlignViewportTest > testShowOrDontShowOccupancy FAILED build 07-Jan-2026 02:41:53 java.lang.AssertionError: Expected occupancy to be non-null in column 5 expected object to not be null build 07-Jan-2026 02:41:53 at org.testng.Assert.fail(Assert.java:110) build 07-Jan-2026 02:41:53 at org.testng.Assert.assertNotNull(Assert.java:1319) build 07-Jan-2026 02:41:53 at jalview.gui.AlignViewportTest.__CLR4_4_1lfq8444593(AlignViewportTest.java:482) build 07-Jan-2026 02:41:53 at jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy(AlignViewportTest.java:442) build 07-Jan-2026 02:44:45 build 07-Jan-2026 02:44:45 Gradle suite > Gradle test > jalview.workers.AlignCaclManager2Test > testRestartDisabledWorker FAILED build 07-Jan-2026 02:44:45 java.lang.AssertionError: expected [2] but found [1] build 07-Jan-2026 02:44:45 at org.testng.Assert.fail(Assert.java:110) build 07-Jan-2026 02:44:45 at org.testng.Assert.failNotEquals(Assert.java:1413) build 07-Jan-2026 02:44:45 at org.testng.Assert.assertEqualsImpl(Assert.java:149) build 07-Jan-2026 02:44:45 at org.testng.Assert.assertEquals(Assert.java:131) build 07-Jan-2026 02:44:45 at org.testng.Assert.assertEquals(Assert.java:1240) build 07-Jan-2026 02:44:45 at org.testng.Assert.assertEquals(Assert.java:1274) build 07-Jan-2026 02:44:45 at jalview.workers.AlignCaclManager2Test.__CLR4_4_1v06epq4l65(AlignCaclManager2Test.java:157) build 07-Jan-2026 02:44:45 at jalview.workers.AlignCaclManager2Test.testRestartDisabledWorker(AlignCaclManager2Test.java:145) error 07-Jan-2026 02:44:56 error 07-Jan-2026 02:44:56 2107 tests completed, 2 failed build 07-Jan-2026 02:44:56 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/testTask0/index.html build 07-Jan-2026 02:44:58 build 07-Jan-2026 02:44:58 > Task :testTask1 build 07-Jan-2026 02:44:58 Running tests WITH clover error 07-Jan-2026 02:44:59 WARNING: An illegal reflective access operation has occurred error 07-Jan-2026 02:44:59 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 07-Jan-2026 02:44:59 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 07-Jan-2026 02:44:59 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 07-Jan-2026 02:44:59 WARNING: All illegal access operations will be denied in a future release build 07-Jan-2026 02:47:00 build 07-Jan-2026 02:47:00 > Task :testTask2 build 07-Jan-2026 02:47:00 Running tests WITH clover error 07-Jan-2026 02:47:01 WARNING: An illegal reflective access operation has occurred error 07-Jan-2026 02:47:01 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 07-Jan-2026 02:47:01 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 07-Jan-2026 02:47:01 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 07-Jan-2026 02:47:01 WARNING: All illegal access operations will be denied in a future release build 07-Jan-2026 02:47:04 build 07-Jan-2026 02:47:04 > Task :testTask3 build 07-Jan-2026 02:47:04 Running tests WITH clover error 07-Jan-2026 02:47:06 WARNING: An illegal reflective access operation has occurred error 07-Jan-2026 02:47:06 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 07-Jan-2026 02:47:06 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 07-Jan-2026 02:47:06 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 07-Jan-2026 02:47:06 WARNING: All illegal access operations will be denied in a future release build 07-Jan-2026 02:47:24 build 07-Jan-2026 02:47:24 > Task :test NO-SOURCE build 07-Jan-2026 02:47:24 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 07-Jan-2026 02:47:24 │jalview:testTask0 results: FAILURE (2107 tests, 2105 successes, 2 failures, 0 skipped) in 4 minutes, 38.641 seconds │ build 07-Jan-2026 02:47:24 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/testTask0/index.html│ build 07-Jan-2026 02:47:24 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 07-Jan-2026 02:47:24 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 1.844 seconds │ build 07-Jan-2026 02:47:24 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/testTask1/index.html│ build 07-Jan-2026 02:47:24 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 07-Jan-2026 02:47:24 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.611 seconds │ build 07-Jan-2026 02:47:24 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/testTask2/index.html│ build 07-Jan-2026 02:47:24 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 07-Jan-2026 02:47:24 │jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 20.955 seconds │ build 07-Jan-2026 02:47:24 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/testTask3/index.html│ build 07-Jan-2026 02:47:24 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 07-Jan-2026 02:47:24 │OVERALL: results: FAILURE (2184 tests, 2181 successes, 2 failures, 1 skipped) in 6 minutes, 66.051 seconds │ build 07-Jan-2026 02:47:24 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ error 07-Jan-2026 02:47:24 error 07-Jan-2026 02:47:24 FAILURE: Build failed with an exception. error 07-Jan-2026 02:47:24 error 07-Jan-2026 02:47:24 * Where: error 07-Jan-2026 02:47:24 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build.gradle' line: 1964 error 07-Jan-2026 02:47:24 error 07-Jan-2026 02:47:24 * What went wrong: error 07-Jan-2026 02:47:24 Failed tests! error 07-Jan-2026 02:47:24 error 07-Jan-2026 02:47:24 * Try: error 07-Jan-2026 02:47:24 > Run with --stacktrace option to get the stack trace. error 07-Jan-2026 02:47:24 > Run with --info or --debug option to get more log output. error 07-Jan-2026 02:47:24 > Run with --scan to get full insights. error 07-Jan-2026 02:47:24 error 07-Jan-2026 02:47:24 * Get more help at https://help.gradle.org error 07-Jan-2026 02:47:24 error 07-Jan-2026 02:47:24 BUILD FAILED in 7m 58s build 07-Jan-2026 02:47:24 build 07-Jan-2026 02:47:24 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 07-Jan-2026 02:47:24 build 07-Jan-2026 02:47:24 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 07-Jan-2026 02:47:24 build 07-Jan-2026 02:47:24 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 07-Jan-2026 02:47:24 build 07-Jan-2026 02:47:24 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 07-Jan-2026 02:47:24 Please consult deprecation warnings for more details. build 07-Jan-2026 02:47:24 21 actionable tasks: 20 executed, 1 up-to-date simple 07-Jan-2026 02:47:24 simple 07-Jan-2026 02:47:24 Failing task since return code of [/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test] was 1 while expected 0 simple 07-Jan-2026 02:47:24 Finished task 'Run tests with openclover under gradle' with result: Failed simple 07-Jan-2026 02:47:24 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 07-Jan-2026 02:47:24 Bamboo Artifactory Plugin version: 2.6.2 command 07-Jan-2026 02:47:24 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests #2 (JB-GDB738-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-GDB738-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_repository_revision_number=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB738-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-GDB738-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB738-JOB1\nbamboo_shortPlanName=feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_repository_48168979_name=Jalview Gitlab\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-GDB738-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 - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_shortPlanKey=GDB738\nbamboo_shortJobKey=JOB1\nbamboo_repository_48168979_git_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_buildTimeStamp=2026-01-07T02:39:23.550Z\nbamboo_repository_previous_revision_number=6c414592dabe553216b6c62e1a28208e99dd8186\nbamboo_planRepository_previousRevision=6c414592dabe553216b6c62e1a28208e99dd8186\nbamboo_repository_48168979_branch_name=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_repository_git_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_buildResultKey=JB-GDB738-JOB1-2\nbamboo_repository_branch_name=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=89c895478e2de885c6475780e1191e8b19fe1dff\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\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 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build 07-Jan-2026 02:47:24 2414 build 07-Jan-2026 02:47:29 build 07-Jan-2026 02:47:29 > Configure project : build 07-Jan-2026 02:47:29 Using properties from file './utils/channels/default/channel_gradle.properties' build 07-Jan-2026 02:47:29 JALVIEW_VERSION is set to '2.12.0' build 07-Jan-2026 02:47:29 HEADLESS BUILD build 07-Jan-2026 02:47:29 J2S ENABLED build 07-Jan-2026 02:47:30 Using a LOCAL profile. build 07-Jan-2026 02:47:30 eclipseDir exists build 07-Jan-2026 02:47:33 build 07-Jan-2026 02:47:33 > Task :cloverHtmlReport build 07-Jan-2026 02:47:33 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 07-Jan-2026 02:47:34 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/clover' build 07-Jan-2026 02:48:29 Done. Processed 137 packages in 55444ms (404ms per package). build 07-Jan-2026 02:48:35 build 07-Jan-2026 02:48:35 > Task :cloverXmlReport build 07-Jan-2026 02:48:35 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 07-Jan-2026 02:48:36 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/clover/clover.xml' build 07-Jan-2026 02:48:36 build 07-Jan-2026 02:48:36 > Task :cloverReport build 07-Jan-2026 02:48:36 build 07-Jan-2026 02:48:36 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 07-Jan-2026 02:48:36 build 07-Jan-2026 02:48:36 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 07-Jan-2026 02:48:36 build 07-Jan-2026 02:48:36 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 07-Jan-2026 02:48:36 build 07-Jan-2026 02:48:36 BUILD SUCCESSFUL in 1m 11s build 07-Jan-2026 02:48:36 2 actionable tasks: 2 executed simple 07-Jan-2026 02:48:36 Finished task 'Clover Report' with result: Success simple 07-Jan-2026 02:48:36 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 07-Jan-2026 02:48:36 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1... simple 07-Jan-2026 02:48:36 Failing task since 2 failing test cases were found. simple 07-Jan-2026 02:48:36 Finished task 'TestNG Parser' with result: Failed simple 07-Jan-2026 02:48:36 Running post build plugin 'NCover Results Collector' simple 07-Jan-2026 02:48:36 Running post build plugin 'Artifact Copier' simple 07-Jan-2026 02:48:36 Publishing an artifact: Clover Report (System) simple 07-Jan-2026 02:48:38 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.045 s simple 07-Jan-2026 02:48:38 Publishing an artifact: TestNG report error 07-Jan-2026 02:48:38 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/test does not exist. simple 07-Jan-2026 02:48:38 The artifact hasn't been successfully published after 2.781 ms simple 07-Jan-2026 02:48:38 Running post build plugin 'Artifactory Release Management Staging' simple 07-Jan-2026 02:48:38 Running post build plugin 'Artifactory Build Info Copier' simple 07-Jan-2026 02:48:38 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 07-Jan-2026 02:48:38 Running post build plugin 'npm Cache Cleanup' simple 07-Jan-2026 02:48:38 Running post build plugin 'Clover Results Collector' simple 07-Jan-2026 02:48:38 Running post build plugin 'Docker Container Cleanup' simple 07-Jan-2026 02:48:38 Finalising the build... simple 07-Jan-2026 02:48:38 Stopping timer. simple 07-Jan-2026 02:48:38 Build JB-GDB738-JOB1-2 completed. simple 07-Jan-2026 02:48:38 Running on server: post build plugin 'NCover Results Collector' simple 07-Jan-2026 02:48:38 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 07-Jan-2026 02:48:38 Running on server: post build plugin 'Clover Delta Calculator' simple 07-Jan-2026 02:48:38 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 07-Jan-2026 02:48:38 All post build plugins have finished simple 07-Jan-2026 02:48:38 Generating build results summary... simple 07-Jan-2026 02:48:39 Saving build results to disk... simple 07-Jan-2026 02:48:39 Logging substituted variables... simple 07-Jan-2026 02:48:39 Indexing build results... simple 07-Jan-2026 02:48:39 Finished building JB-GDB738-JOB1-2.