simple 03-Dec-2025 17:02:57 Build Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests #3 (JB-GDB732-JOB1-3) started building on agent Default Agent simple 03-Dec-2025 17:02:57 simple 03-Dec-2025 17:02:57 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1 simple 03-Dec-2025 17:02:57 Executing build Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests #3 (JB-GDB732-JOB1-3) simple 03-Dec-2025 17:02:57 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 03-Dec-2025 17:02:57 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1 simple 03-Dec-2025 17:02:57 Updating source code to revision: 7d35e28797636155c3de86cbdb1030eaf9110ecc simple 03-Dec-2025 17:02:57 Fetching 'refs/heads/development/Release_2_12_Branch' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 03-Dec-2025 17:02:58 Checking out revision 7d35e28797636155c3de86cbdb1030eaf9110ecc. simple 03-Dec-2025 17:02:58 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 03-Dec-2025 17:02:58 66f03c6..7d35e28 development/Release_2_12_Branch -> origin/development/Release_2_12_Branch simple 03-Dec-2025 17:02:58 fae9009..4d0c90d development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch simple 03-Dec-2025 17:02:59 Already on 'development/Release_2_12_Branch' simple 03-Dec-2025 17:02:59 Your branch is behind 'origin/development/Release_2_12_Branch' by 10 commits, and can be fast-forwarded. simple 03-Dec-2025 17:02:59 (use "git pull" to update your local branch) simple 03-Dec-2025 17:02:59 HEAD is now at 7d35e28 Merge branch 'development/JAL-4107_merge_2115_212' into development/Release_2_12_Branch simple 03-Dec-2025 17:02:59 Updated source code to revision: 7d35e28797636155c3de86cbdb1030eaf9110ecc simple 03-Dec-2025 17:02:59 Finished task 'Checkout Default Repository' with result: Success simple 03-Dec-2025 17:02:59 Running pre-build action: VCS Version Collector simple 03-Dec-2025 17:02:59 Running pre-build action: Artifactory Release Staging simple 03-Dec-2025 17:02:59 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 03-Dec-2025 17:02:59 Bamboo Artifactory Plugin version: 2.6.2 command 03-Dec-2025 17:02:59 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests #3 (JB-GDB732-JOB1-3)'\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-GDB732-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_12_Branch\nbamboo_repository_46498611_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=development/Release_2_12_Branch\nbamboo_repository_revision_number=7d35e28797636155c3de86cbdb1030eaf9110ecc\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB732-JOB1-3\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-GDB732-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB732-JOB1\nbamboo_shortPlanName=development-Release_2_12_Branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=3\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-GDB732-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch\nbamboo_shortPlanKey=GDB732\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=7d35e28797636155c3de86cbdb1030eaf9110ecc\nbamboo_buildTimeStamp=2025-12-03T16:48:58.384Z\nbamboo_repository_previous_revision_number=66f03c613c4cd268ad986900e811777144617bd5\nbamboo_planRepository_previousRevision=66f03c613c4cd268ad986900e811777144617bd5\nbamboo_repository_git_branch=development/Release_2_12_Branch\nbamboo_buildResultKey=JB-GDB732-JOB1-3\nbamboo_repository_branch_name=development/Release_2_12_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=7d35e28797636155c3de86cbdb1030eaf9110ecc\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498611_revision_number=7d35e28797636155c3de86cbdb1030eaf9110ecc\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_repository_46498611_git_branch=development/Release_2_12_Branch\nbamboo_planRepository_branch=development/Release_2_12_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_repository_46498611_git_username=\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=66f03c613c4cd268ad986900e811777144617bd5\nbamboo_repository_46498611_name=Jalview Gitlab\nbamboo_repository_46498611_previous_revision_number=66f03c613c4cd268ad986900e811777144617bd5\nbamboo_planRepository_branchDisplayName=development/Release_2_12_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=development/Release_2_12_Branch\nbamboo_repository_46498611_branch_name=development/Release_2_12_Branch\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-46302793\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-GDB732-JOB1\nbamboo_planKey=JB-GDB732\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=development/Release_2_12_Branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 03-Dec-2025 17:02:59 444 build 03-Dec-2025 17:03:00 build 03-Dec-2025 17:03:00 > Configure project : build 03-Dec-2025 17:03:00 Using properties from file './utils/channels/default/channel_gradle.properties' build 03-Dec-2025 17:03:00 JALVIEW_VERSION is set to '2.12.0' build 03-Dec-2025 17:03:00 HEADLESS BUILD build 03-Dec-2025 17:03:00 J2S ENABLED build 03-Dec-2025 17:03:00 Using a LOCAL profile. build 03-Dec-2025 17:03:00 eclipseDir exists build 03-Dec-2025 17:03:01 build 03-Dec-2025 17:03:01 > Task :clean build 03-Dec-2025 17:03:01 > Task :cleanClover build 03-Dec-2025 17:03:01 > Task :cleanTest UP-TO-DATE build 03-Dec-2025 17:03:03 build 03-Dec-2025 17:03:03 > Task :cloverInstrJava build 03-Dec-2025 17:03:03 Clover: About to instrument 1253 files build 03-Dec-2025 17:03:03 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Dec-2025 17:03:03 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover.db'. build 03-Dec-2025 17:03:03 Processing files at 1.9 source level. error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:08 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:09 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:09 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:09 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:09 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:09 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:09 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:09 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:09 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:09 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:09 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:09 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 03-Dec-2025 17:03:09 WARN: Trying to 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 03-Dec-2025 17:03:16 Clover all over. Instrumented 1253 files (133 packages). build 03-Dec-2025 17:03:19 build 03-Dec-2025 17:03:19 > Task :cloverInstrTests build 03-Dec-2025 17:03:19 Clover: About to instrument test files build 03-Dec-2025 17:03:19 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Dec-2025 17:03:19 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover.db'. build 03-Dec-2025 17:03:19 Processing files at 1.9 source level. build 03-Dec-2025 17:03:22 Clover all over. Instrumented 315 files (58 packages). build 03-Dec-2025 17:03:22 1770 test methods detected. build 03-Dec-2025 17:03:22 build 03-Dec-2025 17:03:22 > Task :cloverInstr build 03-Dec-2025 17:03:24 build 03-Dec-2025 17:03:24 > Task :compileCloverJava build 03-Dec-2025 17:03:24 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 03-Dec-2025 17:03:24 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:03:24 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:03:24 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:03:24 Setting target compatibility to 11 error 03-Dec-2025 17:03:49 Note: Some input files use or override a deprecated API. error 03-Dec-2025 17:03:49 Note: Recompile with -Xlint:deprecation for details. error 03-Dec-2025 17:03:49 Note: Some input files use unchecked or unsafe operations. error 03-Dec-2025 17:03:49 Note: Recompile with -Xlint:unchecked for details. build 03-Dec-2025 17:03:55 build 03-Dec-2025 17:03:55 > Task :processCloverResources NO-SOURCE build 03-Dec-2025 17:03:55 > Task :cloverClasses build 03-Dec-2025 17:03:56 > Task :copyHelp build 03-Dec-2025 17:03:57 > Task :buildIndices build 03-Dec-2025 17:03:57 > Task :copyResources build 03-Dec-2025 17:03:57 > Task :copyChannelResources build 03-Dec-2025 17:03:57 build 03-Dec-2025 17:03:57 > Task :createBuildProperties build 03-Dec-2025 17:03:57 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 03-Dec-2025 17:03:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:03:57 build 03-Dec-2025 17:03:57 > Task :buildResources build 03-Dec-2025 17:03:57 > Task :copyDocs build 03-Dec-2025 17:03:57 build 03-Dec-2025 17:03:57 > Task :convertMdFiles build 03-Dec-2025 17:03:57 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 03-Dec-2025 17:03:57 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/releaseprocess.html build 03-Dec-2025 17:03:57 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 03-Dec-2025 17:03:57 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/JalviewJS-API.html build 03-Dec-2025 17:03:57 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/building.html build 03-Dec-2025 17:03:57 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/addingWebClient.html build 03-Dec-2025 17:03:57 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/jalview-projects.html build 03-Dec-2025 17:03:57 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html build 03-Dec-2025 17:03:57 build 03-Dec-2025 17:03:57 > Task :releasesTemplates build 03-Dec-2025 17:03:57 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 03-Dec-2025 17:03:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:03:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:03:57 Stripping rc/test/etc for TEST build 03-Dec-2025 17:03:57 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 03-Dec-2025 17:03:57 build 03-Dec-2025 17:03:57 > Task :prepare build 03-Dec-2025 17:03:59 build 03-Dec-2025 17:03:59 > Task :compileJava build 03-Dec-2025 17:03:59 Setting target compatibility to 11 error 03-Dec-2025 17:04:06 Note: Some input files use or override a deprecated API. error 03-Dec-2025 17:04:06 Note: Recompile with -Xlint:deprecation for details. error 03-Dec-2025 17:04:06 Note: Some input files use unchecked or unsafe operations. error 03-Dec-2025 17:04:06 Note: Recompile with -Xlint:unchecked for details. build 03-Dec-2025 17:04:09 build 03-Dec-2025 17:04:09 > Task :compileTestJava build 03-Dec-2025 17:04:09 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 03-Dec-2025 17:04:09 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:04:09 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:04:09 Setting target compatibility to 11 error 03-Dec-2025 17:04:16 Note: Some input files use or override a deprecated API. error 03-Dec-2025 17:04:16 Note: Recompile with -Xlint:deprecation for details. error 03-Dec-2025 17:04:16 Note: Some input files use unchecked or unsafe operations. error 03-Dec-2025 17:04:16 Note: Recompile with -Xlint:unchecked for details. build 03-Dec-2025 17:04:18 build 03-Dec-2025 17:04:18 > Task :processTestResources build 03-Dec-2025 17:04:18 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 03-Dec-2025 17:04:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:04:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:04:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:04:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:04:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:04:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:04:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:04:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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 03-Dec-2025 17:04:18 build 03-Dec-2025 17:04:18 > Task :testClasses build 03-Dec-2025 17:04:20 build 03-Dec-2025 17:04:20 > Task :testTask0 build 03-Dec-2025 17:04:20 Running tests WITH clover error 03-Dec-2025 17:04:21 WARNING: An illegal reflective access operation has occurred error 03-Dec-2025 17:04:21 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 03-Dec-2025 17:04:21 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 03-Dec-2025 17:04:21 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 03-Dec-2025 17:04:21 WARNING: All illegal access operations will be denied in a future release build 03-Dec-2025 17:05:19 build 03-Dec-2025 17:05:19 Gradle suite > Gradle test > jalview.bin.CommandLineOperations > testHeadlessModeOutputOperations[7](headless -open examples/uniref50.fa, -html, test/jalview/bin/test_uniref50_out.html, true, 4096, 15000, null) FAILED build 03-Dec-2025 17:05:19 java.lang.AssertionError: Didn't create an output -html file.[headless -open examples/uniref50.fa] expected [true] but found [false] build 03-Dec-2025 17:05:19 at org.testng.Assert.fail(Assert.java:110) build 03-Dec-2025 17:05:19 at org.testng.Assert.failNotEquals(Assert.java:1413) build 03-Dec-2025 17:05:19 at org.testng.Assert.assertTrue(Assert.java:56) build 03-Dec-2025 17:05:19 at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:343) build 03-Dec-2025 17:06:51 build 03-Dec-2025 17:06:51 Gradle suite > Gradle test > jalview.gui.StructureChooserTest > openStructureFileForSequenceTest[3](examples/uniref50.fa, FER1_SPIOL, examples/AlphaFold/AF-P00221-F1-model_v4.cif, Default, examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json, true, false, JMOL, 15, 7, 1, null) FAILED build 03-Dec-2025 17:06:51 java.lang.AssertionError: Wrong number of structure viewers opened expected:<1> but was:<0> build 03-Dec-2025 17:06:51 at org.junit.Assert.fail(Assert.java:89) build 03-Dec-2025 17:06:51 at org.junit.Assert.failNotEquals(Assert.java:835) build 03-Dec-2025 17:06:51 at org.junit.Assert.assertEquals(Assert.java:647) build 03-Dec-2025 17:06:51 at jalview.gui.StructureChooserTest.__CLR4_4_1nqeoac434r(StructureChooserTest.java:358) build 03-Dec-2025 17:06:51 at jalview.gui.StructureChooserTest.openStructureFileForSequenceTest(StructureChooserTest.java:280) build 03-Dec-2025 17:07:17 [178.658s][warning][gc,alloc] AWT-EventQueue-0: Retried waiting for GCLocker too often allocating 135080516 words build 03-Dec-2025 17:07:29 build 03-Dec-2025 17:07:29 Gradle suite > Gradle test > jalview.project.Jalview2xmlTests > noDuplicatePdbMappingsMade FAILED build 03-Dec-2025 17:07:29 java.lang.AssertionError: Expected only two mappings for 1A70 expected [2] but found [0] build 03-Dec-2025 17:07:29 at org.testng.Assert.fail(Assert.java:110) build 03-Dec-2025 17:07:29 at org.testng.Assert.failNotEquals(Assert.java:1413) build 03-Dec-2025 17:07:29 at org.testng.Assert.assertEqualsImpl(Assert.java:149) build 03-Dec-2025 17:07:29 at org.testng.Assert.assertEquals(Assert.java:131) build 03-Dec-2025 17:07:29 at org.testng.Assert.assertEquals(Assert.java:1240) build 03-Dec-2025 17:07:29 at jalview.project.Jalview2xmlTests.__CLR4_4_11umpz94jwx(Jalview2xmlTests.java:355) build 03-Dec-2025 17:07:29 at jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade(Jalview2xmlTests.java:331) build 03-Dec-2025 17:09:48 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/testTask0/index.html error 03-Dec-2025 17:09:48 error 03-Dec-2025 17:09:48 2102 tests completed, 3 failed build 03-Dec-2025 17:09:50 build 03-Dec-2025 17:09:50 > Task :testTask1 build 03-Dec-2025 17:09:50 Running tests WITH clover error 03-Dec-2025 17:09:53 WARNING: An illegal reflective access operation has occurred error 03-Dec-2025 17:09:53 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 03-Dec-2025 17:09:53 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 03-Dec-2025 17:09:53 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 03-Dec-2025 17:09:53 WARNING: All illegal access operations will be denied in a future release build 03-Dec-2025 17:12:33 build 03-Dec-2025 17:12:33 > Task :testTask2 build 03-Dec-2025 17:12:33 Running tests WITH clover error 03-Dec-2025 17:12:35 WARNING: An illegal reflective access operation has occurred error 03-Dec-2025 17:12:35 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 03-Dec-2025 17:12:35 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 03-Dec-2025 17:12:35 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 03-Dec-2025 17:12:35 WARNING: All illegal access operations will be denied in a future release build 03-Dec-2025 17:12:40 build 03-Dec-2025 17:12:40 > Task :testTask3 build 03-Dec-2025 17:12:40 Running tests WITH clover error 03-Dec-2025 17:12:42 WARNING: An illegal reflective access operation has occurred error 03-Dec-2025 17:12:42 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 03-Dec-2025 17:12:42 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 03-Dec-2025 17:12:42 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 03-Dec-2025 17:12:42 WARNING: All illegal access operations will be denied in a future release error 03-Dec-2025 17:13:06 error 03-Dec-2025 17:13:06 FAILURE: Build failed with an exception. error 03-Dec-2025 17:13:06 error 03-Dec-2025 17:13:06 * Where: error 03-Dec-2025 17:13:06 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build.gradle' line: 1964 error 03-Dec-2025 17:13:06 error 03-Dec-2025 17:13:06 * What went wrong: error 03-Dec-2025 17:13:06 Failed tests! error 03-Dec-2025 17:13:06 error 03-Dec-2025 17:13:06 * Try: error 03-Dec-2025 17:13:06 > Run with --stacktrace option to get the stack trace. build 03-Dec-2025 17:13:06 build 03-Dec-2025 17:13:06 > Task :test NO-SOURCE build 03-Dec-2025 17:13:06 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 03-Dec-2025 17:13:06 │jalview:testTask0 results: FAILURE (2102 tests, 2099 successes, 3 failures, 0 skipped) in 5 minutes, 30.030 seconds │ build 03-Dec-2025 17:13:06 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/testTask0/index.html│ build 03-Dec-2025 17:13:06 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Dec-2025 17:13:06 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 42.658 seconds │ build 03-Dec-2025 17:13:06 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/testTask1/index.html│ build 03-Dec-2025 17:13:06 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Dec-2025 17:13:06 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 6.282 seconds │ build 03-Dec-2025 17:13:06 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/testTask2/index.html│ build 03-Dec-2025 17:13:06 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Dec-2025 17:13:06 │jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 28.506 seconds │ build 03-Dec-2025 17:13:06 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/testTask3/index.html│ build 03-Dec-2025 17:13:06 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Dec-2025 17:13:06 │OVERALL: results: FAILURE (2179 tests, 2175 successes, 3 failures, 1 skipped) in 7 minutes, 107.476 seconds │ build 03-Dec-2025 17:13:06 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 03-Dec-2025 17:13:06 build 03-Dec-2025 17:13:06 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 03-Dec-2025 17:13:06 build 03-Dec-2025 17:13:06 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 03-Dec-2025 17:13:06 build 03-Dec-2025 17:13:06 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 03-Dec-2025 17:13:06 build 03-Dec-2025 17:13:06 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 03-Dec-2025 17:13:06 Please consult deprecation warnings for more details. build 03-Dec-2025 17:13:06 21 actionable tasks: 20 executed, 1 up-to-date error 03-Dec-2025 17:13:06 > Run with --info or --debug option to get more log output. error 03-Dec-2025 17:13:06 > Run with --scan to get full insights. error 03-Dec-2025 17:13:06 error 03-Dec-2025 17:13:06 * Get more help at https://help.gradle.org error 03-Dec-2025 17:13:06 error 03-Dec-2025 17:13:06 BUILD FAILED in 10m 7s simple 03-Dec-2025 17:13:07 simple 03-Dec-2025 17:13:07 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 03-Dec-2025 17:13:07 Finished task 'Run tests with openclover under gradle' with result: Failed simple 03-Dec-2025 17:13:07 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 03-Dec-2025 17:13:07 Bamboo Artifactory Plugin version: 2.6.2 command 03-Dec-2025 17:13:07 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests #3 (JB-GDB732-JOB1-3)'\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-GDB732-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_12_Branch\nbamboo_repository_46498611_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=development/Release_2_12_Branch\nbamboo_repository_revision_number=7d35e28797636155c3de86cbdb1030eaf9110ecc\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB732-JOB1-3\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-GDB732-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB732-JOB1\nbamboo_shortPlanName=development-Release_2_12_Branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=3\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-GDB732-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch\nbamboo_shortPlanKey=GDB732\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=7d35e28797636155c3de86cbdb1030eaf9110ecc\nbamboo_buildTimeStamp=2025-12-03T16:48:58.384Z\nbamboo_repository_previous_revision_number=66f03c613c4cd268ad986900e811777144617bd5\nbamboo_planRepository_previousRevision=66f03c613c4cd268ad986900e811777144617bd5\nbamboo_repository_git_branch=development/Release_2_12_Branch\nbamboo_buildResultKey=JB-GDB732-JOB1-3\nbamboo_repository_branch_name=development/Release_2_12_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and 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build 03-Dec-2025 17:13:07 444 build 03-Dec-2025 17:13:14 build 03-Dec-2025 17:13:14 > Configure project : build 03-Dec-2025 17:13:14 Using properties from file './utils/channels/default/channel_gradle.properties' build 03-Dec-2025 17:13:14 JALVIEW_VERSION is set to '2.12.0' build 03-Dec-2025 17:13:14 HEADLESS BUILD build 03-Dec-2025 17:13:14 J2S ENABLED build 03-Dec-2025 17:13:15 Using a LOCAL profile. build 03-Dec-2025 17:13:16 eclipseDir exists build 03-Dec-2025 17:13:18 build 03-Dec-2025 17:13:18 > Task :cloverHtmlReport build 03-Dec-2025 17:13:18 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Dec-2025 17:13:21 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/clover' build 03-Dec-2025 17:14:26 Done. Processed 137 packages in 65589ms (478ms per package). build 03-Dec-2025 17:14:33 build 03-Dec-2025 17:14:33 > Task :cloverXmlReport build 03-Dec-2025 17:14:33 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Dec-2025 17:14:36 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/clover/clover.xml' build 03-Dec-2025 17:14:37 build 03-Dec-2025 17:14:37 > Task :cloverReport build 03-Dec-2025 17:14:37 build 03-Dec-2025 17:14:37 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 03-Dec-2025 17:14:37 build 03-Dec-2025 17:14:37 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 03-Dec-2025 17:14:37 build 03-Dec-2025 17:14:37 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 03-Dec-2025 17:14:37 build 03-Dec-2025 17:14:37 BUILD SUCCESSFUL in 1m 28s build 03-Dec-2025 17:14:37 2 actionable tasks: 2 executed simple 03-Dec-2025 17:14:37 Finished task 'Clover Report' with result: Success simple 03-Dec-2025 17:14:37 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 03-Dec-2025 17:14:37 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1... simple 03-Dec-2025 17:14:37 Failing task since 3 failing test cases were found. simple 03-Dec-2025 17:14:37 Finished task 'TestNG Parser' with result: Failed simple 03-Dec-2025 17:14:37 Running post build plugin 'NCover Results Collector' simple 03-Dec-2025 17:14:37 Running post build plugin 'Artifact Copier' simple 03-Dec-2025 17:14:37 Publishing an artifact: Clover Report (System) simple 03-Dec-2025 17:14:43 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 6.034 s simple 03-Dec-2025 17:14:43 Publishing an artifact: TestNG report error 03-Dec-2025 17:14:43 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/test does not exist. simple 03-Dec-2025 17:14:43 The artifact hasn't been successfully published after 4.858 ms simple 03-Dec-2025 17:14:43 Running post build plugin 'Artifactory Release Management Staging' simple 03-Dec-2025 17:14:43 Running post build plugin 'Artifactory Build Info Copier' simple 03-Dec-2025 17:14:43 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 03-Dec-2025 17:14:43 Running post build plugin 'npm Cache Cleanup' simple 03-Dec-2025 17:14:43 Running post build plugin 'Clover Results Collector' simple 03-Dec-2025 17:14:43 Running post build plugin 'Docker Container Cleanup' simple 03-Dec-2025 17:14:43 Finalising the build... simple 03-Dec-2025 17:14:43 Stopping timer. simple 03-Dec-2025 17:14:43 Build JB-GDB732-JOB1-3 completed. simple 03-Dec-2025 17:14:43 Running on server: post build plugin 'NCover Results Collector' simple 03-Dec-2025 17:14:43 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 03-Dec-2025 17:14:43 Running on server: post build plugin 'Clover Delta Calculator' simple 03-Dec-2025 17:14:43 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 03-Dec-2025 17:14:43 All post build plugins have finished simple 03-Dec-2025 17:14:43 Generating build results summary... simple 03-Dec-2025 17:14:44 Saving build results to disk... simple 03-Dec-2025 17:14:44 Logging substituted variables... simple 03-Dec-2025 17:14:44 Indexing build results... simple 03-Dec-2025 17:14:44 Finished building JB-GDB732-JOB1-3.