simple 10-Dec-2025 07:51:22 Build Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #8 (JB-GDB731-JOB1-8) started building on agent Default Agent simple 10-Dec-2025 07:51:22 simple 10-Dec-2025 07:51:23 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1 simple 10-Dec-2025 07:51:23 Executing build Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #8 (JB-GDB731-JOB1-8) simple 10-Dec-2025 07:51:23 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 10-Dec-2025 07:51:23 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1 simple 10-Dec-2025 07:51:23 Updating source code to revision: b00f7c47ccd3e44f5d4402f33e29b4b95c337419 simple 10-Dec-2025 07:51:23 Fetching 'refs/heads/development/Release_2_11_5_Branch' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 10-Dec-2025 07:51:23 Checking out revision b00f7c47ccd3e44f5d4402f33e29b4b95c337419. simple 10-Dec-2025 07:51:23 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 10-Dec-2025 07:51:23 3ad0f0a..b00f7c4 development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch simple 10-Dec-2025 07:51:23 * [new branch] bug/JAL-4559_old_cli_args_in_JVL_docs -> origin/bug/JAL-4559_old_cli_args_in_JVL_docs simple 10-Dec-2025 07:51:23 c586364..9e8107e releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch simple 10-Dec-2025 07:51:23 Already on 'development/Release_2_11_5_Branch' simple 10-Dec-2025 07:51:23 Your branch is behind 'origin/development/Release_2_11_5_Branch' by 3 commits, and can be fast-forwarded. simple 10-Dec-2025 07:51:23 (use "git pull" to update your local branch) simple 10-Dec-2025 07:51:23 HEAD is now at b00f7c4 JAL-4559 release notes simple 10-Dec-2025 07:51:23 Updated source code to revision: b00f7c47ccd3e44f5d4402f33e29b4b95c337419 simple 10-Dec-2025 07:51:23 Finished task 'Checkout Default Repository' with result: Success simple 10-Dec-2025 07:51:23 Running pre-build action: VCS Version Collector simple 10-Dec-2025 07:51:23 Running pre-build action: Artifactory Release Staging simple 10-Dec-2025 07:51:23 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 10-Dec-2025 07:51:23 Bamboo Artifactory Plugin version: 2.6.2 command 10-Dec-2025 07:51:23 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #8 (JB-GDB731-JOB1-8)'\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-GDB731-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_11_5_Branch\nbamboo_repository_46498610_previous_revision_number=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_repository_revision_number=b00f7c47ccd3e44f5d4402f33e29b4b95c337419\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB731-JOB1-8\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-GDB731-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB731-JOB1\nbamboo_repository_46498610_git_username=\nbamboo_shortPlanName=development-Release_2_11_5_Branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=8\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-GDB731-JOB1-8\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498610_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch\nbamboo_repository_46498610_revision_number=b00f7c47ccd3e44f5d4402f33e29b4b95c337419\nbamboo_shortPlanKey=GDB731\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=b00f7c47ccd3e44f5d4402f33e29b4b95c337419\nbamboo_buildTimeStamp=2025-12-10T07:51:22.960Z\nbamboo_repository_previous_revision_number=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_planRepository_previousRevision=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_repository_git_branch=development/Release_2_11_5_Branch\nbamboo_buildResultKey=JB-GDB731-JOB1-8\nbamboo_repository_branch_name=development/Release_2_11_5_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=b00f7c47ccd3e44f5d4402f33e29b4b95c337419\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_repository_46498610_branch_name=development/Release_2_11_5_Branch\nbamboo_planRepository_branch=development/Release_2_11_5_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_repository_46498610_git_branch=development/Release_2_11_5_Branch\nbamboo_planRepository_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=development/Release_2_11_5_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-46302791\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-GDB731-JOB1\nbamboo_planKey=JB-GDB731\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498610_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=development/Release_2_11_5_Branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 10-Dec-2025 07:51:23 2414 build 10-Dec-2025 07:51:24 Starting a Gradle Daemon (subsequent builds will be faster) build 10-Dec-2025 07:51:30 build 10-Dec-2025 07:51:30 > Configure project : build 10-Dec-2025 07:51:30 Using properties from file './utils/channels/default/channel_gradle.properties' build 10-Dec-2025 07:51:30 JALVIEW_VERSION is set to '2.11.5.1' build 10-Dec-2025 07:51:30 HEADLESS BUILD build 10-Dec-2025 07:51:30 J2S ENABLED build 10-Dec-2025 07:51:30 Using a LOCAL profile. build 10-Dec-2025 07:51:31 eclipseDir exists build 10-Dec-2025 07:51:32 build 10-Dec-2025 07:51:32 > Task :clean build 10-Dec-2025 07:51:32 > Task :cleanClover build 10-Dec-2025 07:51:32 > Task :cleanTest UP-TO-DATE build 10-Dec-2025 07:51:34 build 10-Dec-2025 07:51:34 > Task :cloverInstrJava build 10-Dec-2025 07:51:34 Clover: About to instrument 1109 files build 10-Dec-2025 07:51:34 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 10-Dec-2025 07:51:34 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover.db'. build 10-Dec-2025 07:51:34 Processing files at 1.9 source level. error 10-Dec-2025 07:51:37 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 10-Dec-2025 07:51:37 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 10-Dec-2025 07:51:37 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 10-Dec-2025 07:51:37 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 10-Dec-2025 07:51:37 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 10-Dec-2025 07:51:37 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 10-Dec-2025 07:51:37 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? build 10-Dec-2025 07:51:43 Clover all over. Instrumented 1109 files (113 packages). build 10-Dec-2025 07:51:45 build 10-Dec-2025 07:51:45 > Task :cloverInstrTests build 10-Dec-2025 07:51:45 Clover: About to instrument test files build 10-Dec-2025 07:51:45 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 10-Dec-2025 07:51:45 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover.db'. build 10-Dec-2025 07:51:45 Processing files at 1.9 source level. build 10-Dec-2025 07:51:47 Clover all over. Instrumented 293 files (52 packages). build 10-Dec-2025 07:51:47 1627 test methods detected. build 10-Dec-2025 07:51:47 build 10-Dec-2025 07:51:47 > Task :cloverInstr build 10-Dec-2025 07:51:49 build 10-Dec-2025 07:51:49 > Task :compileCloverJava build 10-Dec-2025 07:51:49 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 10-Dec-2025 07:51:49 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrJava' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 10-Dec-2025 07:51:49 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrTests' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 10-Dec-2025 07:51:49 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-instr'. Reason: Task ':compileCloverJava' uses this output of task ':cloverInstrJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 10-Dec-2025 07:51:49 Setting target compatibility to 11 error 10-Dec-2025 07:52:09 Note: Some input files use or override a deprecated API. error 10-Dec-2025 07:52:09 Note: Recompile with -Xlint:deprecation for details. error 10-Dec-2025 07:52:09 Note: Some input files use unchecked or unsafe operations. error 10-Dec-2025 07:52:09 Note: Recompile with -Xlint:unchecked for details. build 10-Dec-2025 07:52:15 build 10-Dec-2025 07:52:15 > Task :processCloverResources NO-SOURCE build 10-Dec-2025 07:52:15 > Task :cloverClasses build 10-Dec-2025 07:52:15 > Task :copyHelp build 10-Dec-2025 07:52:16 > Task :buildIndices build 10-Dec-2025 07:52:16 > Task :copyResources build 10-Dec-2025 07:52:16 > Task :copyChannelResources build 10-Dec-2025 07:52:16 build 10-Dec-2025 07:52:16 > Task :createBuildProperties build 10-Dec-2025 07:52:16 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 10-Dec-2025 07:52:16 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 10-Dec-2025 07:52:16 build 10-Dec-2025 07:52:16 > Task :buildResources build 10-Dec-2025 07:52:17 > Task :copyDocs build 10-Dec-2025 07:52:17 build 10-Dec-2025 07:52:17 > Task :convertMdFiles build 10-Dec-2025 07:52:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 10-Dec-2025 07:52:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/releaseprocess.html build 10-Dec-2025 07:52:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 10-Dec-2025 07:52:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/building.html build 10-Dec-2025 07:52:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/jalview-projects.html build 10-Dec-2025 07:52:18 build 10-Dec-2025 07:52:18 > Task :releasesTemplates build 10-Dec-2025 07:52:18 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 10-Dec-2025 07:52:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 10-Dec-2025 07:52:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 10-Dec-2025 07:52:18 Stripping rc/test/etc for TEST build 10-Dec-2025 07:52:18 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 10-Dec-2025 07:52:18 build 10-Dec-2025 07:52:18 > Task :prepare build 10-Dec-2025 07:52:20 build 10-Dec-2025 07:52:20 > Task :compileJava build 10-Dec-2025 07:52:20 Setting target compatibility to 11 error 10-Dec-2025 07:52:24 Note: Some input files use or override a deprecated API. error 10-Dec-2025 07:52:24 Note: Recompile with -Xlint:deprecation for details. error 10-Dec-2025 07:52:24 Note: Some input files use unchecked or unsafe operations. error 10-Dec-2025 07:52:24 Note: Recompile with -Xlint:unchecked for details. build 10-Dec-2025 07:52:29 build 10-Dec-2025 07:52:29 > Task :compileTestJava build 10-Dec-2025 07:52:29 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 10-Dec-2025 07:52:29 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 10-Dec-2025 07:52:29 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 10-Dec-2025 07:52:29 Setting target compatibility to 11 error 10-Dec-2025 07:52:34 Note: Some input files use or override a deprecated API. error 10-Dec-2025 07:52:34 Note: Recompile with -Xlint:deprecation for details. error 10-Dec-2025 07:52:34 Note: Some input files use unchecked or unsafe operations. error 10-Dec-2025 07:52:34 Note: Recompile with -Xlint:unchecked for details. build 10-Dec-2025 07:52:35 build 10-Dec-2025 07:52:35 > Task :processTestResources build 10-Dec-2025 07:52:35 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 10-Dec-2025 07:52:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 10-Dec-2025 07:52:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 10-Dec-2025 07:52:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 10-Dec-2025 07:52:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 10-Dec-2025 07:52:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 10-Dec-2025 07:52:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 10-Dec-2025 07:52:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 10-Dec-2025 07:52:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 10-Dec-2025 07:52:35 build 10-Dec-2025 07:52:35 > Task :testClasses build 10-Dec-2025 07:52:37 build 10-Dec-2025 07:52:37 > Task :testTask0 build 10-Dec-2025 07:52:37 Running tests WITH clover error 10-Dec-2025 07:52:40 WARNING: An illegal reflective access operation has occurred error 10-Dec-2025 07:52:40 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 10-Dec-2025 07:52:40 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 10-Dec-2025 07:52:40 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 10-Dec-2025 07:52:40 WARNING: All illegal access operations will be denied in a future release build 10-Dec-2025 07:53:33 build 10-Dec-2025 07:53:33 Gradle suite > Gradle test > jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy FAILED build 10-Dec-2025 07:53:33 java.lang.ArrayIndexOutOfBoundsException: Index 5 out of bounds for length 1 build 10-Dec-2025 07:53:33 at jalview.gui.AlignViewportTest.__CLR4_4_1lfq8443uue(AlignViewportTest.java:478) build 10-Dec-2025 07:53:33 at jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy(AlignViewportTest.java:446) error 10-Dec-2025 07:56:42 error 10-Dec-2025 07:56:42 1835 tests completed, 1 failed build 10-Dec-2025 07:56:42 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask0/index.html build 10-Dec-2025 07:56:45 build 10-Dec-2025 07:56:45 > Task :testTask1 build 10-Dec-2025 07:56:45 Running tests WITH clover error 10-Dec-2025 07:56:46 WARNING: An illegal reflective access operation has occurred error 10-Dec-2025 07:56:46 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 10-Dec-2025 07:56:46 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 10-Dec-2025 07:56:46 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 10-Dec-2025 07:56:46 WARNING: All illegal access operations will be denied in a future release build 10-Dec-2025 07:58:50 build 10-Dec-2025 07:58:50 > Task :testTask2 build 10-Dec-2025 07:58:50 Running tests WITH clover build 10-Dec-2025 07:58:54 build 10-Dec-2025 07:58:54 > Task :testTask3 build 10-Dec-2025 07:58:54 Running tests WITH clover error 10-Dec-2025 07:58:55 WARNING: An illegal reflective access operation has occurred error 10-Dec-2025 07:58:55 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 10-Dec-2025 07:58:55 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 10-Dec-2025 07:58:55 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 10-Dec-2025 07:58:55 WARNING: All illegal access operations will be denied in a future release build 10-Dec-2025 07:59:39 build 10-Dec-2025 07:59:39 > Task :test NO-SOURCE build 10-Dec-2025 07:59:39 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 10-Dec-2025 07:59:39 │jalview:testTask0 results: FAILURE (1835 tests, 1834 successes, 1 failures, 0 skipped) in 4 minutes, 6.391 seconds │ build 10-Dec-2025 07:59:39 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask0/index.html│ build 10-Dec-2025 07:59:39 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 10-Dec-2025 07:59:39 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 5.804 seconds │ build 10-Dec-2025 07:59:39 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask1/index.html│ build 10-Dec-2025 07:59:39 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 10-Dec-2025 07:59:39 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.210 seconds │ build 10-Dec-2025 07:59:39 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask2/index.html│ build 10-Dec-2025 07:59:39 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 10-Dec-2025 07:59:39 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 46.956 seconds │ build 10-Dec-2025 07:59:39 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask3/index.html│ build 10-Dec-2025 07:59:39 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 10-Dec-2025 07:59:39 │OVERALL: results: FAILURE (1923 tests, 1922 successes, 1 failures, 0 skipped) in 6 minutes, 62.361 seconds │ build 10-Dec-2025 07:59:39 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ error 10-Dec-2025 07:59:39 error 10-Dec-2025 07:59:39 FAILURE: Build failed with an exception. error 10-Dec-2025 07:59:39 error 10-Dec-2025 07:59:39 * Where: error 10-Dec-2025 07:59:39 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build.gradle' line: 1967 error 10-Dec-2025 07:59:39 error 10-Dec-2025 07:59:39 * What went wrong: error 10-Dec-2025 07:59:39 Failed tests! error 10-Dec-2025 07:59:39 error 10-Dec-2025 07:59:39 * Try: error 10-Dec-2025 07:59:39 > Run with --stacktrace option to get the stack trace. error 10-Dec-2025 07:59:39 > Run with --info or --debug option to get more log output. error 10-Dec-2025 07:59:39 > Run with --scan to get full insights. error 10-Dec-2025 07:59:39 error 10-Dec-2025 07:59:39 * Get more help at https://help.gradle.org build 10-Dec-2025 07:59:39 build 10-Dec-2025 07:59:39 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 10-Dec-2025 07:59:39 build 10-Dec-2025 07:59:39 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 10-Dec-2025 07:59:39 build 10-Dec-2025 07:59:39 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 10-Dec-2025 07:59:39 build 10-Dec-2025 07:59:39 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 10-Dec-2025 07:59:39 Please consult deprecation warnings for more details. build 10-Dec-2025 07:59:39 21 actionable tasks: 20 executed, 1 up-to-date error 10-Dec-2025 07:59:39 error 10-Dec-2025 07:59:39 BUILD FAILED in 8m 15s simple 10-Dec-2025 07:59:40 simple 10-Dec-2025 07:59:40 Failing task since return code of [/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test] was 1 while expected 0 simple 10-Dec-2025 07:59:40 Finished task 'Run tests with openclover under gradle' with result: Failed simple 10-Dec-2025 07:59:40 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 10-Dec-2025 07:59:40 Bamboo Artifactory Plugin version: 2.6.2 command 10-Dec-2025 07:59:40 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #8 (JB-GDB731-JOB1-8)'\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-GDB731-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_11_5_Branch\nbamboo_repository_46498610_previous_revision_number=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_repository_revision_number=b00f7c47ccd3e44f5d4402f33e29b4b95c337419\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB731-JOB1-8\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-GDB731-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB731-JOB1\nbamboo_repository_46498610_git_username=\nbamboo_shortPlanName=development-Release_2_11_5_Branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=8\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-GDB731-JOB1-8\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498610_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch\nbamboo_repository_46498610_revision_number=b00f7c47ccd3e44f5d4402f33e29b4b95c337419\nbamboo_shortPlanKey=GDB731\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=b00f7c47ccd3e44f5d4402f33e29b4b95c337419\nbamboo_buildTimeStamp=2025-12-10T07:51:22.960Z\nbamboo_repository_previous_revision_number=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_planRepository_previousRevision=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_repository_git_branch=development/Release_2_11_5_Branch\nbamboo_buildResultKey=JB-GDB731-JOB1-8\nbamboo_repository_branch_name=development/Release_2_11_5_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=b00f7c47ccd3e44f5d4402f33e29b4b95c337419\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 test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=true\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46498610_branch_name=development/Release_2_11_5_Branch\nbamboo_planRepository_branch=development/Release_2_11_5_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=3ad0f0a7896b330c0e763c467d1076bede27b59a\nbamboo_repository_46498610_git_branch=development/Release_2_11_5_Branch\nbamboo_planRepository_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=development/Release_2_11_5_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-46302791\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-GDB731-JOB1\nbamboo_planKey=JB-GDB731\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498610_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=development/Release_2_11_5_Branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 10-Dec-2025 07:59:40 2414 build 10-Dec-2025 07:59:44 build 10-Dec-2025 07:59:44 > Configure project : build 10-Dec-2025 07:59:44 Using properties from file './utils/channels/default/channel_gradle.properties' build 10-Dec-2025 07:59:44 JALVIEW_VERSION is set to '2.11.5.1' build 10-Dec-2025 07:59:44 HEADLESS BUILD build 10-Dec-2025 07:59:44 J2S ENABLED build 10-Dec-2025 07:59:45 Using a LOCAL profile. build 10-Dec-2025 07:59:45 eclipseDir exists build 10-Dec-2025 07:59:48 build 10-Dec-2025 07:59:48 > Task :cloverHtmlReport build 10-Dec-2025 07:59:48 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 10-Dec-2025 07:59:49 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/clover' build 10-Dec-2025 08:00:33 Done. Processed 117 packages in 44762ms (382ms per package). build 10-Dec-2025 08:00:38 build 10-Dec-2025 08:00:38 > Task :cloverXmlReport build 10-Dec-2025 08:00:38 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 10-Dec-2025 08:00:39 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/clover/clover.xml' build 10-Dec-2025 08:00:39 build 10-Dec-2025 08:00:39 > Task :cloverReport build 10-Dec-2025 08:00:39 build 10-Dec-2025 08:00:39 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 10-Dec-2025 08:00:39 build 10-Dec-2025 08:00:39 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 10-Dec-2025 08:00:39 build 10-Dec-2025 08:00:39 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 10-Dec-2025 08:00:39 build 10-Dec-2025 08:00:39 BUILD SUCCESSFUL in 59s build 10-Dec-2025 08:00:39 2 actionable tasks: 2 executed simple 10-Dec-2025 08:00:39 Finished task 'Clover Report' with result: Success simple 10-Dec-2025 08:00:39 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 10-Dec-2025 08:00:39 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1... simple 10-Dec-2025 08:00:39 Failing task since 1 failing test cases were found. simple 10-Dec-2025 08:00:39 Finished task 'TestNG Parser' with result: Failed simple 10-Dec-2025 08:00:39 Running post build plugin 'NCover Results Collector' simple 10-Dec-2025 08:00:39 Running post build plugin 'Artifact Copier' simple 10-Dec-2025 08:00:39 Publishing an artifact: Clover Report (System) simple 10-Dec-2025 08:00:41 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.841 s simple 10-Dec-2025 08:00:41 Publishing an artifact: TestNG report error 10-Dec-2025 08:00:41 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/test does not exist. simple 10-Dec-2025 08:00:41 The artifact hasn't been successfully published after 1.192 ms simple 10-Dec-2025 08:00:41 Running post build plugin 'Artifactory Release Management Staging' simple 10-Dec-2025 08:00:41 Running post build plugin 'Artifactory Build Info Copier' simple 10-Dec-2025 08:00:41 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 10-Dec-2025 08:00:41 Running post build plugin 'npm Cache Cleanup' simple 10-Dec-2025 08:00:41 Running post build plugin 'Clover Results Collector' simple 10-Dec-2025 08:00:41 Running post build plugin 'Docker Container Cleanup' simple 10-Dec-2025 08:00:41 Finalising the build... simple 10-Dec-2025 08:00:41 Stopping timer. simple 10-Dec-2025 08:00:41 Build JB-GDB731-JOB1-8 completed. simple 10-Dec-2025 08:00:41 Running on server: post build plugin 'NCover Results Collector' simple 10-Dec-2025 08:00:41 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 10-Dec-2025 08:00:41 Running on server: post build plugin 'Clover Delta Calculator' simple 10-Dec-2025 08:00:41 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 10-Dec-2025 08:00:41 All post build plugins have finished simple 10-Dec-2025 08:00:41 Generating build results summary... simple 10-Dec-2025 08:00:41 Saving build results to disk... simple 10-Dec-2025 08:00:41 Logging substituted variables... simple 10-Dec-2025 08:00:41 Indexing build results... simple 10-Dec-2025 08:00:41 Finished building JB-GDB731-JOB1-8.