simple 08-Dec-2025 11:12:05 Build Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #5 (JB-GDB731-JOB1-5) started building on agent Default Agent simple 08-Dec-2025 11:12:05 simple 08-Dec-2025 11:12:05 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1 simple 08-Dec-2025 11:12:05 Executing build Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #5 (JB-GDB731-JOB1-5) simple 08-Dec-2025 11:12:05 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 08-Dec-2025 11:12:05 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1 simple 08-Dec-2025 11:12:05 Updating source code to revision: a3717c01ff25f6dd430c1f09e1703931eb52d3e3 simple 08-Dec-2025 11:12:05 Fetching 'refs/heads/development/Release_2_11_5_Branch' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 08-Dec-2025 11:12:05 Checking out revision a3717c01ff25f6dd430c1f09e1703931eb52d3e3. simple 08-Dec-2025 11:12:05 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 08-Dec-2025 11:12:05 4d0c90d..a3717c0 development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch simple 08-Dec-2025 11:12:05 * [new branch] bug/JAL-4107_jalviewjs_fixes_on_2_12_branch -> origin/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch simple 08-Dec-2025 11:12:05 7d35e28..ef35c02 development/Release_2_12_Branch -> origin/development/Release_2_12_Branch simple 08-Dec-2025 11:12:05 * [new branch] patch/JAL-4606_again_and_again -> origin/patch/JAL-4606_again_and_again simple 08-Dec-2025 11:12:06 Already on 'development/Release_2_11_5_Branch' simple 08-Dec-2025 11:12:06 Your branch is behind 'origin/development/Release_2_11_5_Branch' by 9 commits, and can be fast-forwarded. simple 08-Dec-2025 11:12:06 (use "git pull" to update your local branch) simple 08-Dec-2025 11:12:06 HEAD is now at a3717c0 JAL-4617 update release notes for JAL-4631 simple 08-Dec-2025 11:12:06 Updated source code to revision: a3717c01ff25f6dd430c1f09e1703931eb52d3e3 simple 08-Dec-2025 11:12:06 Finished task 'Checkout Default Repository' with result: Success simple 08-Dec-2025 11:12:06 Running pre-build action: VCS Version Collector simple 08-Dec-2025 11:12:06 Running pre-build action: Artifactory Release Staging simple 08-Dec-2025 11:12:06 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 08-Dec-2025 11:12:06 Bamboo Artifactory Plugin version: 2.6.2 command 08-Dec-2025 11:12:06 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #5 (JB-GDB731-JOB1-5)'\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=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\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=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB731-JOB1-5\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=5\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-JOB1-5\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=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_shortPlanKey=GDB731\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_buildTimeStamp=2025-12-08T11:09:23.023Z\nbamboo_repository_previous_revision_number=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\nbamboo_planRepository_previousRevision=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\nbamboo_repository_git_branch=development/Release_2_11_5_Branch\nbamboo_buildResultKey=JB-GDB731-JOB1-5\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=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\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=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\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 08-Dec-2025 11:12:06 2414 build 08-Dec-2025 11:12:07 build 08-Dec-2025 11:12:07 > Configure project : build 08-Dec-2025 11:12:07 Using properties from file './utils/channels/default/channel_gradle.properties' build 08-Dec-2025 11:12:07 JALVIEW_VERSION is set to '2.11.5.1' build 08-Dec-2025 11:12:07 HEADLESS BUILD build 08-Dec-2025 11:12:07 J2S ENABLED build 08-Dec-2025 11:12:07 Using a LOCAL profile. build 08-Dec-2025 11:12:07 eclipseDir exists build 08-Dec-2025 11:12:08 build 08-Dec-2025 11:12:08 > Task :clean build 08-Dec-2025 11:12:08 > Task :cleanClover build 08-Dec-2025 11:12:08 > Task :cleanTest UP-TO-DATE build 08-Dec-2025 11:12:10 build 08-Dec-2025 11:12:10 > Task :cloverInstrJava build 08-Dec-2025 11:12:10 Clover: About to instrument 1109 files build 08-Dec-2025 11:12:10 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 08-Dec-2025 11:12:10 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover.db'. build 08-Dec-2025 11:12:10 Processing files at 1.9 source level. error 08-Dec-2025 11:12:12 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 08-Dec-2025 11:12:12 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 08-Dec-2025 11:12:12 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 08-Dec-2025 11:12:12 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 08-Dec-2025 11:12:12 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 08-Dec-2025 11:12:12 WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? error 08-Dec-2025 11:12:12 WARN: Trying to 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 08-Dec-2025 11:12:18 Clover all over. Instrumented 1109 files (113 packages). build 08-Dec-2025 11:12:20 build 08-Dec-2025 11:12:20 > Task :cloverInstrTests build 08-Dec-2025 11:12:20 Clover: About to instrument test files build 08-Dec-2025 11:12:20 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 08-Dec-2025 11:12:20 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover.db'. build 08-Dec-2025 11:12:20 Processing files at 1.9 source level. build 08-Dec-2025 11:12:22 Clover all over. Instrumented 293 files (52 packages). build 08-Dec-2025 11:12:22 1627 test methods detected. build 08-Dec-2025 11:12:23 build 08-Dec-2025 11:12:23 > Task :cloverInstr build 08-Dec-2025 11:12:25 build 08-Dec-2025 11:12:25 > Task :compileCloverJava build 08-Dec-2025 11:12:25 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 08-Dec-2025 11:12:25 - 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 08-Dec-2025 11:12:25 - 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 08-Dec-2025 11:12:25 - 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 08-Dec-2025 11:12:25 Setting target compatibility to 11 error 08-Dec-2025 11:12:41 Note: Some input files use or override a deprecated API. error 08-Dec-2025 11:12:41 Note: Recompile with -Xlint:deprecation for details. error 08-Dec-2025 11:12:41 Note: Some input files use unchecked or unsafe operations. error 08-Dec-2025 11:12:41 Note: Recompile with -Xlint:unchecked for details. build 08-Dec-2025 11:12:47 build 08-Dec-2025 11:12:47 > Task :processCloverResources NO-SOURCE build 08-Dec-2025 11:12:47 > Task :cloverClasses build 08-Dec-2025 11:12:47 > Task :copyHelp build 08-Dec-2025 11:12:48 > Task :buildIndices build 08-Dec-2025 11:12:48 > Task :copyResources build 08-Dec-2025 11:12:48 > Task :copyChannelResources build 08-Dec-2025 11:12:48 build 08-Dec-2025 11:12:48 > Task :createBuildProperties build 08-Dec-2025 11:12:48 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 08-Dec-2025 11:12:48 - 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 08-Dec-2025 11:12:48 build 08-Dec-2025 11:12:48 > Task :buildResources build 08-Dec-2025 11:12:49 > Task :copyDocs build 08-Dec-2025 11:12:49 build 08-Dec-2025 11:12:49 > Task :convertMdFiles build 08-Dec-2025 11:12:49 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 08-Dec-2025 11:12:49 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/releaseprocess.html build 08-Dec-2025 11:12:49 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 08-Dec-2025 11:12:49 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/building.html build 08-Dec-2025 11:12:49 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/jalview-projects.html build 08-Dec-2025 11:12:49 build 08-Dec-2025 11:12:49 > Task :releasesTemplates build 08-Dec-2025 11:12:49 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 08-Dec-2025 11:12:49 - 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 08-Dec-2025 11:12:49 - 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 08-Dec-2025 11:12:49 Stripping rc/test/etc for TEST build 08-Dec-2025 11:12:49 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 08-Dec-2025 11:12:49 build 08-Dec-2025 11:12:49 > Task :prepare build 08-Dec-2025 11:12:51 build 08-Dec-2025 11:12:51 > Task :compileJava build 08-Dec-2025 11:12:51 Setting target compatibility to 11 error 08-Dec-2025 11:12:56 Note: Some input files use or override a deprecated API. error 08-Dec-2025 11:12:56 Note: Recompile with -Xlint:deprecation for details. error 08-Dec-2025 11:12:56 Note: Some input files use unchecked or unsafe operations. error 08-Dec-2025 11:12:56 Note: Recompile with -Xlint:unchecked for details. build 08-Dec-2025 11:12:58 build 08-Dec-2025 11:12:58 > Task :compileTestJava build 08-Dec-2025 11:12:58 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 08-Dec-2025 11:12:58 - 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 08-Dec-2025 11:12:58 - 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 08-Dec-2025 11:12:58 Setting target compatibility to 11 error 08-Dec-2025 11:13:02 Note: Some input files use or override a deprecated API. error 08-Dec-2025 11:13:02 Note: Recompile with -Xlint:deprecation for details. error 08-Dec-2025 11:13:02 Note: Some input files use unchecked or unsafe operations. error 08-Dec-2025 11:13:02 Note: Recompile with -Xlint:unchecked for details. build 08-Dec-2025 11:13:03 build 08-Dec-2025 11:13:03 > Task :processTestResources build 08-Dec-2025 11:13:03 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 08-Dec-2025 11:13:03 - 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 08-Dec-2025 11:13:03 - 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 08-Dec-2025 11:13:03 - 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 08-Dec-2025 11:13:03 - 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 08-Dec-2025 11:13:03 - 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 08-Dec-2025 11:13:03 - 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 08-Dec-2025 11:13:03 - 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 08-Dec-2025 11:13:03 - 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 08-Dec-2025 11:13:03 build 08-Dec-2025 11:13:03 > Task :testClasses build 08-Dec-2025 11:13:05 build 08-Dec-2025 11:13:05 > Task :testTask0 build 08-Dec-2025 11:13:05 Running tests WITH clover error 08-Dec-2025 11:13:07 WARNING: An illegal reflective access operation has occurred error 08-Dec-2025 11:13:07 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 08-Dec-2025 11:13:07 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 08-Dec-2025 11:13:07 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 08-Dec-2025 11:13:07 WARNING: All illegal access operations will be denied in a future release build 08-Dec-2025 11:17:25 build 08-Dec-2025 11:17:25 > Task :testTask1 build 08-Dec-2025 11:17:25 Running tests WITH clover error 08-Dec-2025 11:17:26 WARNING: An illegal reflective access operation has occurred error 08-Dec-2025 11:17:26 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 08-Dec-2025 11:17:26 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 08-Dec-2025 11:17:26 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 08-Dec-2025 11:17:26 WARNING: All illegal access operations will be denied in a future release build 08-Dec-2025 11:19:35 build 08-Dec-2025 11:19:35 > Task :testTask2 build 08-Dec-2025 11:19:35 Running tests WITH clover build 08-Dec-2025 11:19:38 build 08-Dec-2025 11:19:38 > Task :testTask3 build 08-Dec-2025 11:19:38 Running tests WITH clover error 08-Dec-2025 11:19:39 WARNING: An illegal reflective access operation has occurred error 08-Dec-2025 11:19:39 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 08-Dec-2025 11:19:39 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 08-Dec-2025 11:19:39 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 08-Dec-2025 11:19:39 WARNING: All illegal access operations will be denied in a future release build 08-Dec-2025 11:20:25 build 08-Dec-2025 11:20:25 > Task :test NO-SOURCE build 08-Dec-2025 11:20:25 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 08-Dec-2025 11:20:25 │jalview:testTask0 results: SUCCESS (1835 tests, 1835 successes, 0 failures, 0 skipped) in 4 minutes, 19.074 seconds │ build 08-Dec-2025 11:20:25 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask0/index.html│ build 08-Dec-2025 11:20:25 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 08-Dec-2025 11:20:25 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 9.816 seconds │ build 08-Dec-2025 11:20:25 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask1/index.html│ build 08-Dec-2025 11:20:25 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 08-Dec-2025 11:20:25 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.336 seconds │ build 08-Dec-2025 11:20:25 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask2/index.html│ build 08-Dec-2025 11:20:25 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 08-Dec-2025 11:20:25 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 48.959 seconds │ build 08-Dec-2025 11:20:25 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask3/index.html│ build 08-Dec-2025 11:20:25 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 08-Dec-2025 11:20:25 │OVERALL: results: SUCCESS (1923 tests, 1923 successes, 0 failures, 0 skipped) in 6 minutes, 81.185 seconds │ build 08-Dec-2025 11:20:25 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 08-Dec-2025 11:20:25 build 08-Dec-2025 11:20:25 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 08-Dec-2025 11:20:25 build 08-Dec-2025 11:20:25 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 08-Dec-2025 11:20:25 build 08-Dec-2025 11:20:25 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 08-Dec-2025 11:20:25 build 08-Dec-2025 11:20:25 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 08-Dec-2025 11:20:25 Please consult deprecation warnings for more details. build 08-Dec-2025 11:20:25 build 08-Dec-2025 11:20:25 BUILD SUCCESSFUL in 8m 19s build 08-Dec-2025 11:20:25 21 actionable tasks: 20 executed, 1 up-to-date simple 08-Dec-2025 11:20:26 Finished task 'Run tests with openclover under gradle' with result: Success simple 08-Dec-2025 11:20:26 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 08-Dec-2025 11:20:26 Bamboo Artifactory Plugin version: 2.6.2 command 08-Dec-2025 11:20:26 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #5 (JB-GDB731-JOB1-5)'\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=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\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=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB731-JOB1-5\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=5\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-JOB1-5\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=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_shortPlanKey=GDB731\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\nbamboo_buildTimeStamp=2025-12-08T11:09:23.023Z\nbamboo_repository_previous_revision_number=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\nbamboo_planRepository_previousRevision=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\nbamboo_repository_git_branch=development/Release_2_11_5_Branch\nbamboo_buildResultKey=JB-GDB731-JOB1-5\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=a3717c01ff25f6dd430c1f09e1703931eb52d3e3\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=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_jobFailed=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\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 08-Dec-2025 11:20:26 2414 build 08-Dec-2025 11:20:31 build 08-Dec-2025 11:20:31 > Configure project : build 08-Dec-2025 11:20:31 Using properties from file './utils/channels/default/channel_gradle.properties' build 08-Dec-2025 11:20:31 JALVIEW_VERSION is set to '2.11.5.1' build 08-Dec-2025 11:20:31 HEADLESS BUILD build 08-Dec-2025 11:20:31 J2S ENABLED build 08-Dec-2025 11:20:32 Using a LOCAL profile. build 08-Dec-2025 11:20:32 eclipseDir exists build 08-Dec-2025 11:20:35 build 08-Dec-2025 11:20:35 > Task :cloverHtmlReport build 08-Dec-2025 11:20:35 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 08-Dec-2025 11:20:36 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/clover' build 08-Dec-2025 11:21:23 Done. Processed 117 packages in 46948ms (401ms per package). build 08-Dec-2025 11:21:27 build 08-Dec-2025 11:21:27 > Task :cloverXmlReport build 08-Dec-2025 11:21:27 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 08-Dec-2025 11:21:29 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/clover/clover.xml' build 08-Dec-2025 11:21:29 build 08-Dec-2025 11:21:29 > Task :cloverReport build 08-Dec-2025 11:21:29 build 08-Dec-2025 11:21:29 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 08-Dec-2025 11:21:29 build 08-Dec-2025 11:21:29 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 08-Dec-2025 11:21:29 build 08-Dec-2025 11:21:29 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 08-Dec-2025 11:21:29 build 08-Dec-2025 11:21:29 BUILD SUCCESSFUL in 1m 3s build 08-Dec-2025 11:21:29 2 actionable tasks: 2 executed simple 08-Dec-2025 11:21:30 Finished task 'Clover Report' with result: Success simple 08-Dec-2025 11:21:30 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 08-Dec-2025 11:21:30 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1... simple 08-Dec-2025 11:21:30 Finished task 'TestNG Parser' with result: Success simple 08-Dec-2025 11:21:30 Running post build plugin 'NCover Results Collector' simple 08-Dec-2025 11:21:30 Running post build plugin 'Artifact Copier' simple 08-Dec-2025 11:21:30 Publishing an artifact: Clover Report (System) simple 08-Dec-2025 11:21:31 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.819 s simple 08-Dec-2025 11:21:31 Publishing an artifact: TestNG report error 08-Dec-2025 11:21:31 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 08-Dec-2025 11:21:31 The artifact hasn't been successfully published after 1.176 ms simple 08-Dec-2025 11:21:31 Running post build plugin 'Artifactory Release Management Staging' simple 08-Dec-2025 11:21:31 Running post build plugin 'Artifactory Build Info Copier' simple 08-Dec-2025 11:21:31 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 08-Dec-2025 11:21:31 Running post build plugin 'npm Cache Cleanup' simple 08-Dec-2025 11:21:31 Running post build plugin 'Clover Results Collector' simple 08-Dec-2025 11:21:31 Running post build plugin 'Docker Container Cleanup' simple 08-Dec-2025 11:21:31 Finalising the build... simple 08-Dec-2025 11:21:31 Stopping timer. simple 08-Dec-2025 11:21:31 Build JB-GDB731-JOB1-5 completed. simple 08-Dec-2025 11:21:31 Running on server: post build plugin 'NCover Results Collector' simple 08-Dec-2025 11:21:31 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 08-Dec-2025 11:21:31 Running on server: post build plugin 'Clover Delta Calculator' simple 08-Dec-2025 11:21:32 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 08-Dec-2025 11:21:32 All post build plugins have finished simple 08-Dec-2025 11:21:32 Generating build results summary... simple 08-Dec-2025 11:21:32 Saving build results to disk... simple 08-Dec-2025 11:21:32 Logging substituted variables... simple 08-Dec-2025 11:21:32 Indexing build results... simple 08-Dec-2025 11:21:32 Finished building JB-GDB731-JOB1-5.