simple 05-Dec-2025 17:45:22 Build Jalview Builds - Gradle Develop Build - patch-JAL-4606_again_and_again - Clover and Tests #9 (JB-GDB735-JOB1-9) started building on agent Default Agent simple 05-Dec-2025 17:45:22 simple 05-Dec-2025 17:45:22 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1 simple 05-Dec-2025 17:45:22 Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4606_again_and_again - Clover and Tests #9 (JB-GDB735-JOB1-9) simple 05-Dec-2025 17:45:22 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 05-Dec-2025 17:45:22 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1 simple 05-Dec-2025 17:45:22 Updating source code to revision: 23d77417fa19d86491740b13213c4e5f6fe8c8ca simple 05-Dec-2025 17:45:22 Fetching 'refs/heads/patch/JAL-4606_again_and_again' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 05-Dec-2025 17:45:22 Checking out revision 23d77417fa19d86491740b13213c4e5f6fe8c8ca. simple 05-Dec-2025 17:45:22 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 05-Dec-2025 17:45:22 de432b7..23d7741 patch/JAL-4606_again_and_again -> origin/patch/JAL-4606_again_and_again simple 05-Dec-2025 17:45:22 Already on 'patch/JAL-4606_again_and_again' simple 05-Dec-2025 17:45:22 Your branch is behind 'origin/patch/JAL-4606_again_and_again' by 1 commit, and can be fast-forwarded. simple 05-Dec-2025 17:45:22 (use "git pull" to update your local branch) simple 05-Dec-2025 17:45:22 HEAD is now at 23d7741 JAL-4606 JAL-4638 - try to report exceptions and 'ignore' them rather than wait for them to be resolved. simple 05-Dec-2025 17:45:22 Updated source code to revision: 23d77417fa19d86491740b13213c4e5f6fe8c8ca simple 05-Dec-2025 17:45:22 Finished task 'Checkout Default Repository' with result: Success simple 05-Dec-2025 17:45:22 Running pre-build action: VCS Version Collector simple 05-Dec-2025 17:45:22 Running pre-build action: Artifactory Release Staging simple 05-Dec-2025 17:45:22 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 05-Dec-2025 17:45:22 Bamboo Artifactory Plugin version: 2.6.2 command 05-Dec-2025 17:45:22 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4606_again_and_again - Clover and Tests #9 (JB-GDB735-JOB1-9)'\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-GDB735-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4606_again_and_again\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4606_again_and_again\nbamboo_repository_revision_number=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB735-JOB1-9\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_46498622_previous_revision_number=de432b741cf810c75c9c231c9b4367d7fa1c25f4\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1\nbamboo_repository_46498622_git_username=\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB735-JOB1\nbamboo_repository_46498622_branch_name=patch/JAL-4606_again_and_again\nbamboo_shortPlanName=patch-JAL-4606_again_and_again\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=9\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-GDB735-JOB1-9\nbamboo_repository_46498622_name=Jalview Gitlab\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498622_revision_number=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4606_again_and_again\nbamboo_shortPlanKey=GDB735\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_buildTimeStamp=2025-12-05T17:45:22.155Z\nbamboo_repository_previous_revision_number=de432b741cf810c75c9c231c9b4367d7fa1c25f4\nbamboo_planRepository_previousRevision=de432b741cf810c75c9c231c9b4367d7fa1c25f4\nbamboo_repository_git_branch=patch/JAL-4606_again_and_again\nbamboo_buildResultKey=JB-GDB735-JOB1-9\nbamboo_repository_branch_name=patch/JAL-4606_again_and_again\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4606_again_and_again - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498622_git_branch=patch/JAL-4606_again_and_again\nbamboo_planRepository_1_revision=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=patch/JAL-4606_again_and_again\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=de432b741cf810c75c9c231c9b4367d7fa1c25f4\nbamboo_planRepository_branchDisplayName=patch/JAL-4606_again_and_again\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4606_again_and_again\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-46302813\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498622_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-GDB735-JOB1\nbamboo_planKey=JB-GDB735\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4606_again_and_again\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 05-Dec-2025 17:45:22 2414 build 05-Dec-2025 17:45:23 build 05-Dec-2025 17:45:23 > Configure project : build 05-Dec-2025 17:45:23 Using properties from file './utils/channels/default/channel_gradle.properties' build 05-Dec-2025 17:45:23 JALVIEW_VERSION is set to '2.11.5.1' build 05-Dec-2025 17:45:23 HEADLESS BUILD build 05-Dec-2025 17:45:23 J2S ENABLED build 05-Dec-2025 17:45:23 Using a LOCAL profile. build 05-Dec-2025 17:45:23 eclipseDir exists build 05-Dec-2025 17:45:24 build 05-Dec-2025 17:45:24 > Task :clean build 05-Dec-2025 17:45:24 > Task :cleanClover build 05-Dec-2025 17:45:24 > Task :cleanTest UP-TO-DATE build 05-Dec-2025 17:45:26 build 05-Dec-2025 17:45:26 > Task :cloverInstrJava build 05-Dec-2025 17:45:26 Clover: About to instrument 1109 files build 05-Dec-2025 17:45:26 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 05-Dec-2025 17:45:26 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/clover/clover.db'. build 05-Dec-2025 17:45:26 Processing files at 1.9 source level. error 05-Dec-2025 17:45:27 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 05-Dec-2025 17:45:27 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 05-Dec-2025 17:45:27 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 05-Dec-2025 17:45:27 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 05-Dec-2025 17:45:27 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 05-Dec-2025 17:45:27 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 05-Dec-2025 17:45:27 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 05-Dec-2025 17:45:33 Clover all over. Instrumented 1109 files (113 packages). build 05-Dec-2025 17:45:35 build 05-Dec-2025 17:45:35 > Task :cloverInstrTests build 05-Dec-2025 17:45:35 Clover: About to instrument test files build 05-Dec-2025 17:45:35 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 05-Dec-2025 17:45:35 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/clover/clover.db'. build 05-Dec-2025 17:45:35 Processing files at 1.9 source level. build 05-Dec-2025 17:45:37 Clover all over. Instrumented 293 files (52 packages). build 05-Dec-2025 17:45:37 1627 test methods detected. build 05-Dec-2025 17:45:37 build 05-Dec-2025 17:45:37 > Task :cloverInstr build 05-Dec-2025 17:45:39 build 05-Dec-2025 17:45:39 > Task :compileCloverJava build 05-Dec-2025 17:45:39 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 05-Dec-2025 17:45:39 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:45:39 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:45:39 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:45:39 Setting target compatibility to 11 error 05-Dec-2025 17:45:50 Note: Some input files use or override a deprecated API. error 05-Dec-2025 17:45:50 Note: Recompile with -Xlint:deprecation for details. error 05-Dec-2025 17:45:50 Note: Some input files use unchecked or unsafe operations. error 05-Dec-2025 17:45:50 Note: Recompile with -Xlint:unchecked for details. build 05-Dec-2025 17:45:54 build 05-Dec-2025 17:45:54 > Task :processCloverResources NO-SOURCE build 05-Dec-2025 17:45:54 > Task :cloverClasses build 05-Dec-2025 17:45:54 > Task :copyHelp build 05-Dec-2025 17:45:55 > Task :buildIndices build 05-Dec-2025 17:45:55 > Task :copyResources build 05-Dec-2025 17:45:55 > Task :copyChannelResources build 05-Dec-2025 17:45:55 build 05-Dec-2025 17:45:55 > Task :createBuildProperties build 05-Dec-2025 17:45:55 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 05-Dec-2025 17:45:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:45:55 build 05-Dec-2025 17:45:55 > Task :buildResources build 05-Dec-2025 17:45:55 > Task :copyDocs build 05-Dec-2025 17:45:55 build 05-Dec-2025 17:45:55 > Task :convertMdFiles build 05-Dec-2025 17:45:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 05-Dec-2025 17:45:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/resources/doc_build/doc/releaseprocess.html build 05-Dec-2025 17:45:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 05-Dec-2025 17:45:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/resources/doc_build/doc/building.html build 05-Dec-2025 17:45:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/resources/doc_build/doc/jalview-projects.html build 05-Dec-2025 17:45:55 build 05-Dec-2025 17:45:55 > Task :releasesTemplates build 05-Dec-2025 17:45:55 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 05-Dec-2025 17:45:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:45:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:45:55 Stripping rc/test/etc for TEST build 05-Dec-2025 17:45:55 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 05-Dec-2025 17:45:55 build 05-Dec-2025 17:45:55 > Task :prepare build 05-Dec-2025 17:45:57 build 05-Dec-2025 17:45:57 > Task :compileJava build 05-Dec-2025 17:45:57 Setting target compatibility to 11 error 05-Dec-2025 17:46:01 Note: Some input files use or override a deprecated API. error 05-Dec-2025 17:46:01 Note: Recompile with -Xlint:deprecation for details. error 05-Dec-2025 17:46:01 Note: Some input files use unchecked or unsafe operations. error 05-Dec-2025 17:46:01 Note: Recompile with -Xlint:unchecked for details. build 05-Dec-2025 17:46:03 build 05-Dec-2025 17:46:03 > Task :compileTestJava build 05-Dec-2025 17:46:03 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 05-Dec-2025 17:46:03 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:46:03 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:46:03 Setting target compatibility to 11 error 05-Dec-2025 17:46:06 Note: Some input files use or override a deprecated API. error 05-Dec-2025 17:46:06 Note: Recompile with -Xlint:deprecation for details. error 05-Dec-2025 17:46:06 Note: Some input files use unchecked or unsafe operations. error 05-Dec-2025 17:46:06 Note: Recompile with -Xlint:unchecked for details. build 05-Dec-2025 17:46:07 build 05-Dec-2025 17:46:07 > Task :processTestResources build 05-Dec-2025 17:46:07 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 05-Dec-2025 17:46:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:46:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:46:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:46:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:46:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:46:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:46:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:46:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-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 05-Dec-2025 17:46:07 build 05-Dec-2025 17:46:07 > Task :testClasses build 05-Dec-2025 17:46:09 build 05-Dec-2025 17:46:09 > Task :testTask0 build 05-Dec-2025 17:46:09 Running tests WITH clover error 05-Dec-2025 17:46:10 WARNING: An illegal reflective access operation has occurred error 05-Dec-2025 17:46:10 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 05-Dec-2025 17:46:10 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 05-Dec-2025 17:46:10 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 05-Dec-2025 17:46:10 WARNING: All illegal access operations will be denied in a future release build 05-Dec-2025 17:50:20 build 05-Dec-2025 17:50:20 > Task :testTask1 build 05-Dec-2025 17:50:20 Running tests WITH clover error 05-Dec-2025 17:50:21 WARNING: An illegal reflective access operation has occurred error 05-Dec-2025 17:50:21 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 05-Dec-2025 17:50:21 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 05-Dec-2025 17:50:21 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 05-Dec-2025 17:50:21 WARNING: All illegal access operations will be denied in a future release build 05-Dec-2025 17:52:29 build 05-Dec-2025 17:52:29 > Task :testTask2 build 05-Dec-2025 17:52:29 Running tests WITH clover build 05-Dec-2025 17:52:33 build 05-Dec-2025 17:52:33 > Task :testTask3 build 05-Dec-2025 17:52:33 Running tests WITH clover error 05-Dec-2025 17:52:34 WARNING: An illegal reflective access operation has occurred error 05-Dec-2025 17:52:34 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 05-Dec-2025 17:52:34 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 05-Dec-2025 17:52:34 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 05-Dec-2025 17:52:34 WARNING: All illegal access operations will be denied in a future release build 05-Dec-2025 17:53:19 build 05-Dec-2025 17:53:19 > Task :test NO-SOURCE build 05-Dec-2025 17:53:19 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 05-Dec-2025 17:53:19 │jalview:testTask0 results: SUCCESS (1835 tests, 1835 successes, 0 failures, 0 skipped) in 4 minutes, 10.785 seconds │ build 05-Dec-2025 17:53:19 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/reports/tests/testTask0/index.html│ build 05-Dec-2025 17:53:19 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 05-Dec-2025 17:53:19 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 9.018 seconds │ build 05-Dec-2025 17:53:19 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/reports/tests/testTask1/index.html│ build 05-Dec-2025 17:53:19 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 05-Dec-2025 17:53:19 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.200 seconds │ build 05-Dec-2025 17:53:19 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/reports/tests/testTask2/index.html│ build 05-Dec-2025 17:53:19 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 05-Dec-2025 17:53:19 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 48.162 seconds │ build 05-Dec-2025 17:53:19 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/reports/tests/testTask3/index.html│ build 05-Dec-2025 17:53:19 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 05-Dec-2025 17:53:19 │OVERALL: results: SUCCESS (1923 tests, 1923 successes, 0 failures, 0 skipped) in 6 minutes, 71.165 seconds │ build 05-Dec-2025 17:53:19 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 05-Dec-2025 17:53:19 build 05-Dec-2025 17:53:19 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 05-Dec-2025 17:53:19 build 05-Dec-2025 17:53:19 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 05-Dec-2025 17:53:19 build 05-Dec-2025 17:53:19 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 05-Dec-2025 17:53:19 build 05-Dec-2025 17:53:19 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 05-Dec-2025 17:53:19 Please consult deprecation warnings for more details. build 05-Dec-2025 17:53:19 build 05-Dec-2025 17:53:19 BUILD SUCCESSFUL in 7m 56s build 05-Dec-2025 17:53:19 21 actionable tasks: 20 executed, 1 up-to-date simple 05-Dec-2025 17:53:19 Finished task 'Run tests with openclover under gradle' with result: Success simple 05-Dec-2025 17:53:19 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 05-Dec-2025 17:53:19 Bamboo Artifactory Plugin version: 2.6.2 command 05-Dec-2025 17:53:19 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4606_again_and_again - Clover and Tests #9 (JB-GDB735-JOB1-9)'\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-GDB735-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4606_again_and_again\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4606_again_and_again\nbamboo_repository_revision_number=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB735-JOB1-9\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_46498622_previous_revision_number=de432b741cf810c75c9c231c9b4367d7fa1c25f4\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1\nbamboo_repository_46498622_git_username=\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB735-JOB1\nbamboo_repository_46498622_branch_name=patch/JAL-4606_again_and_again\nbamboo_shortPlanName=patch-JAL-4606_again_and_again\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=9\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-GDB735-JOB1-9\nbamboo_repository_46498622_name=Jalview Gitlab\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498622_revision_number=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4606_again_and_again\nbamboo_shortPlanKey=GDB735\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_buildTimeStamp=2025-12-05T17:45:22.155Z\nbamboo_repository_previous_revision_number=de432b741cf810c75c9c231c9b4367d7fa1c25f4\nbamboo_planRepository_previousRevision=de432b741cf810c75c9c231c9b4367d7fa1c25f4\nbamboo_repository_git_branch=patch/JAL-4606_again_and_again\nbamboo_buildResultKey=JB-GDB735-JOB1-9\nbamboo_repository_branch_name=patch/JAL-4606_again_and_again\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4606_again_and_again - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498622_git_branch=patch/JAL-4606_again_and_again\nbamboo_planRepository_1_revision=23d77417fa19d86491740b13213c4e5f6fe8c8ca\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_planRepository_branch=patch/JAL-4606_again_and_again\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=de432b741cf810c75c9c231c9b4367d7fa1c25f4\nbamboo_planRepository_branchDisplayName=patch/JAL-4606_again_and_again\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4606_again_and_again\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-46302813\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498622_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-GDB735-JOB1\nbamboo_planKey=JB-GDB735\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4606_again_and_again\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 05-Dec-2025 17:53:19 2414 build 05-Dec-2025 17:53:24 build 05-Dec-2025 17:53:24 > Configure project : build 05-Dec-2025 17:53:24 Using properties from file './utils/channels/default/channel_gradle.properties' build 05-Dec-2025 17:53:24 JALVIEW_VERSION is set to '2.11.5.1' build 05-Dec-2025 17:53:24 HEADLESS BUILD build 05-Dec-2025 17:53:24 J2S ENABLED build 05-Dec-2025 17:53:24 Using a LOCAL profile. build 05-Dec-2025 17:53:25 eclipseDir exists build 05-Dec-2025 17:53:27 build 05-Dec-2025 17:53:27 > Task :cloverHtmlReport build 05-Dec-2025 17:53:27 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 05-Dec-2025 17:53:28 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/reports/clover' build 05-Dec-2025 17:54:15 Done. Processed 117 packages in 46911ms (400ms per package). build 05-Dec-2025 17:54:20 build 05-Dec-2025 17:54:20 > Task :cloverXmlReport build 05-Dec-2025 17:54:20 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 05-Dec-2025 17:54:22 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/reports/clover/clover.xml' build 05-Dec-2025 17:54:22 build 05-Dec-2025 17:54:22 > Task :cloverReport build 05-Dec-2025 17:54:22 build 05-Dec-2025 17:54:22 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 05-Dec-2025 17:54:22 build 05-Dec-2025 17:54:22 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 05-Dec-2025 17:54:22 build 05-Dec-2025 17:54:22 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 05-Dec-2025 17:54:22 build 05-Dec-2025 17:54:22 BUILD SUCCESSFUL in 1m 2s build 05-Dec-2025 17:54:22 2 actionable tasks: 2 executed simple 05-Dec-2025 17:54:22 Finished task 'Clover Report' with result: Success simple 05-Dec-2025 17:54:22 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 05-Dec-2025 17:54:22 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1... simple 05-Dec-2025 17:54:22 Finished task 'TestNG Parser' with result: Success simple 05-Dec-2025 17:54:22 Running post build plugin 'NCover Results Collector' simple 05-Dec-2025 17:54:22 Running post build plugin 'Artifact Copier' simple 05-Dec-2025 17:54:22 Publishing an artifact: Clover Report (System) simple 05-Dec-2025 17:54:24 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.665 s simple 05-Dec-2025 17:54:24 Publishing an artifact: TestNG report error 05-Dec-2025 17:54:24 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB735-JOB1/build/reports/tests/test does not exist. simple 05-Dec-2025 17:54:24 The artifact hasn't been successfully published after 728.1 μs simple 05-Dec-2025 17:54:24 Running post build plugin 'Artifactory Release Management Staging' simple 05-Dec-2025 17:54:24 Running post build plugin 'Artifactory Build Info Copier' simple 05-Dec-2025 17:54:24 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 05-Dec-2025 17:54:24 Running post build plugin 'npm Cache Cleanup' simple 05-Dec-2025 17:54:24 Running post build plugin 'Clover Results Collector' simple 05-Dec-2025 17:54:24 Running post build plugin 'Docker Container Cleanup' simple 05-Dec-2025 17:54:24 Finalising the build... simple 05-Dec-2025 17:54:24 Stopping timer. simple 05-Dec-2025 17:54:24 Build JB-GDB735-JOB1-9 completed. simple 05-Dec-2025 17:54:24 Running on server: post build plugin 'NCover Results Collector' simple 05-Dec-2025 17:54:24 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 05-Dec-2025 17:54:24 Running on server: post build plugin 'Clover Delta Calculator' simple 05-Dec-2025 17:54:24 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 05-Dec-2025 17:54:24 All post build plugins have finished simple 05-Dec-2025 17:54:24 Generating build results summary... simple 05-Dec-2025 17:54:24 Saving build results to disk... simple 05-Dec-2025 17:54:24 Logging substituted variables... simple 05-Dec-2025 17:54:24 Indexing build results... simple 05-Dec-2025 17:54:24 Finished building JB-GDB735-JOB1-9.