simple 14-Jan-2026 02:58:13 Build Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests #1 (JB-GDB740-JOB1-1) started building on agent Default Agent simple 14-Jan-2026 02:58:13 simple 14-Jan-2026 02:58:13 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1 simple 14-Jan-2026 02:58:13 Executing build Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests #1 (JB-GDB740-JOB1-1) simple 14-Jan-2026 02:58:13 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 14-Jan-2026 02:58:13 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1 simple 14-Jan-2026 02:58:13 Updating source code to revision: ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25 simple 14-Jan-2026 02:58:13 Fetching 'refs/heads/citation.cff' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 14-Jan-2026 02:58:14 Checking out revision ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25. simple 14-Jan-2026 02:58:14 Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/.git'. simple 14-Jan-2026 02:58:14 Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1'... simple 14-Jan-2026 02:58:14 done. simple 14-Jan-2026 02:58:20 Switched to a new branch 'citation.cff' simple 14-Jan-2026 02:58:20 Branch citation.cff set up to track remote branch citation.cff from origin. simple 14-Jan-2026 02:58:20 Updated source code to revision: ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25 simple 14-Jan-2026 02:58:20 Finished task 'Checkout Default Repository' with result: Success simple 14-Jan-2026 02:58:20 Running pre-build action: VCS Version Collector simple 14-Jan-2026 02:58:20 Running pre-build action: Artifactory Release Staging simple 14-Jan-2026 02:58:20 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 14-Jan-2026 02:58:20 Bamboo Artifactory Plugin version: 2.6.2 command 14-Jan-2026 02:58:20 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests #1 (JB-GDB740-JOB1-1)'\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-GDB740-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=citation.cff\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=citation.cff\nbamboo_repository_revision_number=ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB740-JOB1-1\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-GDB740-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB740-JOB1\nbamboo_repository_48168989_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortPlanName=citation.cff\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\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-GDB740-JOB1-1\nbamboo_repository_48168989_git_branch=citation.cff\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - citation.cff\nbamboo_shortPlanKey=GDB740\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25\nbamboo_buildTimeStamp=2026-01-14T02:58:13.804Z\nbamboo_repository_git_branch=citation.cff\nbamboo_buildResultKey=JB-GDB740-JOB1-1\nbamboo_repository_branch_name=citation.cff\nbamboo_repository_48168989_name=Jalview Gitlab\nbamboo_repository_48168989_branch_name=citation.cff\nbamboo_repository_48168989_git_username=\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25\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_48168989_revision_number=ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25\nbamboo_planRepository_branch=citation.cff\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=citation.cff\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=citation.cff\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-47972409\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-GDB740-JOB1\nbamboo_planKey=JB-GDB740\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=citation.cff\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 14-Jan-2026 02:58:20 2414 build 14-Jan-2026 02:58:21 Starting a Gradle Daemon (subsequent builds will be faster) build 14-Jan-2026 02:58:27 build 14-Jan-2026 02:58:27 > Configure project : build 14-Jan-2026 02:58:27 Using properties from file './utils/channels/default/channel_gradle.properties' build 14-Jan-2026 02:58:27 JALVIEW_VERSION is set to '2.11.5.1' build 14-Jan-2026 02:58:27 HEADLESS BUILD build 14-Jan-2026 02:58:27 J2S ENABLED build 14-Jan-2026 02:58:27 Using a LOCAL profile. build 14-Jan-2026 02:58:28 eclipseDir exists build 14-Jan-2026 02:58:29 build 14-Jan-2026 02:58:29 > Task :clean build 14-Jan-2026 02:58:29 > Task :cleanClover build 14-Jan-2026 02:58:29 > Task :cleanTest UP-TO-DATE build 14-Jan-2026 02:58:31 build 14-Jan-2026 02:58:31 > Task :cloverInstrJava build 14-Jan-2026 02:58:31 Clover: About to instrument 1109 files build 14-Jan-2026 02:58:31 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 14-Jan-2026 02:58:31 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/clover/clover.db'. build 14-Jan-2026 02:58:31 Processing files at 1.9 source level. error 14-Jan-2026 02:58:35 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 14-Jan-2026 02:58:35 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 14-Jan-2026 02:58:35 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 14-Jan-2026 02:58:35 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 14-Jan-2026 02:58:35 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 14-Jan-2026 02:58:35 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 14-Jan-2026 02:58:35 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 14-Jan-2026 02:58:40 Clover all over. Instrumented 1109 files (113 packages). build 14-Jan-2026 02:58:42 build 14-Jan-2026 02:58:42 > Task :cloverInstrTests build 14-Jan-2026 02:58:42 Clover: About to instrument test files build 14-Jan-2026 02:58:42 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 14-Jan-2026 02:58:42 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/clover/clover.db'. build 14-Jan-2026 02:58:42 Processing files at 1.9 source level. build 14-Jan-2026 02:58:45 Clover all over. Instrumented 293 files (52 packages). build 14-Jan-2026 02:58:45 1627 test methods detected. build 14-Jan-2026 02:58:45 build 14-Jan-2026 02:58:45 > Task :cloverInstr build 14-Jan-2026 02:58:49 build 14-Jan-2026 02:58:49 > Task :compileCloverJava build 14-Jan-2026 02:58:49 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 14-Jan-2026 02:58:49 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:58:49 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:58:49 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:58:49 Setting target compatibility to 11 error 14-Jan-2026 02:59:09 Note: Some input files use or override a deprecated API. error 14-Jan-2026 02:59:09 Note: Recompile with -Xlint:deprecation for details. error 14-Jan-2026 02:59:09 Note: Some input files use unchecked or unsafe operations. error 14-Jan-2026 02:59:09 Note: Recompile with -Xlint:unchecked for details. build 14-Jan-2026 02:59:15 build 14-Jan-2026 02:59:15 > Task :processCloverResources NO-SOURCE build 14-Jan-2026 02:59:15 > Task :cloverClasses build 14-Jan-2026 02:59:15 > Task :copyHelp build 14-Jan-2026 02:59:16 > Task :buildIndices build 14-Jan-2026 02:59:16 > Task :copyResources build 14-Jan-2026 02:59:16 > Task :copyChannelResources build 14-Jan-2026 02:59:16 build 14-Jan-2026 02:59:16 > Task :createBuildProperties build 14-Jan-2026 02:59:16 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 14-Jan-2026 02:59:16 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:59:16 build 14-Jan-2026 02:59:16 > Task :buildResources build 14-Jan-2026 02:59:16 > Task :copyDocs build 14-Jan-2026 02:59:17 build 14-Jan-2026 02:59:17 > Task :convertMdFiles build 14-Jan-2026 02:59:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 14-Jan-2026 02:59:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/releaseprocess.html build 14-Jan-2026 02:59:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 14-Jan-2026 02:59:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/building.html build 14-Jan-2026 02:59:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/jalview-projects.html build 14-Jan-2026 02:59:17 build 14-Jan-2026 02:59:17 > Task :releasesTemplates build 14-Jan-2026 02:59:17 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 14-Jan-2026 02:59:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:59:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:59:17 Stripping rc/test/etc for TEST build 14-Jan-2026 02:59:17 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 14-Jan-2026 02:59:17 build 14-Jan-2026 02:59:17 > Task :prepare build 14-Jan-2026 02:59:19 build 14-Jan-2026 02:59:19 > Task :compileJava build 14-Jan-2026 02:59:19 Setting target compatibility to 11 error 14-Jan-2026 02:59:24 Note: Some input files use or override a deprecated API. error 14-Jan-2026 02:59:24 Note: Recompile with -Xlint:deprecation for details. error 14-Jan-2026 02:59:24 Note: Some input files use unchecked or unsafe operations. error 14-Jan-2026 02:59:24 Note: Recompile with -Xlint:unchecked for details. build 14-Jan-2026 02:59:28 build 14-Jan-2026 02:59:28 > Task :compileTestJava build 14-Jan-2026 02:59:28 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 14-Jan-2026 02:59:28 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:59:28 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:59:28 Setting target compatibility to 11 error 14-Jan-2026 02:59:32 Note: Some input files use or override a deprecated API. error 14-Jan-2026 02:59:32 Note: Recompile with -Xlint:deprecation for details. error 14-Jan-2026 02:59:32 Note: Some input files use unchecked or unsafe operations. error 14-Jan-2026 02:59:32 Note: Recompile with -Xlint:unchecked for details. build 14-Jan-2026 02:59:33 build 14-Jan-2026 02:59:33 > Task :processTestResources build 14-Jan-2026 02:59:33 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 14-Jan-2026 02:59:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:59:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:59:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:59:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:59:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:59:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:59:33 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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 14-Jan-2026 02:59:33 build 14-Jan-2026 02:59:33 > Task :testClasses build 14-Jan-2026 02:59:35 build 14-Jan-2026 02:59:35 > Task :testTask0 build 14-Jan-2026 02:59:35 Running tests WITH clover error 14-Jan-2026 02:59:37 WARNING: An illegal reflective access operation has occurred error 14-Jan-2026 02:59:37 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 14-Jan-2026 02:59:37 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 14-Jan-2026 02:59:37 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 14-Jan-2026 02:59:37 WARNING: All illegal access operations will be denied in a future release build 14-Jan-2026 03:03:37 build 14-Jan-2026 03:03:37 > Task :testTask1 build 14-Jan-2026 03:03:37 Running tests WITH clover error 14-Jan-2026 03:03:38 WARNING: An illegal reflective access operation has occurred error 14-Jan-2026 03:03:38 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 14-Jan-2026 03:03:38 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 14-Jan-2026 03:03:38 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 14-Jan-2026 03:03:38 WARNING: All illegal access operations will be denied in a future release build 14-Jan-2026 03:05:46 build 14-Jan-2026 03:05:46 > Task :testTask2 build 14-Jan-2026 03:05:46 Running tests WITH clover build 14-Jan-2026 03:05:49 build 14-Jan-2026 03:05:49 > Task :testTask3 build 14-Jan-2026 03:05:49 Running tests WITH clover error 14-Jan-2026 03:05:50 WARNING: An illegal reflective access operation has occurred error 14-Jan-2026 03:05:50 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 14-Jan-2026 03:05:50 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 14-Jan-2026 03:05:50 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 14-Jan-2026 03:05:50 WARNING: All illegal access operations will be denied in a future release build 14-Jan-2026 03:06:37 build 14-Jan-2026 03:06:37 > Task :test NO-SOURCE build 14-Jan-2026 03:06:37 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 14-Jan-2026 03:06:37 │jalview:testTask0 results: SUCCESS (1835 tests, 1835 successes, 0 failures, 0 skipped) in 4 minutes, 0.629 seconds │ build 14-Jan-2026 03:06:37 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/testTask0/index.html│ build 14-Jan-2026 03:06:37 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 14-Jan-2026 03:06:37 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 9.095 seconds │ build 14-Jan-2026 03:06:37 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/testTask1/index.html│ build 14-Jan-2026 03:06:37 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 14-Jan-2026 03:06:37 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.240 seconds │ build 14-Jan-2026 03:06:37 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/testTask2/index.html│ build 14-Jan-2026 03:06:37 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 14-Jan-2026 03:06:37 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 49.614 seconds │ build 14-Jan-2026 03:06:37 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/testTask3/index.html│ build 14-Jan-2026 03:06:37 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 14-Jan-2026 03:06:37 │OVERALL: results: SUCCESS (1923 tests, 1923 successes, 0 failures, 0 skipped) in 6 minutes, 62.578 seconds │ build 14-Jan-2026 03:06:37 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 14-Jan-2026 03:06:37 build 14-Jan-2026 03:06:37 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 14-Jan-2026 03:06:37 build 14-Jan-2026 03:06:37 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 14-Jan-2026 03:06:37 build 14-Jan-2026 03:06:37 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 14-Jan-2026 03:06:37 build 14-Jan-2026 03:06:37 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 14-Jan-2026 03:06:37 Please consult deprecation warnings for more details. build 14-Jan-2026 03:06:37 build 14-Jan-2026 03:06:37 BUILD SUCCESSFUL in 8m 17s build 14-Jan-2026 03:06:37 21 actionable tasks: 20 executed, 1 up-to-date simple 14-Jan-2026 03:06:37 Finished task 'Run tests with openclover under gradle' with result: Success simple 14-Jan-2026 03:06:37 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 14-Jan-2026 03:06:37 Bamboo Artifactory Plugin version: 2.6.2 command 14-Jan-2026 03:06:37 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests #1 (JB-GDB740-JOB1-1)'\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-GDB740-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=citation.cff\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=citation.cff\nbamboo_repository_revision_number=ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB740-JOB1-1\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-GDB740-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB740-JOB1\nbamboo_repository_48168989_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortPlanName=citation.cff\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\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-GDB740-JOB1-1\nbamboo_repository_48168989_git_branch=citation.cff\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - citation.cff\nbamboo_shortPlanKey=GDB740\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25\nbamboo_buildTimeStamp=2026-01-14T02:58:13.804Z\nbamboo_repository_git_branch=citation.cff\nbamboo_buildResultKey=JB-GDB740-JOB1-1\nbamboo_repository_branch_name=citation.cff\nbamboo_repository_48168989_name=Jalview Gitlab\nbamboo_repository_48168989_branch_name=citation.cff\nbamboo_repository_48168989_git_username=\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25\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_48168989_revision_number=ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25\nbamboo_planRepository_branch=citation.cff\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_branchDisplayName=citation.cff\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=citation.cff\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-47972409\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-GDB740-JOB1\nbamboo_planKey=JB-GDB740\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=citation.cff\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 14-Jan-2026 03:06:37 2414 build 14-Jan-2026 03:06:42 build 14-Jan-2026 03:06:42 > Configure project : build 14-Jan-2026 03:06:42 Using properties from file './utils/channels/default/channel_gradle.properties' build 14-Jan-2026 03:06:42 JALVIEW_VERSION is set to '2.11.5.1' build 14-Jan-2026 03:06:42 HEADLESS BUILD build 14-Jan-2026 03:06:42 J2S ENABLED build 14-Jan-2026 03:06:42 Using a LOCAL profile. build 14-Jan-2026 03:06:43 eclipseDir exists build 14-Jan-2026 03:06:46 build 14-Jan-2026 03:06:46 > Task :cloverHtmlReport build 14-Jan-2026 03:06:46 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 14-Jan-2026 03:06:46 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/clover' build 14-Jan-2026 03:07:32 Done. Processed 117 packages in 45440ms (388ms per package). build 14-Jan-2026 03:07:36 build 14-Jan-2026 03:07:36 > Task :cloverXmlReport build 14-Jan-2026 03:07:36 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 14-Jan-2026 03:07:37 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/clover/clover.xml' build 14-Jan-2026 03:07:37 build 14-Jan-2026 03:07:37 > Task :cloverReport build 14-Jan-2026 03:07:37 build 14-Jan-2026 03:07:37 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 14-Jan-2026 03:07:37 build 14-Jan-2026 03:07:37 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 14-Jan-2026 03:07:37 build 14-Jan-2026 03:07:37 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 14-Jan-2026 03:07:37 build 14-Jan-2026 03:07:37 BUILD SUCCESSFUL in 1m build 14-Jan-2026 03:07:37 2 actionable tasks: 2 executed simple 14-Jan-2026 03:07:38 Finished task 'Clover Report' with result: Success simple 14-Jan-2026 03:07:38 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 14-Jan-2026 03:07:38 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1... simple 14-Jan-2026 03:07:38 Finished task 'TestNG Parser' with result: Success simple 14-Jan-2026 03:07:38 Running post build plugin 'NCover Results Collector' simple 14-Jan-2026 03:07:38 Running post build plugin 'Artifact Copier' simple 14-Jan-2026 03:07:38 Publishing an artifact: Clover Report (System) simple 14-Jan-2026 03:07:40 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.113 s simple 14-Jan-2026 03:07:40 Publishing an artifact: TestNG report error 14-Jan-2026 03:07:40 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/test does not exist. simple 14-Jan-2026 03:07:40 The artifact hasn't been successfully published after 1.546 ms simple 14-Jan-2026 03:07:40 Running post build plugin 'Artifactory Release Management Staging' simple 14-Jan-2026 03:07:40 Running post build plugin 'Artifactory Build Info Copier' simple 14-Jan-2026 03:07:40 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 14-Jan-2026 03:07:40 Running post build plugin 'npm Cache Cleanup' simple 14-Jan-2026 03:07:40 Running post build plugin 'Clover Results Collector' simple 14-Jan-2026 03:07:40 Running post build plugin 'Docker Container Cleanup' simple 14-Jan-2026 03:07:40 Finalising the build... simple 14-Jan-2026 03:07:40 Stopping timer. simple 14-Jan-2026 03:07:40 Build JB-GDB740-JOB1-1 completed. simple 14-Jan-2026 03:07:40 Running on server: post build plugin 'NCover Results Collector' simple 14-Jan-2026 03:07:40 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 14-Jan-2026 03:07:40 Running on server: post build plugin 'Clover Delta Calculator' simple 14-Jan-2026 03:07:40 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 14-Jan-2026 03:07:40 All post build plugins have finished simple 14-Jan-2026 03:07:40 Generating build results summary... simple 14-Jan-2026 03:07:40 Saving build results to disk... simple 14-Jan-2026 03:07:40 Logging substituted variables... simple 14-Jan-2026 03:07:40 Indexing build results... simple 14-Jan-2026 03:07:40 Finished building JB-GDB740-JOB1-1.