simple 11-Feb-2026 11:22:23 Build Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests #4 (JB-GDB740-JOB1-4) started building on agent Default Agent simple 11-Feb-2026 11:22:23 simple 11-Feb-2026 11:22:23 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1 simple 11-Feb-2026 11:22:23 Executing build Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests #4 (JB-GDB740-JOB1-4) simple 11-Feb-2026 11:22:23 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 11-Feb-2026 11:22:23 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1 simple 11-Feb-2026 11:22:23 Updating source code to revision: 1617d0ed323d507874712592b848e1ffdcec2883 simple 11-Feb-2026 11:22:23 Fetching 'refs/heads/citation.cff' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 11-Feb-2026 11:22:23 Checking out revision 1617d0ed323d507874712592b848e1ffdcec2883. simple 11-Feb-2026 11:22:23 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 11-Feb-2026 11:22:23 6f3ab10..1617d0e citation.cff -> origin/citation.cff simple 11-Feb-2026 11:22:24 Already on 'citation.cff' simple 11-Feb-2026 11:22:24 Your branch is behind 'origin/citation.cff' by 1 commit, and can be fast-forwarded. simple 11-Feb-2026 11:22:24 (use "git pull" to update your local branch) simple 11-Feb-2026 11:22:24 HEAD is now at 1617d0e JAL-4651 make it all valid simple 11-Feb-2026 11:22:24 Updated source code to revision: 1617d0ed323d507874712592b848e1ffdcec2883 simple 11-Feb-2026 11:22:24 Finished task 'Checkout Default Repository' with result: Success simple 11-Feb-2026 11:22:24 Running pre-build action: VCS Version Collector simple 11-Feb-2026 11:22:24 Running pre-build action: Artifactory Release Staging simple 11-Feb-2026 11:22:24 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 11-Feb-2026 11:22:24 Bamboo Artifactory Plugin version: 2.6.2 command 11-Feb-2026 11:22:24 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests #4 (JB-GDB740-JOB1-4)'\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=1617d0ed323d507874712592b848e1ffdcec2883\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB740-JOB1-4\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=4\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-JOB1-4\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_repository_48168989_previous_revision_number=6f3ab10eeeb41f56f66de76b7b65d8ef9364c322\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1617d0ed323d507874712592b848e1ffdcec2883\nbamboo_buildTimeStamp=2026-02-11T11:22:23.489Z\nbamboo_repository_previous_revision_number=6f3ab10eeeb41f56f66de76b7b65d8ef9364c322\nbamboo_planRepository_previousRevision=6f3ab10eeeb41f56f66de76b7b65d8ef9364c322\nbamboo_repository_git_branch=citation.cff\nbamboo_buildResultKey=JB-GDB740-JOB1-4\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=1617d0ed323d507874712592b848e1ffdcec2883\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=1617d0ed323d507874712592b848e1ffdcec2883\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_1_previousRevision=6f3ab10eeeb41f56f66de76b7b65d8ef9364c322\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 11-Feb-2026 11:22:24 2414 build 11-Feb-2026 11:22:26 build 11-Feb-2026 11:22:26 > Configure project : build 11-Feb-2026 11:22:26 Using properties from file './utils/channels/default/channel_gradle.properties' build 11-Feb-2026 11:22:26 JALVIEW_VERSION is set to '2.11.5.1' build 11-Feb-2026 11:22:26 HEADLESS BUILD build 11-Feb-2026 11:22:26 J2S ENABLED build 11-Feb-2026 11:22:26 Using a LOCAL profile. build 11-Feb-2026 11:22:26 eclipseDir exists build 11-Feb-2026 11:22:27 build 11-Feb-2026 11:22:27 > Task :clean build 11-Feb-2026 11:22:27 > Task :cleanClover build 11-Feb-2026 11:22:27 > Task :cleanTest UP-TO-DATE build 11-Feb-2026 11:22:29 build 11-Feb-2026 11:22:29 > Task :cloverInstrJava build 11-Feb-2026 11:22:29 Clover: About to instrument 1109 files build 11-Feb-2026 11:22:29 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 11-Feb-2026 11:22:29 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/clover/clover.db'. build 11-Feb-2026 11:22:29 Processing files at 1.9 source level. error 11-Feb-2026 11:22:31 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 11-Feb-2026 11:22:31 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 11-Feb-2026 11:22:31 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 11-Feb-2026 11:22:31 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 11-Feb-2026 11:22:31 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 11-Feb-2026 11:22:31 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 11-Feb-2026 11:22:31 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 11-Feb-2026 11:22:38 Clover all over. Instrumented 1109 files (113 packages). build 11-Feb-2026 11:22:40 build 11-Feb-2026 11:22:40 > Task :cloverInstrTests build 11-Feb-2026 11:22:40 Clover: About to instrument test files build 11-Feb-2026 11:22:40 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 11-Feb-2026 11:22:40 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/clover/clover.db'. build 11-Feb-2026 11:22:40 Processing files at 1.9 source level. build 11-Feb-2026 11:22:42 Clover all over. Instrumented 293 files (52 packages). build 11-Feb-2026 11:22:42 1627 test methods detected. build 11-Feb-2026 11:22:42 build 11-Feb-2026 11:22:42 > Task :cloverInstr build 11-Feb-2026 11:22:44 build 11-Feb-2026 11:22:44 > Task :compileCloverJava build 11-Feb-2026 11:22:44 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 11-Feb-2026 11:22:44 - 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 11-Feb-2026 11:22:44 - 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 11-Feb-2026 11:22:44 - 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 11-Feb-2026 11:22:44 Setting target compatibility to 11 error 11-Feb-2026 11:22:56 Note: Some input files use or override a deprecated API. error 11-Feb-2026 11:22:56 Note: Recompile with -Xlint:deprecation for details. error 11-Feb-2026 11:22:56 Note: Some input files use unchecked or unsafe operations. error 11-Feb-2026 11:22:56 Note: Recompile with -Xlint:unchecked for details. build 11-Feb-2026 11:23:02 build 11-Feb-2026 11:23:02 > Task :processCloverResources NO-SOURCE build 11-Feb-2026 11:23:02 > Task :cloverClasses build 11-Feb-2026 11:23:02 > Task :copyHelp build 11-Feb-2026 11:23:03 > Task :buildIndices build 11-Feb-2026 11:23:03 > Task :copyResources build 11-Feb-2026 11:23:03 > Task :copyChannelResources build 11-Feb-2026 11:23:03 build 11-Feb-2026 11:23:03 > Task :createBuildProperties build 11-Feb-2026 11:23:03 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 11-Feb-2026 11:23:03 - 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 11-Feb-2026 11:23:03 build 11-Feb-2026 11:23:03 > Task :buildResources build 11-Feb-2026 11:23:03 > Task :copyDocs build 11-Feb-2026 11:23:03 build 11-Feb-2026 11:23:03 > Task :convertMdFiles build 11-Feb-2026 11:23:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 11-Feb-2026 11:23:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/releaseprocess.html build 11-Feb-2026 11:23:03 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 11-Feb-2026 11:23:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/building.html build 11-Feb-2026 11:23:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/jalview-projects.html build 11-Feb-2026 11:23:04 build 11-Feb-2026 11:23:04 > Task :releasesTemplates build 11-Feb-2026 11:23:04 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 11-Feb-2026 11:23:04 - 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 11-Feb-2026 11:23:04 - 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 11-Feb-2026 11:23:04 Stripping rc/test/etc for TEST build 11-Feb-2026 11:23:04 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 11-Feb-2026 11:23:04 build 11-Feb-2026 11:23:04 > Task :prepare build 11-Feb-2026 11:23:06 build 11-Feb-2026 11:23:06 > Task :compileJava build 11-Feb-2026 11:23:06 Setting target compatibility to 11 error 11-Feb-2026 11:23:10 Note: Some input files use or override a deprecated API. error 11-Feb-2026 11:23:10 Note: Recompile with -Xlint:deprecation for details. error 11-Feb-2026 11:23:10 Note: Some input files use unchecked or unsafe operations. error 11-Feb-2026 11:23:10 Note: Recompile with -Xlint:unchecked for details. build 11-Feb-2026 11:23:13 build 11-Feb-2026 11:23:13 > Task :compileTestJava build 11-Feb-2026 11:23:13 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 11-Feb-2026 11:23:13 - 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 11-Feb-2026 11:23:13 - 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 11-Feb-2026 11:23:13 Setting target compatibility to 11 error 11-Feb-2026 11:23:16 Note: Some input files use or override a deprecated API. error 11-Feb-2026 11:23:16 Note: Recompile with -Xlint:deprecation for details. error 11-Feb-2026 11:23:16 Note: Some input files use unchecked or unsafe operations. error 11-Feb-2026 11:23:16 Note: Recompile with -Xlint:unchecked for details. build 11-Feb-2026 11:23:17 build 11-Feb-2026 11:23:17 > Task :processTestResources build 11-Feb-2026 11:23:17 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 11-Feb-2026 11:23:17 - 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 ':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 11-Feb-2026 11:23:17 - 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 11-Feb-2026 11:23:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/help_build'. 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 11-Feb-2026 11:23:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/help_build'. 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 11-Feb-2026 11:23:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/help_build'. 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 11-Feb-2026 11:23:17 - 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 11-Feb-2026 11:23:17 - 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 11-Feb-2026 11:23:17 - 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 11-Feb-2026 11:23:17 build 11-Feb-2026 11:23:17 > Task :testClasses build 11-Feb-2026 11:23:19 build 11-Feb-2026 11:23:19 > Task :testTask0 build 11-Feb-2026 11:23:19 Running tests WITH clover error 11-Feb-2026 11:23:21 WARNING: An illegal reflective access operation has occurred error 11-Feb-2026 11:23:21 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 11-Feb-2026 11:23:21 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 11-Feb-2026 11:23:21 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 11-Feb-2026 11:23:21 WARNING: All illegal access operations will be denied in a future release build 11-Feb-2026 11:27:48 build 11-Feb-2026 11:27:48 > Task :testTask1 build 11-Feb-2026 11:27:48 Running tests WITH clover error 11-Feb-2026 11:27:50 WARNING: An illegal reflective access operation has occurred error 11-Feb-2026 11:27:50 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 11-Feb-2026 11:27:50 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 11-Feb-2026 11:27:50 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 11-Feb-2026 11:27:50 WARNING: All illegal access operations will be denied in a future release build 11-Feb-2026 11:30:08 build 11-Feb-2026 11:30:08 > Task :testTask2 build 11-Feb-2026 11:30:08 Running tests WITH clover build 11-Feb-2026 11:30:11 build 11-Feb-2026 11:30:11 > Task :testTask3 build 11-Feb-2026 11:30:11 Running tests WITH clover error 11-Feb-2026 11:30:13 WARNING: An illegal reflective access operation has occurred error 11-Feb-2026 11:30:13 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 11-Feb-2026 11:30:13 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 11-Feb-2026 11:30:13 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 11-Feb-2026 11:30:13 WARNING: All illegal access operations will be denied in a future release build 11-Feb-2026 11:31:04 build 11-Feb-2026 11:31:04 > Task :test NO-SOURCE build 11-Feb-2026 11:31:04 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 11-Feb-2026 11:31:04 │jalview:testTask0 results: SUCCESS (1835 tests, 1835 successes, 0 failures, 0 skipped) in 4 minutes, 28.761 seconds │ build 11-Feb-2026 11:31:04 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/testTask0/index.html│ build 11-Feb-2026 11:31:04 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Feb-2026 11:31:04 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 19.560 seconds │ build 11-Feb-2026 11:31:04 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/testTask1/index.html│ build 11-Feb-2026 11:31:04 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Feb-2026 11:31:04 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.198 seconds │ build 11-Feb-2026 11:31:04 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/testTask2/index.html│ build 11-Feb-2026 11:31:04 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Feb-2026 11:31:04 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 54.220 seconds │ build 11-Feb-2026 11:31:04 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/testTask3/index.html│ build 11-Feb-2026 11:31:04 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Feb-2026 11:31:04 │OVERALL: results: SUCCESS (1923 tests, 1923 successes, 0 failures, 0 skipped) in 6 minutes, 105.739 seconds │ build 11-Feb-2026 11:31:04 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 11-Feb-2026 11:31:04 build 11-Feb-2026 11:31:04 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 11-Feb-2026 11:31:04 build 11-Feb-2026 11:31:04 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 11-Feb-2026 11:31:04 build 11-Feb-2026 11:31:04 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 11-Feb-2026 11:31:04 build 11-Feb-2026 11:31:04 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 11-Feb-2026 11:31:04 Please consult deprecation warnings for more details. build 11-Feb-2026 11:31:04 build 11-Feb-2026 11:31:04 BUILD SUCCESSFUL in 8m 39s build 11-Feb-2026 11:31:04 21 actionable tasks: 20 executed, 1 up-to-date simple 11-Feb-2026 11:31:04 Finished task 'Run tests with openclover under gradle' with result: Success simple 11-Feb-2026 11:31:04 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 11-Feb-2026 11:31:04 Bamboo Artifactory Plugin version: 2.6.2 command 11-Feb-2026 11:31:04 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests #4 (JB-GDB740-JOB1-4)'\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=1617d0ed323d507874712592b848e1ffdcec2883\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB740-JOB1-4\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=4\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-JOB1-4\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_repository_48168989_previous_revision_number=6f3ab10eeeb41f56f66de76b7b65d8ef9364c322\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1617d0ed323d507874712592b848e1ffdcec2883\nbamboo_buildTimeStamp=2026-02-11T11:22:23.489Z\nbamboo_repository_previous_revision_number=6f3ab10eeeb41f56f66de76b7b65d8ef9364c322\nbamboo_planRepository_previousRevision=6f3ab10eeeb41f56f66de76b7b65d8ef9364c322\nbamboo_repository_git_branch=citation.cff\nbamboo_buildResultKey=JB-GDB740-JOB1-4\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=1617d0ed323d507874712592b848e1ffdcec2883\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=1617d0ed323d507874712592b848e1ffdcec2883\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_1_previousRevision=6f3ab10eeeb41f56f66de76b7b65d8ef9364c322\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 11-Feb-2026 11:31:04 2414 build 11-Feb-2026 11:31:10 build 11-Feb-2026 11:31:10 > Configure project : build 11-Feb-2026 11:31:10 Using properties from file './utils/channels/default/channel_gradle.properties' build 11-Feb-2026 11:31:10 JALVIEW_VERSION is set to '2.11.5.1' build 11-Feb-2026 11:31:10 HEADLESS BUILD build 11-Feb-2026 11:31:10 J2S ENABLED build 11-Feb-2026 11:31:10 Using a LOCAL profile. build 11-Feb-2026 11:31:11 eclipseDir exists build 11-Feb-2026 11:31:13 build 11-Feb-2026 11:31:13 > Task :cloverHtmlReport build 11-Feb-2026 11:31:13 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 11-Feb-2026 11:31:15 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/clover' build 11-Feb-2026 11:32:01 Done. Processed 117 packages in 46445ms (396ms per package). build 11-Feb-2026 11:32:06 build 11-Feb-2026 11:32:06 > Task :cloverXmlReport build 11-Feb-2026 11:32:06 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 11-Feb-2026 11:32:08 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/clover/clover.xml' build 11-Feb-2026 11:32:08 build 11-Feb-2026 11:32:08 > Task :cloverReport build 11-Feb-2026 11:32:08 build 11-Feb-2026 11:32:08 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 11-Feb-2026 11:32:08 build 11-Feb-2026 11:32:08 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 11-Feb-2026 11:32:08 build 11-Feb-2026 11:32:08 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 11-Feb-2026 11:32:08 build 11-Feb-2026 11:32:08 BUILD SUCCESSFUL in 1m 3s build 11-Feb-2026 11:32:08 2 actionable tasks: 2 executed simple 11-Feb-2026 11:32:08 Finished task 'Clover Report' with result: Success simple 11-Feb-2026 11:32:08 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 11-Feb-2026 11:32:08 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1... simple 11-Feb-2026 11:32:08 Finished task 'TestNG Parser' with result: Success simple 11-Feb-2026 11:32:08 Running post build plugin 'NCover Results Collector' simple 11-Feb-2026 11:32:08 Running post build plugin 'Artifact Copier' simple 11-Feb-2026 11:32:08 Publishing an artifact: Clover Report (System) simple 11-Feb-2026 11:32:10 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.589 s simple 11-Feb-2026 11:32:10 Publishing an artifact: TestNG report error 11-Feb-2026 11:32:10 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 11-Feb-2026 11:32:10 The artifact hasn't been successfully published after 2.197 ms simple 11-Feb-2026 11:32:10 Running post build plugin 'Artifactory Release Management Staging' simple 11-Feb-2026 11:32:10 Running post build plugin 'Artifactory Build Info Copier' simple 11-Feb-2026 11:32:10 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 11-Feb-2026 11:32:10 Running post build plugin 'npm Cache Cleanup' simple 11-Feb-2026 11:32:10 Running post build plugin 'Clover Results Collector' simple 11-Feb-2026 11:32:10 Running post build plugin 'Docker Container Cleanup' simple 11-Feb-2026 11:32:10 Finalising the build... simple 11-Feb-2026 11:32:10 Stopping timer. simple 11-Feb-2026 11:32:10 Build JB-GDB740-JOB1-4 completed. simple 11-Feb-2026 11:32:10 Running on server: post build plugin 'NCover Results Collector' simple 11-Feb-2026 11:32:10 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 11-Feb-2026 11:32:10 Running on server: post build plugin 'Clover Delta Calculator' simple 11-Feb-2026 11:32:10 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 11-Feb-2026 11:32:10 All post build plugins have finished simple 11-Feb-2026 11:32:10 Generating build results summary... simple 11-Feb-2026 11:32:10 Saving build results to disk... simple 11-Feb-2026 11:32:10 Logging substituted variables... simple 11-Feb-2026 11:32:10 Indexing build results... simple 11-Feb-2026 11:32:10 Finished building JB-GDB740-JOB1-4.