simple 07-Mar-2025 09:41:10 Build Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #8 (JB-GDB661-JOB1-8) started building on agent Default Agent simple 07-Mar-2025 09:41:10 simple 07-Mar-2025 09:41:10 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1 simple 07-Mar-2025 09:41:10 Executing build Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #8 (JB-GDB661-JOB1-8) simple 07-Mar-2025 09:41:10 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 07-Mar-2025 09:41:10 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1 simple 07-Mar-2025 09:41:10 Updating source code to revision: fbda4585b2681eea8794f267dc30b6e98bfad030 simple 07-Mar-2025 09:41:10 Fetching 'refs/heads/feature/JAL-4386_JAL-4435_reformat_node_labels' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 07-Mar-2025 09:41:10 Checking out revision fbda4585b2681eea8794f267dc30b6e98bfad030. simple 07-Mar-2025 09:41:12 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 07-Mar-2025 09:41:12 d9b1091..fbda458 feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels simple 07-Mar-2025 09:41:12 * [new branch] jims_2_12/JAL-4519_error_reporting_and_slivka -> origin/jims_2_12/JAL-4519_error_reporting_and_slivka simple 07-Mar-2025 09:41:12 * [new branch] spike/JAL-4517_customNodenamesInNewick -> origin/spike/JAL-4517_customNodenamesInNewick simple 07-Mar-2025 09:41:12 Already on 'feature/JAL-4386_JAL-4435_reformat_node_labels' simple 07-Mar-2025 09:41:12 Your branch is behind 'origin/feature/JAL-4386_JAL-4435_reformat_node_labels' by 3 commits, and can be fast-forwarded. simple 07-Mar-2025 09:41:12 (use "git pull" to update your local branch) simple 07-Mar-2025 09:41:12 HEAD is now at fbda458 Merge branch 'spike/JAL-4517_customNodenamesInNewick' into 'feature/JAL-4386_JAL-4435_reformat_node_labels' simple 07-Mar-2025 09:41:12 Updated source code to revision: fbda4585b2681eea8794f267dc30b6e98bfad030 simple 07-Mar-2025 09:41:12 Finished task 'Checkout Default Repository' with result: Success simple 07-Mar-2025 09:41:12 Running pre-build action: VCS Version Collector simple 07-Mar-2025 09:41:12 Running pre-build action: Artifactory Release Staging simple 07-Mar-2025 09:41:12 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 07-Mar-2025 09:41:12 Bamboo Artifactory Plugin version: 2.6.2 command 07-Mar-2025 09:41:12 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #8 (JB-GDB661-JOB1-8)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_revision_number=fbda4585b2681eea8794f267dc30b6e98bfad030\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB661-JOB1-8\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB661-JOB1\nbamboo_repository_46498272_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_46498272_name=Jalview Gitlab\nbamboo_shortPlanName=feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=8\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_46498272_revision_number=fbda4585b2681eea8794f267dc30b6e98bfad030\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB661-JOB1-8\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_shortPlanKey=GDB661\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=fbda4585b2681eea8794f267dc30b6e98bfad030\nbamboo_buildTimeStamp=2025-03-07T09:41:09.979Z\nbamboo_repository_previous_revision_number=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_planRepository_previousRevision=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_repository_46498272_previous_revision_number=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDB661-JOB1-8\nbamboo_repository_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=fbda4585b2681eea8794f267dc30b6e98bfad030\nSHLVL=1\nbamboo_repository_46498272_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498272_git_username=\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=feature/JAL-4386_JAL-4435_reformat_node_labels\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=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_planRepository_branchDisplayName=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498272_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302129\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-GDB661-JOB1\nbamboo_planKey=JB-GDB661\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 07-Mar-2025 09:41:12 444 build 07-Mar-2025 09:41:13 Starting a Gradle Daemon (subsequent builds will be faster) build 07-Mar-2025 09:41:24 build 07-Mar-2025 09:41:24 > Configure project : build 07-Mar-2025 09:41:24 Using properties from file './utils/channels/default/channel_gradle.properties' build 07-Mar-2025 09:41:24 JALVIEW_VERSION is set to '2.11.4.0' build 07-Mar-2025 09:41:24 HEADLESS BUILD build 07-Mar-2025 09:41:24 J2S ENABLED build 07-Mar-2025 09:41:25 Using a LOCAL profile. build 07-Mar-2025 09:41:27 eclipseDir exists build 07-Mar-2025 09:41:28 build 07-Mar-2025 09:41:28 > Task :clean build 07-Mar-2025 09:41:28 > Task :cleanClover build 07-Mar-2025 09:41:28 > Task :cleanTest UP-TO-DATE build 07-Mar-2025 09:41:30 build 07-Mar-2025 09:41:30 > Task :cloverInstrJava build 07-Mar-2025 09:41:30 Clover: About to instrument 1102 files build 07-Mar-2025 09:41:31 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 07-Mar-2025 09:41:31 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/clover/clover.db'. build 07-Mar-2025 09:41:31 Processing files at 1.9 source level. error 07-Mar-2025 09:41:36 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 07-Mar-2025 09:41:36 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 07-Mar-2025 09:41:36 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 07-Mar-2025 09:41:36 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 07-Mar-2025 09:41:36 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 07-Mar-2025 09:41:36 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 07-Mar-2025 09:41:36 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 07-Mar-2025 09:41:44 Clover all over. Instrumented 1102 files (111 packages). build 07-Mar-2025 09:41:46 build 07-Mar-2025 09:41:46 > Task :cloverInstrTests build 07-Mar-2025 09:41:46 Clover: About to instrument test files build 07-Mar-2025 09:41:46 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 07-Mar-2025 09:41:46 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/clover/clover.db'. build 07-Mar-2025 09:41:46 Processing files at 1.9 source level. build 07-Mar-2025 09:41:51 Clover all over. Instrumented 290 files (52 packages). build 07-Mar-2025 09:41:51 1591 test methods detected. build 07-Mar-2025 09:41:51 build 07-Mar-2025 09:41:51 > Task :cloverInstr build 07-Mar-2025 09:41:53 build 07-Mar-2025 09:41:53 > Task :compileCloverJava build 07-Mar-2025 09:41:53 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 07-Mar-2025 09:41:53 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:41:53 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:41:53 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:41:53 Setting target compatibility to 11 error 07-Mar-2025 09:42:15 Note: Some input files use or override a deprecated API. error 07-Mar-2025 09:42:15 Note: Recompile with -Xlint:deprecation for details. error 07-Mar-2025 09:42:15 Note: Some input files use unchecked or unsafe operations. error 07-Mar-2025 09:42:15 Note: Recompile with -Xlint:unchecked for details. build 07-Mar-2025 09:42:24 build 07-Mar-2025 09:42:24 > Task :processCloverResources NO-SOURCE build 07-Mar-2025 09:42:24 > Task :cloverClasses build 07-Mar-2025 09:42:25 > Task :copyHelp build 07-Mar-2025 09:42:27 > Task :buildIndices build 07-Mar-2025 09:42:27 > Task :copyResources build 07-Mar-2025 09:42:27 > Task :copyChannelResources build 07-Mar-2025 09:42:27 build 07-Mar-2025 09:42:27 > Task :createBuildProperties build 07-Mar-2025 09:42:27 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 07-Mar-2025 09:42:27 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:42:27 build 07-Mar-2025 09:42:27 > Task :buildResources build 07-Mar-2025 09:42:27 > Task :copyDocs build 07-Mar-2025 09:42:28 build 07-Mar-2025 09:42:28 > Task :convertMdFiles build 07-Mar-2025 09:42:28 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 07-Mar-2025 09:42:28 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/resources/doc_build/doc/releaseprocess.html build 07-Mar-2025 09:42:28 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 07-Mar-2025 09:42:28 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/resources/doc_build/doc/building.html build 07-Mar-2025 09:42:28 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/resources/doc_build/doc/jalview-projects.html build 07-Mar-2025 09:42:29 build 07-Mar-2025 09:42:29 > Task :releasesTemplates build 07-Mar-2025 09:42:29 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 07-Mar-2025 09:42:29 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:42:29 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:42:29 Stripping rc/test/etc for TEST build 07-Mar-2025 09:42:29 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 07-Mar-2025 09:42:29 build 07-Mar-2025 09:42:29 > Task :prepare build 07-Mar-2025 09:42:31 build 07-Mar-2025 09:42:31 > Task :compileJava build 07-Mar-2025 09:42:31 Setting target compatibility to 11 error 07-Mar-2025 09:42:37 Note: Some input files use or override a deprecated API. error 07-Mar-2025 09:42:37 Note: Recompile with -Xlint:deprecation for details. error 07-Mar-2025 09:42:37 Note: Some input files use unchecked or unsafe operations. error 07-Mar-2025 09:42:37 Note: Recompile with -Xlint:unchecked for details. build 07-Mar-2025 09:42:41 build 07-Mar-2025 09:42:41 > Task :compileTestJava build 07-Mar-2025 09:42:41 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 07-Mar-2025 09:42:41 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:42:41 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:42:41 Setting target compatibility to 11 error 07-Mar-2025 09:42:46 Note: Some input files use or override a deprecated API. error 07-Mar-2025 09:42:46 Note: Recompile with -Xlint:deprecation for details. error 07-Mar-2025 09:42:46 Note: Some input files use unchecked or unsafe operations. error 07-Mar-2025 09:42:46 Note: Recompile with -Xlint:unchecked for details. build 07-Mar-2025 09:42:47 build 07-Mar-2025 09:42:47 > Task :processTestResources build 07-Mar-2025 09:42:47 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 07-Mar-2025 09:42:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:42:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:42:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:42:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:42:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:42:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:42:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:42:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-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 07-Mar-2025 09:42:47 build 07-Mar-2025 09:42:47 > Task :testClasses build 07-Mar-2025 09:42:49 build 07-Mar-2025 09:42:49 > Task :testTask0 build 07-Mar-2025 09:42:49 Running tests WITH clover error 07-Mar-2025 09:42:52 WARNING: An illegal reflective access operation has occurred error 07-Mar-2025 09:42:52 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 07-Mar-2025 09:42:52 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 07-Mar-2025 09:42:52 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 07-Mar-2025 09:42:52 WARNING: All illegal access operations will be denied in a future release build 07-Mar-2025 09:46:53 build 07-Mar-2025 09:46:53 > Task :testTask1 build 07-Mar-2025 09:46:53 Running tests WITH clover error 07-Mar-2025 09:46:55 WARNING: An illegal reflective access operation has occurred error 07-Mar-2025 09:46:55 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 07-Mar-2025 09:46:55 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 07-Mar-2025 09:46:55 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 07-Mar-2025 09:46:55 WARNING: All illegal access operations will be denied in a future release build 07-Mar-2025 09:48:29 build 07-Mar-2025 09:48:29 > Task :testTask2 build 07-Mar-2025 09:48:29 Running tests WITH clover build 07-Mar-2025 09:48:33 build 07-Mar-2025 09:48:33 > Task :testTask3 build 07-Mar-2025 09:48:33 Running tests WITH clover error 07-Mar-2025 09:48:35 WARNING: An illegal reflective access operation has occurred error 07-Mar-2025 09:48:35 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 07-Mar-2025 09:48:35 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 07-Mar-2025 09:48:35 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 07-Mar-2025 09:48:35 WARNING: All illegal access operations will be denied in a future release build 07-Mar-2025 09:49:18 build 07-Mar-2025 09:49:18 > Task :test NO-SOURCE build 07-Mar-2025 09:49:18 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 07-Mar-2025 09:49:18 │jalview:testTask0 results: [32mSUCCESS[0m (1693 tests, [32m1693[0m successes, 0 failures, 0 skipped) in 4 minutes, 3.067 seconds │ build 07-Mar-2025 09:49:18 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/reports/tests/testTask0/index.html│ build 07-Mar-2025 09:49:18 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 07-Mar-2025 09:49:18 │jalview:testTask1 results: [32mSUCCESS[0m (49 tests, [32m49[0m successes, 0 failures, 0 skipped) in 1 minutes, 36.576 seconds │ build 07-Mar-2025 09:49:18 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/reports/tests/testTask1/index.html│ build 07-Mar-2025 09:49:18 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 07-Mar-2025 09:49:18 │jalview:testTask2 results: [32mSUCCESS[0m (1 tests, [32m1[0m successes, 0 failures, 0 skipped) in 3.603 seconds │ build 07-Mar-2025 09:49:18 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/reports/tests/testTask2/index.html│ build 07-Mar-2025 09:49:18 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 07-Mar-2025 09:49:18 │jalview:testTask3 results: [32mSUCCESS[0m (25 tests, [32m25[0m successes, 0 failures, 0 skipped) in 46.586 seconds │ build 07-Mar-2025 09:49:18 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/reports/tests/testTask3/index.html│ build 07-Mar-2025 09:49:18 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 07-Mar-2025 09:49:18 │OVERALL: results: [32mSUCCESS[0m (1768 tests, [32m1768[0m successes, 0 failures, 0 skipped) in 5 minutes, 89.832 seconds │ build 07-Mar-2025 09:49:18 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 07-Mar-2025 09:49:18 build 07-Mar-2025 09:49:18 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 07-Mar-2025 09:49:18 build 07-Mar-2025 09:49:18 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 07-Mar-2025 09:49:18 build 07-Mar-2025 09:49:18 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 07-Mar-2025 09:49:18 build 07-Mar-2025 09:49:18 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 07-Mar-2025 09:49:18 Please consult deprecation warnings for more details. build 07-Mar-2025 09:49:18 build 07-Mar-2025 09:49:18 BUILD SUCCESSFUL in 8m 5s build 07-Mar-2025 09:49:18 21 actionable tasks: 20 executed, 1 up-to-date simple 07-Mar-2025 09:49:18 Finished task 'Run tests with openclover under gradle' with result: Success simple 07-Mar-2025 09:49:18 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 07-Mar-2025 09:49:18 Bamboo Artifactory Plugin version: 2.6.2 command 07-Mar-2025 09:49:18 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #8 (JB-GDB661-JOB1-8)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1\n ... using extra environment variables: 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Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=8\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_46498272_revision_number=fbda4585b2681eea8794f267dc30b6e98bfad030\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB661-JOB1-8\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_shortPlanKey=GDB661\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=fbda4585b2681eea8794f267dc30b6e98bfad030\nbamboo_buildTimeStamp=2025-03-07T09:41:09.979Z\nbamboo_repository_previous_revision_number=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_planRepository_previousRevision=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_repository_46498272_previous_revision_number=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDB661-JOB1-8\nbamboo_repository_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=fbda4585b2681eea8794f267dc30b6e98bfad030\nSHLVL=1\nbamboo_repository_46498272_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498272_git_username=\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=feature/JAL-4386_JAL-4435_reformat_node_labels\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=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_planRepository_branchDisplayName=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498272_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302129\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-GDB661-JOB1\nbamboo_planKey=JB-GDB661\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 07-Mar-2025 09:49:19 444 build 07-Mar-2025 09:49:27 build 07-Mar-2025 09:49:27 > Configure project : build 07-Mar-2025 09:49:27 Using properties from file './utils/channels/default/channel_gradle.properties' build 07-Mar-2025 09:49:27 JALVIEW_VERSION is set to '2.11.4.0' build 07-Mar-2025 09:49:27 HEADLESS BUILD build 07-Mar-2025 09:49:27 J2S ENABLED build 07-Mar-2025 09:49:28 Using a LOCAL profile. build 07-Mar-2025 09:49:29 eclipseDir exists build 07-Mar-2025 09:49:31 build 07-Mar-2025 09:49:31 > Task :cloverHtmlReport build 07-Mar-2025 09:49:31 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 07-Mar-2025 09:49:33 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/reports/clover' build 07-Mar-2025 09:50:11 Done. Processed 115 packages in 38281ms (332ms per package). build 07-Mar-2025 09:50:17 build 07-Mar-2025 09:50:17 > Task :cloverXmlReport build 07-Mar-2025 09:50:17 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 07-Mar-2025 09:50:20 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/reports/clover/clover.xml' build 07-Mar-2025 09:50:20 build 07-Mar-2025 09:50:20 > Task :cloverReport build 07-Mar-2025 09:50:20 build 07-Mar-2025 09:50:20 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 07-Mar-2025 09:50:20 build 07-Mar-2025 09:50:20 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 07-Mar-2025 09:50:20 build 07-Mar-2025 09:50:20 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 07-Mar-2025 09:50:20 build 07-Mar-2025 09:50:20 BUILD SUCCESSFUL in 1m 1s build 07-Mar-2025 09:50:20 2 actionable tasks: 2 executed simple 07-Mar-2025 09:50:20 Finished task 'Clover Report' with result: Success simple 07-Mar-2025 09:50:20 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 07-Mar-2025 09:50:20 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1... simple 07-Mar-2025 09:50:20 Finished task 'TestNG Parser' with result: Success simple 07-Mar-2025 09:50:20 Running post build plugin 'NCover Results Collector' simple 07-Mar-2025 09:50:20 Running post build plugin 'Artifact Copier' simple 07-Mar-2025 09:50:20 Publishing an artifact: Clover Report (System) simple 07-Mar-2025 09:50:22 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.149 s simple 07-Mar-2025 09:50:22 Publishing an artifact: TestNG report error 07-Mar-2025 09:50:22 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/reports/tests/test does not exist. simple 07-Mar-2025 09:50:22 The artifact hasn't been successfully published after 1.513 ms simple 07-Mar-2025 09:50:22 Running post build plugin 'Artifactory Release Management Staging' simple 07-Mar-2025 09:50:22 Running post build plugin 'Artifactory Build Info Copier' simple 07-Mar-2025 09:50:22 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 07-Mar-2025 09:50:22 Running post build plugin 'npm Cache Cleanup' simple 07-Mar-2025 09:50:22 Running post build plugin 'Clover Results Collector' simple 07-Mar-2025 09:50:22 Running post build plugin 'Docker Container Cleanup' simple 07-Mar-2025 09:50:22 Finalising the build... simple 07-Mar-2025 09:50:22 Stopping timer. simple 07-Mar-2025 09:50:22 Build JB-GDB661-JOB1-8 completed. simple 07-Mar-2025 09:50:22 Running on server: post build plugin 'NCover Results Collector' simple 07-Mar-2025 09:50:22 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 07-Mar-2025 09:50:22 Running on server: post build plugin 'Clover Delta Calculator' simple 07-Mar-2025 09:50:22 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 07-Mar-2025 09:50:22 All post build plugins have finished simple 07-Mar-2025 09:50:22 Generating build results summary... simple 07-Mar-2025 09:50:22 Saving build results to disk... simple 07-Mar-2025 09:50:22 Logging substituted variables... simple 07-Mar-2025 09:50:22 Indexing build results... simple 07-Mar-2025 09:50:22 Finished building JB-GDB661-JOB1-8.