simple 26-Feb-2025 18:26:09 Build Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #7 (JB-GDB661-JOB1-7) started building on agent Default Agent simple 26-Feb-2025 18:26:09 simple 26-Feb-2025 18:26:09 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1 simple 26-Feb-2025 18:26:09 Executing build Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #7 (JB-GDB661-JOB1-7) simple 26-Feb-2025 18:26:09 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 26-Feb-2025 18:26:09 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1 simple 26-Feb-2025 18:26:09 Updating source code to revision: d9b10917dcf53abeb15fd632531e699905025179 simple 26-Feb-2025 18:26:09 Fetching 'refs/heads/feature/JAL-4386_JAL-4435_reformat_node_labels' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 26-Feb-2025 18:26:09 Checking out revision d9b10917dcf53abeb15fd632531e699905025179. simple 26-Feb-2025 18:26:09 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 26-Feb-2025 18:26:09 23ebbc3..d9b1091 feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels simple 26-Feb-2025 18:26:09 Already on 'feature/JAL-4386_JAL-4435_reformat_node_labels' simple 26-Feb-2025 18:26:09 Your branch is behind 'origin/feature/JAL-4386_JAL-4435_reformat_node_labels' by 1 commit, and can be fast-forwarded. simple 26-Feb-2025 18:26:09 (use "git pull" to update your local branch) simple 26-Feb-2025 18:26:09 HEAD is now at d9b1091 JAL-4515 Add Coloured Backgrounds for Grouped Nodes in Similarity Tree simple 26-Feb-2025 18:26:09 Updated source code to revision: d9b10917dcf53abeb15fd632531e699905025179 simple 26-Feb-2025 18:26:09 Finished task 'Checkout Default Repository' with result: Success simple 26-Feb-2025 18:26:09 Running pre-build action: VCS Version Collector simple 26-Feb-2025 18:26:09 Running pre-build action: Artifactory Release Staging simple 26-Feb-2025 18:26:09 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 26-Feb-2025 18:26:09 Bamboo Artifactory Plugin version: 2.6.2 command 26-Feb-2025 18:26:09 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #7 (JB-GDB661-JOB1-7)'\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=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB661-JOB1-7\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=7\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_46498272_revision_number=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB661-JOB1-7\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=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_buildTimeStamp=2025-02-26T18:26:09.379Z\nbamboo_repository_previous_revision_number=23ebbc38fce7bf2abc5b1129e0f3592e3b792e2e\nbamboo_planRepository_previousRevision=23ebbc38fce7bf2abc5b1129e0f3592e3b792e2e\nbamboo_repository_46498272_previous_revision_number=23ebbc38fce7bf2abc5b1129e0f3592e3b792e2e\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDB661-JOB1-7\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=d9b10917dcf53abeb15fd632531e699905025179\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=23ebbc38fce7bf2abc5b1129e0f3592e3b792e2e\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 26-Feb-2025 18:26:09 444 build 26-Feb-2025 18:26:10 Starting a Gradle Daemon (subsequent builds will be faster) build 26-Feb-2025 18:26:20 build 26-Feb-2025 18:26:20 > Configure project : build 26-Feb-2025 18:26:20 Using properties from file './utils/channels/default/channel_gradle.properties' build 26-Feb-2025 18:26:20 JALVIEW_VERSION is set to '2.11.4.0' build 26-Feb-2025 18:26:20 HEADLESS BUILD build 26-Feb-2025 18:26:20 J2S ENABLED build 26-Feb-2025 18:26:20 Using a LOCAL profile. build 26-Feb-2025 18:26:22 eclipseDir exists build 26-Feb-2025 18:26:23 build 26-Feb-2025 18:26:23 > Task :clean build 26-Feb-2025 18:26:23 > Task :cleanClover build 26-Feb-2025 18:26:23 > Task :cleanTest UP-TO-DATE build 26-Feb-2025 18:26:25 build 26-Feb-2025 18:26:25 > Task :cloverInstrJava build 26-Feb-2025 18:26:25 Clover: About to instrument 1102 files build 26-Feb-2025 18:26:25 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 26-Feb-2025 18:26:25 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/clover/clover.db'. build 26-Feb-2025 18:26:25 Processing files at 1.9 source level. error 26-Feb-2025 18:26:28 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 26-Feb-2025 18:26:28 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 26-Feb-2025 18:26:28 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 26-Feb-2025 18:26:28 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 26-Feb-2025 18:26:28 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 26-Feb-2025 18:26:28 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 26-Feb-2025 18:26:28 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 26-Feb-2025 18:26:35 Clover all over. Instrumented 1102 files (111 packages). build 26-Feb-2025 18:26:38 build 26-Feb-2025 18:26:38 > Task :cloverInstrTests build 26-Feb-2025 18:26:38 Clover: About to instrument test files build 26-Feb-2025 18:26:38 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 26-Feb-2025 18:26:38 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/clover/clover.db'. build 26-Feb-2025 18:26:38 Processing files at 1.9 source level. build 26-Feb-2025 18:26:42 Clover all over. Instrumented 290 files (52 packages). build 26-Feb-2025 18:26:42 1591 test methods detected. build 26-Feb-2025 18:26:42 build 26-Feb-2025 18:26:42 > Task :cloverInstr build 26-Feb-2025 18:26:44 build 26-Feb-2025 18:26:44 > Task :compileCloverJava build 26-Feb-2025 18:26:44 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 26-Feb-2025 18:26:44 - 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 26-Feb-2025 18:26:44 - 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 26-Feb-2025 18:26:44 - 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 26-Feb-2025 18:26:44 Setting target compatibility to 11 error 26-Feb-2025 18:27:05 Note: Some input files use or override a deprecated API. error 26-Feb-2025 18:27:05 Note: Recompile with -Xlint:deprecation for details. error 26-Feb-2025 18:27:05 Note: Some input files use unchecked or unsafe operations. error 26-Feb-2025 18:27:05 Note: Recompile with -Xlint:unchecked for details. build 26-Feb-2025 18:27:10 build 26-Feb-2025 18:27:10 > Task :processCloverResources NO-SOURCE build 26-Feb-2025 18:27:10 > Task :cloverClasses build 26-Feb-2025 18:27:11 > Task :copyHelp build 26-Feb-2025 18:27:12 > Task :buildIndices build 26-Feb-2025 18:27:13 > Task :copyResources build 26-Feb-2025 18:27:13 > Task :copyChannelResources build 26-Feb-2025 18:27:13 build 26-Feb-2025 18:27:13 > Task :createBuildProperties build 26-Feb-2025 18:27:13 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 26-Feb-2025 18:27:13 - 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 26-Feb-2025 18:27:13 build 26-Feb-2025 18:27:13 > Task :buildResources build 26-Feb-2025 18:27:13 > Task :copyDocs build 26-Feb-2025 18:27:14 build 26-Feb-2025 18:27:14 > Task :convertMdFiles build 26-Feb-2025 18:27:14 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 26-Feb-2025 18:27:14 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/resources/doc_build/doc/releaseprocess.html build 26-Feb-2025 18:27:14 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 26-Feb-2025 18:27:14 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/resources/doc_build/doc/building.html build 26-Feb-2025 18:27:14 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/resources/doc_build/doc/jalview-projects.html build 26-Feb-2025 18:27:14 build 26-Feb-2025 18:27:14 > Task :releasesTemplates build 26-Feb-2025 18:27:14 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 26-Feb-2025 18:27:14 - 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 26-Feb-2025 18:27:14 - 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 26-Feb-2025 18:27:14 Stripping rc/test/etc for TEST build 26-Feb-2025 18:27:14 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 26-Feb-2025 18:27:14 build 26-Feb-2025 18:27:14 > Task :prepare build 26-Feb-2025 18:27:16 build 26-Feb-2025 18:27:16 > Task :compileJava build 26-Feb-2025 18:27:16 Setting target compatibility to 11 error 26-Feb-2025 18:27:22 Note: Some input files use or override a deprecated API. error 26-Feb-2025 18:27:22 Note: Recompile with -Xlint:deprecation for details. error 26-Feb-2025 18:27:22 Note: Some input files use unchecked or unsafe operations. error 26-Feb-2025 18:27:22 Note: Recompile with -Xlint:unchecked for details. build 26-Feb-2025 18:27:26 build 26-Feb-2025 18:27:26 > Task :compileTestJava build 26-Feb-2025 18:27:26 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 26-Feb-2025 18:27:26 - 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 26-Feb-2025 18:27:26 - 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 26-Feb-2025 18:27:26 Setting target compatibility to 11 error 26-Feb-2025 18:27:30 Note: Some input files use or override a deprecated API. error 26-Feb-2025 18:27:30 Note: Recompile with -Xlint:deprecation for details. error 26-Feb-2025 18:27:30 Note: Some input files use unchecked or unsafe operations. error 26-Feb-2025 18:27:30 Note: Recompile with -Xlint:unchecked for details. build 26-Feb-2025 18:27:31 build 26-Feb-2025 18:27:31 > Task :processTestResources build 26-Feb-2025 18:27:31 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 26-Feb-2025 18:27:31 - 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 26-Feb-2025 18:27:31 - 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 26-Feb-2025 18:27:31 - 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 26-Feb-2025 18:27:31 - 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 26-Feb-2025 18:27:31 - 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 26-Feb-2025 18:27:31 - 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 26-Feb-2025 18:27:31 - 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 26-Feb-2025 18:27:31 - 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 26-Feb-2025 18:27:31 build 26-Feb-2025 18:27:31 > Task :testClasses build 26-Feb-2025 18:27:33 build 26-Feb-2025 18:27:33 > Task :testTask0 build 26-Feb-2025 18:27:33 Running tests WITH clover error 26-Feb-2025 18:27:35 WARNING: An illegal reflective access operation has occurred error 26-Feb-2025 18:27:35 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 26-Feb-2025 18:27:35 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 26-Feb-2025 18:27:35 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 26-Feb-2025 18:27:35 WARNING: All illegal access operations will be denied in a future release build 26-Feb-2025 18:31:27 build 26-Feb-2025 18:31:27 > Task :testTask1 build 26-Feb-2025 18:31:27 Running tests WITH clover error 26-Feb-2025 18:31:28 WARNING: An illegal reflective access operation has occurred error 26-Feb-2025 18:31:28 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 26-Feb-2025 18:31:28 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 26-Feb-2025 18:31:28 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 26-Feb-2025 18:31:28 WARNING: All illegal access operations will be denied in a future release build 26-Feb-2025 18:33:01 build 26-Feb-2025 18:33:01 > Task :testTask2 build 26-Feb-2025 18:33:01 Running tests WITH clover build 26-Feb-2025 18:33:05 build 26-Feb-2025 18:33:05 > Task :testTask3 build 26-Feb-2025 18:33:05 Running tests WITH clover error 26-Feb-2025 18:33:06 WARNING: An illegal reflective access operation has occurred error 26-Feb-2025 18:33:06 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 26-Feb-2025 18:33:06 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 26-Feb-2025 18:33:06 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 26-Feb-2025 18:33:06 WARNING: All illegal access operations will be denied in a future release build 26-Feb-2025 18:33:52 build 26-Feb-2025 18:33:52 > Task :test NO-SOURCE build 26-Feb-2025 18:33:52 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 26-Feb-2025 18:33:52 │jalview:testTask0 results: [32mSUCCESS[0m (1693 tests, [32m1693[0m successes, 0 failures, 0 skipped) in 3 minutes, 52.600 seconds │ build 26-Feb-2025 18:33:52 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/reports/tests/testTask0/index.html│ build 26-Feb-2025 18:33:52 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 26-Feb-2025 18:33:52 │jalview:testTask1 results: [32mSUCCESS[0m (49 tests, [32m49[0m successes, 0 failures, 0 skipped) in 1 minutes, 34.473 seconds │ build 26-Feb-2025 18:33:52 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/reports/tests/testTask1/index.html│ build 26-Feb-2025 18:33:52 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 26-Feb-2025 18:33:52 │jalview:testTask2 results: [32mSUCCESS[0m (1 tests, [32m1[0m successes, 0 failures, 0 skipped) in 3.480 seconds │ build 26-Feb-2025 18:33:52 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/reports/tests/testTask2/index.html│ build 26-Feb-2025 18:33:52 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 26-Feb-2025 18:33:52 │jalview:testTask3 results: [32mSUCCESS[0m (25 tests, [32m25[0m successes, 0 failures, 0 skipped) in 48.862 seconds │ build 26-Feb-2025 18:33:52 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/reports/tests/testTask3/index.html│ build 26-Feb-2025 18:33:52 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 26-Feb-2025 18:33:52 │OVERALL: results: [32mSUCCESS[0m (1768 tests, [32m1768[0m successes, 0 failures, 0 skipped) in 4 minutes, 139.415 seconds │ build 26-Feb-2025 18:33:52 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 26-Feb-2025 18:33:52 build 26-Feb-2025 18:33:52 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 26-Feb-2025 18:33:52 build 26-Feb-2025 18:33:52 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 26-Feb-2025 18:33:52 build 26-Feb-2025 18:33:52 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 26-Feb-2025 18:33:52 build 26-Feb-2025 18:33:52 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 26-Feb-2025 18:33:52 Please consult deprecation warnings for more details. build 26-Feb-2025 18:33:52 build 26-Feb-2025 18:33:52 BUILD SUCCESSFUL in 7m 42s build 26-Feb-2025 18:33:52 21 actionable tasks: 20 executed, 1 up-to-date simple 26-Feb-2025 18:33:52 Finished task 'Run tests with openclover under gradle' with result: Success simple 26-Feb-2025 18:33:52 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 26-Feb-2025 18:33:52 Bamboo Artifactory Plugin version: 2.6.2 command 26-Feb-2025 18:33:52 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #7 (JB-GDB661-JOB1-7)'\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: \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=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB661-JOB1-7\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=7\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_46498272_revision_number=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB661-JOB1-7\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=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_buildTimeStamp=2025-02-26T18:26:09.379Z\nbamboo_repository_previous_revision_number=23ebbc38fce7bf2abc5b1129e0f3592e3b792e2e\nbamboo_planRepository_previousRevision=23ebbc38fce7bf2abc5b1129e0f3592e3b792e2e\nbamboo_repository_46498272_previous_revision_number=23ebbc38fce7bf2abc5b1129e0f3592e3b792e2e\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDB661-JOB1-7\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=d9b10917dcf53abeb15fd632531e699905025179\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=23ebbc38fce7bf2abc5b1129e0f3592e3b792e2e\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 26-Feb-2025 18:33:52 444 build 26-Feb-2025 18:33:59 build 26-Feb-2025 18:33:59 > Configure project : build 26-Feb-2025 18:33:59 Using properties from file './utils/channels/default/channel_gradle.properties' build 26-Feb-2025 18:33:59 JALVIEW_VERSION is set to '2.11.4.0' build 26-Feb-2025 18:33:59 HEADLESS BUILD build 26-Feb-2025 18:33:59 J2S ENABLED build 26-Feb-2025 18:33:59 Using a LOCAL profile. build 26-Feb-2025 18:34:01 eclipseDir exists build 26-Feb-2025 18:34:03 build 26-Feb-2025 18:34:03 > Task :cloverHtmlReport build 26-Feb-2025 18:34:03 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 26-Feb-2025 18:34:04 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/reports/clover' build 26-Feb-2025 18:34:42 Done. Processed 115 packages in 38055ms (330ms per package). build 26-Feb-2025 18:34:47 build 26-Feb-2025 18:34:47 > Task :cloverXmlReport build 26-Feb-2025 18:34:47 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 26-Feb-2025 18:34:48 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1/build/reports/clover/clover.xml' build 26-Feb-2025 18:34:48 build 26-Feb-2025 18:34:48 > Task :cloverReport build 26-Feb-2025 18:34:48 build 26-Feb-2025 18:34:48 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 26-Feb-2025 18:34:48 build 26-Feb-2025 18:34:48 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 26-Feb-2025 18:34:48 build 26-Feb-2025 18:34:48 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 26-Feb-2025 18:34:48 build 26-Feb-2025 18:34:48 BUILD SUCCESSFUL in 56s build 26-Feb-2025 18:34:48 2 actionable tasks: 2 executed simple 26-Feb-2025 18:34:48 Finished task 'Clover Report' with result: Success simple 26-Feb-2025 18:34:48 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 26-Feb-2025 18:34:48 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB661-JOB1... simple 26-Feb-2025 18:34:48 Finished task 'TestNG Parser' with result: Success simple 26-Feb-2025 18:34:48 Running post build plugin 'NCover Results Collector' simple 26-Feb-2025 18:34:48 Running post build plugin 'Artifact Copier' simple 26-Feb-2025 18:34:48 Publishing an artifact: Clover Report (System) simple 26-Feb-2025 18:34:50 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.387 s simple 26-Feb-2025 18:34:50 Publishing an artifact: TestNG report error 26-Feb-2025 18:34:50 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 26-Feb-2025 18:34:50 The artifact hasn't been successfully published after 1.318 ms simple 26-Feb-2025 18:34:50 Running post build plugin 'Artifactory Release Management Staging' simple 26-Feb-2025 18:34:50 Running post build plugin 'Artifactory Build Info Copier' simple 26-Feb-2025 18:34:50 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 26-Feb-2025 18:34:50 Running post build plugin 'npm Cache Cleanup' simple 26-Feb-2025 18:34:50 Running post build plugin 'Clover Results Collector' simple 26-Feb-2025 18:34:50 Running post build plugin 'Docker Container Cleanup' simple 26-Feb-2025 18:34:50 Finalising the build... simple 26-Feb-2025 18:34:50 Stopping timer. simple 26-Feb-2025 18:34:50 Build JB-GDB661-JOB1-7 completed. simple 26-Feb-2025 18:34:50 Running on server: post build plugin 'NCover Results Collector' simple 26-Feb-2025 18:34:50 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 26-Feb-2025 18:34:50 Running on server: post build plugin 'Clover Delta Calculator' simple 26-Feb-2025 18:34:50 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 26-Feb-2025 18:34:50 All post build plugins have finished simple 26-Feb-2025 18:34:50 Generating build results summary... simple 26-Feb-2025 18:34:50 Saving build results to disk... simple 26-Feb-2025 18:34:50 Logging substituted variables... simple 26-Feb-2025 18:34:50 Indexing build results... simple 26-Feb-2025 18:34:50 Finished building JB-GDB661-JOB1-7.