simple 06-Mar-2025 16:31:03 Build Jalview Builds - Gradle Develop Build - spike-JAL-4517_customNodenamesInNewick - Clover and Tests #1 (JB-GDB666-JOB1-1) started building on agent Default Agent simple 06-Mar-2025 16:31:03 simple 06-Mar-2025 16:31:03 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1 simple 06-Mar-2025 16:31:03 Executing build Jalview Builds - Gradle Develop Build - spike-JAL-4517_customNodenamesInNewick - Clover and Tests #1 (JB-GDB666-JOB1-1) simple 06-Mar-2025 16:31:03 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 06-Mar-2025 16:31:03 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1 simple 06-Mar-2025 16:31:03 Updating source code to revision: c3f846fb911da7304ae2f7d049618db92adb5a80 simple 06-Mar-2025 16:31:03 Fetching 'refs/heads/spike/JAL-4517_customNodenamesInNewick' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 06-Mar-2025 16:31:03 Checking out revision c3f846fb911da7304ae2f7d049618db92adb5a80. simple 06-Mar-2025 16:31:03 Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/.git'. simple 06-Mar-2025 16:31:04 Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1'... simple 06-Mar-2025 16:31:04 done. simple 06-Mar-2025 16:31:14 Branch spike/JAL-4517_customNodenamesInNewick set up to track remote branch spike/JAL-4517_customNodenamesInNewick from origin. simple 06-Mar-2025 16:31:14 Switched to a new branch 'spike/JAL-4517_customNodenamesInNewick' simple 06-Mar-2025 16:31:14 Updated source code to revision: c3f846fb911da7304ae2f7d049618db92adb5a80 simple 06-Mar-2025 16:31:14 Finished task 'Checkout Default Repository' with result: Success simple 06-Mar-2025 16:31:14 Running pre-build action: VCS Version Collector simple 06-Mar-2025 16:31:14 Running pre-build action: Artifactory Release Staging simple 06-Mar-2025 16:31:14 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 06-Mar-2025 16:31:14 Bamboo Artifactory Plugin version: 2.6.2 command 06-Mar-2025 16:31:14 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-JAL-4517_customNodenamesInNewick - Clover and Tests #1 (JB-GDB666-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=spike/JAL-4517_customNodenamesInNewick\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=spike/JAL-4517_customNodenamesInNewick\nbamboo_repository_revision_number=c3f846fb911da7304ae2f7d049618db92adb5a80\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB666-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_repository_46498287_branch_name=spike/JAL-4517_customNodenamesInNewick\nbamboo_buildKey=JB-GDB666-JOB1\nbamboo_shortPlanName=spike-JAL-4517_customNodenamesInNewick\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB666-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - spike-JAL-4517_customNodenamesInNewick\nbamboo_shortPlanKey=GDB666\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498287_git_branch=spike/JAL-4517_customNodenamesInNewick\nbamboo_repository_46498287_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=c3f846fb911da7304ae2f7d049618db92adb5a80\nbamboo_buildTimeStamp=2025-03-06T16:31:03.604Z\nbamboo_repository_git_branch=spike/JAL-4517_customNodenamesInNewick\nbamboo_buildResultKey=JB-GDB666-JOB1-1\nbamboo_repository_branch_name=spike/JAL-4517_customNodenamesInNewick\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-JAL-4517_customNodenamesInNewick - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=c3f846fb911da7304ae2f7d049618db92adb5a80\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=spike/JAL-4517_customNodenamesInNewick\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_repository_46498287_revision_number=c3f846fb911da7304ae2f7d049618db92adb5a80\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=spike/JAL-4517_customNodenamesInNewick\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=spike/JAL-4517_customNodenamesInNewick\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498287_name=Jalview Gitlab\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302159\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-GDB666-JOB1\nbamboo_planKey=JB-GDB666\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498287_git_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=spike/JAL-4517_customNodenamesInNewick\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 06-Mar-2025 16:31:14 444 build 06-Mar-2025 16:31:20 Starting a Gradle Daemon (subsequent builds will be faster) build 06-Mar-2025 16:31:38 build 06-Mar-2025 16:31:38 > Configure project : build 06-Mar-2025 16:31:38 Using properties from file './utils/channels/default/channel_gradle.properties' build 06-Mar-2025 16:31:38 JALVIEW_VERSION is set to '2.11.4.0' build 06-Mar-2025 16:31:38 HEADLESS BUILD build 06-Mar-2025 16:31:38 J2S ENABLED build 06-Mar-2025 16:31:38 Using a LOCAL profile. build 06-Mar-2025 16:31:40 eclipseDir exists build 06-Mar-2025 16:31:40 build 06-Mar-2025 16:31:40 > Task :clean build 06-Mar-2025 16:31:40 > Task :cleanClover build 06-Mar-2025 16:31:40 > Task :cleanTest UP-TO-DATE build 06-Mar-2025 16:31:43 build 06-Mar-2025 16:31:43 > Task :cloverInstrJava build 06-Mar-2025 16:31:43 Clover: About to instrument 1102 files build 06-Mar-2025 16:31:43 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Mar-2025 16:31:43 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/clover/clover.db'. build 06-Mar-2025 16:31:43 Processing files at 1.9 source level. error 06-Mar-2025 16:31:47 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 06-Mar-2025 16:31:47 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 06-Mar-2025 16:31:47 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 06-Mar-2025 16:31:47 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 06-Mar-2025 16:31:47 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 06-Mar-2025 16:31:47 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 06-Mar-2025 16:31:47 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 06-Mar-2025 16:31:54 Clover all over. Instrumented 1102 files (111 packages). build 06-Mar-2025 16:31:56 build 06-Mar-2025 16:31:56 > Task :cloverInstrTests build 06-Mar-2025 16:31:56 Clover: About to instrument test files build 06-Mar-2025 16:31:56 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Mar-2025 16:31:56 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/clover/clover.db'. build 06-Mar-2025 16:31:56 Processing files at 1.9 source level. build 06-Mar-2025 16:31:59 Clover all over. Instrumented 290 files (52 packages). build 06-Mar-2025 16:31:59 1591 test methods detected. build 06-Mar-2025 16:32:00 build 06-Mar-2025 16:32:00 > Task :cloverInstr build 06-Mar-2025 16:32:03 build 06-Mar-2025 16:32:03 > Task :compileCloverJava build 06-Mar-2025 16:32:03 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 06-Mar-2025 16:32:03 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:03 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:03 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:03 Setting target compatibility to 11 error 06-Mar-2025 16:32:26 Note: Some input files use or override a deprecated API. error 06-Mar-2025 16:32:26 Note: Recompile with -Xlint:deprecation for details. error 06-Mar-2025 16:32:26 Note: Some input files use unchecked or unsafe operations. error 06-Mar-2025 16:32:26 Note: Recompile with -Xlint:unchecked for details. build 06-Mar-2025 16:32:33 build 06-Mar-2025 16:32:33 > Task :processCloverResources NO-SOURCE build 06-Mar-2025 16:32:33 > Task :cloverClasses build 06-Mar-2025 16:32:33 > Task :copyHelp build 06-Mar-2025 16:32:34 > Task :buildIndices build 06-Mar-2025 16:32:35 > Task :copyResources build 06-Mar-2025 16:32:35 > Task :copyChannelResources build 06-Mar-2025 16:32:35 build 06-Mar-2025 16:32:35 > Task :createBuildProperties build 06-Mar-2025 16:32:35 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 06-Mar-2025 16:32:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:35 build 06-Mar-2025 16:32:35 > Task :buildResources build 06-Mar-2025 16:32:35 > Task :copyDocs build 06-Mar-2025 16:32:35 build 06-Mar-2025 16:32:35 > Task :convertMdFiles build 06-Mar-2025 16:32:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 06-Mar-2025 16:32:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/resources/doc_build/doc/releaseprocess.html build 06-Mar-2025 16:32:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 06-Mar-2025 16:32:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/resources/doc_build/doc/building.html build 06-Mar-2025 16:32:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/resources/doc_build/doc/jalview-projects.html build 06-Mar-2025 16:32:36 build 06-Mar-2025 16:32:36 > Task :releasesTemplates build 06-Mar-2025 16:32:36 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 06-Mar-2025 16:32:36 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:36 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:36 Stripping rc/test/etc for TEST build 06-Mar-2025 16:32:36 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 06-Mar-2025 16:32:36 build 06-Mar-2025 16:32:36 > Task :prepare build 06-Mar-2025 16:32:38 build 06-Mar-2025 16:32:38 > Task :compileJava build 06-Mar-2025 16:32:38 Setting target compatibility to 11 error 06-Mar-2025 16:32:44 Note: Some input files use or override a deprecated API. error 06-Mar-2025 16:32:44 Note: Recompile with -Xlint:deprecation for details. error 06-Mar-2025 16:32:44 Note: Some input files use unchecked or unsafe operations. error 06-Mar-2025 16:32:44 Note: Recompile with -Xlint:unchecked for details. build 06-Mar-2025 16:32:48 build 06-Mar-2025 16:32:48 > Task :compileTestJava build 06-Mar-2025 16:32:48 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 06-Mar-2025 16:32:48 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:48 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:48 Setting target compatibility to 11 error 06-Mar-2025 16:32:53 Note: Some input files use or override a deprecated API. error 06-Mar-2025 16:32:53 Note: Recompile with -Xlint:deprecation for details. error 06-Mar-2025 16:32:53 Note: Some input files use unchecked or unsafe operations. error 06-Mar-2025 16:32:53 Note: Recompile with -Xlint:unchecked for details. build 06-Mar-2025 16:32:54 build 06-Mar-2025 16:32:54 > Task :processTestResources build 06-Mar-2025 16:32:54 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 06-Mar-2025 16:32:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-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 06-Mar-2025 16:32:54 build 06-Mar-2025 16:32:54 > Task :testClasses build 06-Mar-2025 16:32:56 build 06-Mar-2025 16:32:56 > Task :testTask0 build 06-Mar-2025 16:32:56 Running tests WITH clover error 06-Mar-2025 16:33:00 WARNING: An illegal reflective access operation has occurred error 06-Mar-2025 16:33:00 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 06-Mar-2025 16:33:00 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 06-Mar-2025 16:33:00 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 06-Mar-2025 16:33:00 WARNING: All illegal access operations will be denied in a future release build 06-Mar-2025 16:36:44 build 06-Mar-2025 16:36:44 > Task :testTask1 build 06-Mar-2025 16:36:44 Running tests WITH clover error 06-Mar-2025 16:36:46 WARNING: An illegal reflective access operation has occurred error 06-Mar-2025 16:36:46 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 06-Mar-2025 16:36:46 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 06-Mar-2025 16:36:46 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 06-Mar-2025 16:36:46 WARNING: All illegal access operations will be denied in a future release build 06-Mar-2025 16:38:20 build 06-Mar-2025 16:38:20 > Task :testTask2 build 06-Mar-2025 16:38:20 Running tests WITH clover build 06-Mar-2025 16:38:23 build 06-Mar-2025 16:38:23 > Task :testTask3 build 06-Mar-2025 16:38:23 Running tests WITH clover error 06-Mar-2025 16:38:25 WARNING: An illegal reflective access operation has occurred error 06-Mar-2025 16:38:25 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 06-Mar-2025 16:38:25 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 06-Mar-2025 16:38:25 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 06-Mar-2025 16:38:25 WARNING: All illegal access operations will be denied in a future release build 06-Mar-2025 16:39:10 build 06-Mar-2025 16:39:10 > Task :test NO-SOURCE build 06-Mar-2025 16:39:10 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 06-Mar-2025 16:39:10 │jalview:testTask0 results: [32mSUCCESS[0m (1693 tests, [32m1693[0m successes, 0 failures, 0 skipped) in 3 minutes, 47.446 seconds │ build 06-Mar-2025 16:39:10 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/reports/tests/testTask0/index.html│ build 06-Mar-2025 16:39:10 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Mar-2025 16:39:10 │jalview:testTask1 results: [32mSUCCESS[0m (49 tests, [32m49[0m successes, 0 failures, 0 skipped) in 1 minutes, 35.809 seconds │ build 06-Mar-2025 16:39:10 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/reports/tests/testTask1/index.html│ build 06-Mar-2025 16:39:10 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Mar-2025 16:39:10 │jalview:testTask2 results: [32mSUCCESS[0m (1 tests, [32m1[0m successes, 0 failures, 0 skipped) in 3.163 seconds │ build 06-Mar-2025 16:39:10 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/reports/tests/testTask2/index.html│ build 06-Mar-2025 16:39:10 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Mar-2025 16:39:10 │jalview:testTask3 results: [32mSUCCESS[0m (25 tests, [32m25[0m successes, 0 failures, 0 skipped) in 48.753 seconds │ build 06-Mar-2025 16:39:10 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/reports/tests/testTask3/index.html│ build 06-Mar-2025 16:39:10 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Mar-2025 16:39:10 │OVERALL: results: [32mSUCCESS[0m (1768 tests, [32m1768[0m successes, 0 failures, 0 skipped) in 4 minutes, 135.171 seconds │ build 06-Mar-2025 16:39:10 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 06-Mar-2025 16:39:10 build 06-Mar-2025 16:39:10 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 06-Mar-2025 16:39:10 build 06-Mar-2025 16:39:10 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 06-Mar-2025 16:39:10 build 06-Mar-2025 16:39:10 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 06-Mar-2025 16:39:10 build 06-Mar-2025 16:39:10 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 06-Mar-2025 16:39:10 Please consult deprecation warnings for more details. build 06-Mar-2025 16:39:10 build 06-Mar-2025 16:39:10 BUILD SUCCESSFUL in 7m 55s build 06-Mar-2025 16:39:10 21 actionable tasks: 20 executed, 1 up-to-date simple 06-Mar-2025 16:39:11 Finished task 'Run tests with openclover under gradle' with result: Success simple 06-Mar-2025 16:39:11 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 06-Mar-2025 16:39:11 Bamboo Artifactory Plugin version: 2.6.2 command 06-Mar-2025 16:39:11 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-JAL-4517_customNodenamesInNewick - Clover and Tests #1 (JB-GDB666-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=spike/JAL-4517_customNodenamesInNewick\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=spike/JAL-4517_customNodenamesInNewick\nbamboo_repository_revision_number=c3f846fb911da7304ae2f7d049618db92adb5a80\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB666-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_repository_46498287_branch_name=spike/JAL-4517_customNodenamesInNewick\nbamboo_buildKey=JB-GDB666-JOB1\nbamboo_shortPlanName=spike-JAL-4517_customNodenamesInNewick\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB666-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - spike-JAL-4517_customNodenamesInNewick\nbamboo_shortPlanKey=GDB666\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498287_git_branch=spike/JAL-4517_customNodenamesInNewick\nbamboo_repository_46498287_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=c3f846fb911da7304ae2f7d049618db92adb5a80\nbamboo_buildTimeStamp=2025-03-06T16:31:03.604Z\nbamboo_repository_git_branch=spike/JAL-4517_customNodenamesInNewick\nbamboo_buildResultKey=JB-GDB666-JOB1-1\nbamboo_repository_branch_name=spike/JAL-4517_customNodenamesInNewick\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-JAL-4517_customNodenamesInNewick - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=c3f846fb911da7304ae2f7d049618db92adb5a80\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=spike/JAL-4517_customNodenamesInNewick\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_repository_46498287_revision_number=c3f846fb911da7304ae2f7d049618db92adb5a80\nbamboo_jobFailed=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=spike/JAL-4517_customNodenamesInNewick\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=spike/JAL-4517_customNodenamesInNewick\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498287_name=Jalview Gitlab\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302159\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-GDB666-JOB1\nbamboo_planKey=JB-GDB666\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498287_git_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=spike/JAL-4517_customNodenamesInNewick\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 06-Mar-2025 16:39:11 444 build 06-Mar-2025 16:39:16 build 06-Mar-2025 16:39:16 > Configure project : build 06-Mar-2025 16:39:16 Using properties from file './utils/channels/default/channel_gradle.properties' build 06-Mar-2025 16:39:16 JALVIEW_VERSION is set to '2.11.4.0' build 06-Mar-2025 16:39:16 HEADLESS BUILD build 06-Mar-2025 16:39:16 J2S ENABLED build 06-Mar-2025 16:39:17 Using a LOCAL profile. build 06-Mar-2025 16:39:17 eclipseDir exists build 06-Mar-2025 16:39:20 build 06-Mar-2025 16:39:20 > Task :cloverHtmlReport build 06-Mar-2025 16:39:20 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Mar-2025 16:39:21 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/reports/clover' build 06-Mar-2025 16:39:58 Done. Processed 115 packages in 37011ms (321ms per package). build 06-Mar-2025 16:40:03 build 06-Mar-2025 16:40:03 > Task :cloverXmlReport build 06-Mar-2025 16:40:03 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Mar-2025 16:40:04 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/reports/clover/clover.xml' build 06-Mar-2025 16:40:04 build 06-Mar-2025 16:40:04 > Task :cloverReport build 06-Mar-2025 16:40:04 build 06-Mar-2025 16:40:04 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 06-Mar-2025 16:40:04 build 06-Mar-2025 16:40:04 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 06-Mar-2025 16:40:04 build 06-Mar-2025 16:40:04 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 06-Mar-2025 16:40:04 build 06-Mar-2025 16:40:04 BUILD SUCCESSFUL in 53s build 06-Mar-2025 16:40:04 2 actionable tasks: 2 executed simple 06-Mar-2025 16:40:06 Finished task 'Clover Report' with result: Success simple 06-Mar-2025 16:40:06 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 06-Mar-2025 16:40:06 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1... simple 06-Mar-2025 16:40:06 Finished task 'TestNG Parser' with result: Success simple 06-Mar-2025 16:40:06 Running post build plugin 'NCover Results Collector' simple 06-Mar-2025 16:40:06 Running post build plugin 'Artifact Copier' simple 06-Mar-2025 16:40:06 Publishing an artifact: Clover Report (System) simple 06-Mar-2025 16:40:08 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.468 s simple 06-Mar-2025 16:40:08 Publishing an artifact: TestNG report error 06-Mar-2025 16:40:08 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB666-JOB1/build/reports/tests/test does not exist. simple 06-Mar-2025 16:40:08 The artifact hasn't been successfully published after 1.469 ms simple 06-Mar-2025 16:40:08 Running post build plugin 'Artifactory Release Management Staging' simple 06-Mar-2025 16:40:08 Running post build plugin 'Artifactory Build Info Copier' simple 06-Mar-2025 16:40:08 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 06-Mar-2025 16:40:08 Running post build plugin 'npm Cache Cleanup' simple 06-Mar-2025 16:40:08 Running post build plugin 'Clover Results Collector' simple 06-Mar-2025 16:40:08 Running post build plugin 'Docker Container Cleanup' simple 06-Mar-2025 16:40:08 Finalising the build... simple 06-Mar-2025 16:40:08 Stopping timer. simple 06-Mar-2025 16:40:08 Build JB-GDB666-JOB1-1 completed. simple 06-Mar-2025 16:40:08 Running on server: post build plugin 'NCover Results Collector' simple 06-Mar-2025 16:40:08 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 06-Mar-2025 16:40:08 Running on server: post build plugin 'Clover Delta Calculator' simple 06-Mar-2025 16:40:08 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 06-Mar-2025 16:40:08 All post build plugins have finished simple 06-Mar-2025 16:40:08 Generating build results summary... simple 06-Mar-2025 16:40:08 Saving build results to disk... simple 06-Mar-2025 16:40:08 Logging substituted variables... simple 06-Mar-2025 16:40:08 Indexing build results... simple 06-Mar-2025 16:40:08 Finished building JB-GDB666-JOB1-1.