simple 06-Dec-2024 13:47:00 Build Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #9 (JB-GDB633-JOB1-9) started building on agent Default Agent simple 06-Dec-2024 13:47:00 simple 06-Dec-2024 13:47:00 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1 simple 06-Dec-2024 13:47:00 Executing build Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #9 (JB-GDB633-JOB1-9) simple 06-Dec-2024 13:47:00 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 06-Dec-2024 13:47:00 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1 simple 06-Dec-2024 13:47:00 Updating source code to revision: 39291a3fa3b81f3a82111b067ffd51c87b14fe8d simple 06-Dec-2024 13:47:00 Fetching 'refs/heads/feature/JAL-4386_JAL-4435_reformat_node_labels' from 'http://source.jalview.org/git/jalview.git'. simple 06-Dec-2024 13:47:00 Checking out revision 39291a3fa3b81f3a82111b067ffd51c87b14fe8d. simple 06-Dec-2024 13:47:00 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 06-Dec-2024 13:47:00 c8ec18c..39291a3 feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels simple 06-Dec-2024 13:47:00 Already on 'feature/JAL-4386_JAL-4435_reformat_node_labels' simple 06-Dec-2024 13:47:00 Your branch is behind 'origin/feature/JAL-4386_JAL-4435_reformat_node_labels' by 1 commit, and can be fast-forwarded. simple 06-Dec-2024 13:47:00 (use "git pull" to update your local branch) simple 06-Dec-2024 13:47:00 HEAD is now at 39291a3 JAL-4435 Corrections on coloured line visualisation simple 06-Dec-2024 13:47:00 Updated source code to revision: 39291a3fa3b81f3a82111b067ffd51c87b14fe8d simple 06-Dec-2024 13:47:00 Finished task 'Checkout Default Repository' with result: Success simple 06-Dec-2024 13:47:00 Running pre-build action: VCS Version Collector simple 06-Dec-2024 13:47:00 Running pre-build action: Artifactory Release Staging simple 06-Dec-2024 13:47:00 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 06-Dec-2024 13:47:00 Bamboo Artifactory Plugin version: 2.6.2 command 06-Dec-2024 13:47:00 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #9 (JB-GDB633-JOB1-9)'\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-GDB633-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=39291a3fa3b81f3a82111b067ffd51c87b14fe8d\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB633-JOB1-9\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-GDB633-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB633-JOB1\nbamboo_shortPlanName=feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_46498136_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_repository_46498136_revision_number=39291a3fa3b81f3a82111b067ffd51c87b14fe8d\nbamboo_buildNumber=9\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-GDB633-JOB1-9\nbamboo_repository_46498136_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/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=GDB633\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=39291a3fa3b81f3a82111b067ffd51c87b14fe8d\nbamboo_buildTimeStamp=2024-12-06T13:47:00.413Z\nbamboo_repository_previous_revision_number=c8ec18cdaf58a232459fe4a2bc6fa2bb70678c32\nbamboo_planRepository_previousRevision=c8ec18cdaf58a232459fe4a2bc6fa2bb70678c32\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDB633-JOB1-9\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=39291a3fa3b81f3a82111b067ffd51c87b14fe8d\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_repository_46498136_previous_revision_number=c8ec18cdaf58a232459fe4a2bc6fa2bb70678c32\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=c8ec18cdaf58a232459fe4a2bc6fa2bb70678c32\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\nbamboo_repository_46498136_branch_name=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_46498136_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301871\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=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_repository_46498136_name=Jalview Git\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-GDB633-JOB1\nbamboo_planKey=JB-GDB633\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/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 06-Dec-2024 13:47:00 444 build 06-Dec-2024 13:47:01 build 06-Dec-2024 13:47:01 > Configure project : build 06-Dec-2024 13:47:01 Using properties from file './utils/channels/default/channel_gradle.properties' build 06-Dec-2024 13:47:01 JALVIEW_VERSION is set to '2.11.4.0' build 06-Dec-2024 13:47:01 HEADLESS BUILD build 06-Dec-2024 13:47:01 J2S ENABLED build 06-Dec-2024 13:47:01 Using a LOCAL profile. build 06-Dec-2024 13:47:01 eclipseDir exists build 06-Dec-2024 13:47:01 build 06-Dec-2024 13:47:01 > Task :clean build 06-Dec-2024 13:47:01 > Task :cleanClover build 06-Dec-2024 13:47:01 > Task :cleanTest UP-TO-DATE build 06-Dec-2024 13:47:04 build 06-Dec-2024 13:47:04 > Task :cloverInstrJava build 06-Dec-2024 13:47:04 Clover: About to instrument 1102 files build 06-Dec-2024 13:47:04 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Dec-2024 13:47:04 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover.db'. build 06-Dec-2024 13:47:04 Processing files at 1.9 source level. error 06-Dec-2024 13:47:06 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-Dec-2024 13:47:06 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-Dec-2024 13:47:06 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-Dec-2024 13:47:06 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-Dec-2024 13:47:06 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-Dec-2024 13:47:06 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-Dec-2024 13:47:06 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-Dec-2024 13:47:13 Clover all over. Instrumented 1102 files (111 packages). build 06-Dec-2024 13:47:15 build 06-Dec-2024 13:47:15 > Task :cloverInstrTests build 06-Dec-2024 13:47:15 Clover: About to instrument test files build 06-Dec-2024 13:47:15 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Dec-2024 13:47:15 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover.db'. build 06-Dec-2024 13:47:15 Processing files at 1.9 source level. build 06-Dec-2024 13:47:18 Clover all over. Instrumented 290 files (52 packages). build 06-Dec-2024 13:47:18 1591 test methods detected. build 06-Dec-2024 13:47:18 build 06-Dec-2024 13:47:18 > Task :cloverInstr build 06-Dec-2024 13:47:20 build 06-Dec-2024 13:47:20 > Task :compileCloverJava build 06-Dec-2024 13:47:20 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 06-Dec-2024 13:47:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:20 Setting target compatibility to 11 error 06-Dec-2024 13:47:32 Note: Some input files use or override a deprecated API. error 06-Dec-2024 13:47:32 Note: Recompile with -Xlint:deprecation for details. error 06-Dec-2024 13:47:32 Note: Some input files use unchecked or unsafe operations. error 06-Dec-2024 13:47:32 Note: Recompile with -Xlint:unchecked for details. build 06-Dec-2024 13:47:37 build 06-Dec-2024 13:47:37 > Task :processCloverResources NO-SOURCE build 06-Dec-2024 13:47:37 > Task :cloverClasses build 06-Dec-2024 13:47:38 > Task :copyHelp build 06-Dec-2024 13:47:39 > Task :buildIndices build 06-Dec-2024 13:47:39 > Task :copyResources build 06-Dec-2024 13:47:39 > Task :copyChannelResources build 06-Dec-2024 13:47:39 build 06-Dec-2024 13:47:39 > Task :createBuildProperties build 06-Dec-2024 13:47:39 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 06-Dec-2024 13:47:39 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:39 build 06-Dec-2024 13:47:39 > Task :buildResources build 06-Dec-2024 13:47:39 > Task :copyDocs build 06-Dec-2024 13:47:39 build 06-Dec-2024 13:47:39 > Task :convertMdFiles build 06-Dec-2024 13:47:39 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 06-Dec-2024 13:47:39 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/releaseprocess.html build 06-Dec-2024 13:47:39 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 06-Dec-2024 13:47:39 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/building.html build 06-Dec-2024 13:47:39 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/jalview-projects.html build 06-Dec-2024 13:47:40 build 06-Dec-2024 13:47:40 > Task :releasesTemplates build 06-Dec-2024 13:47:40 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 06-Dec-2024 13:47:40 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:40 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:40 Stripping rc/test/etc for TEST build 06-Dec-2024 13:47:40 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 06-Dec-2024 13:47:40 build 06-Dec-2024 13:47:40 > Task :prepare build 06-Dec-2024 13:47:42 build 06-Dec-2024 13:47:42 > Task :compileJava build 06-Dec-2024 13:47:42 Setting target compatibility to 11 error 06-Dec-2024 13:47:47 Note: Some input files use or override a deprecated API. error 06-Dec-2024 13:47:47 Note: Recompile with -Xlint:deprecation for details. error 06-Dec-2024 13:47:47 Note: Some input files use unchecked or unsafe operations. error 06-Dec-2024 13:47:47 Note: Recompile with -Xlint:unchecked for details. build 06-Dec-2024 13:47:49 build 06-Dec-2024 13:47:49 > Task :compileTestJava build 06-Dec-2024 13:47:49 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 06-Dec-2024 13:47:49 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:49 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:49 Setting target compatibility to 11 error 06-Dec-2024 13:47:53 Note: Some input files use or override a deprecated API. error 06-Dec-2024 13:47:53 Note: Recompile with -Xlint:deprecation for details. error 06-Dec-2024 13:47:53 Note: Some input files use unchecked or unsafe operations. error 06-Dec-2024 13:47:53 Note: Recompile with -Xlint:unchecked for details. build 06-Dec-2024 13:47:54 build 06-Dec-2024 13:47:54 > Task :processTestResources build 06-Dec-2024 13:47:54 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 06-Dec-2024 13:47:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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-Dec-2024 13:47:54 build 06-Dec-2024 13:47:54 > Task :testClasses build 06-Dec-2024 13:47:56 build 06-Dec-2024 13:47:56 > Task :testTask0 build 06-Dec-2024 13:47:56 Running tests WITH clover error 06-Dec-2024 13:47:59 WARNING: An illegal reflective access operation has occurred error 06-Dec-2024 13:47:59 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 06-Dec-2024 13:47:59 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 06-Dec-2024 13:47:59 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 06-Dec-2024 13:47:59 WARNING: All illegal access operations will be denied in a future release build 06-Dec-2024 13:51:47 build 06-Dec-2024 13:51:47 > Task :testTask1 build 06-Dec-2024 13:51:47 Running tests WITH clover error 06-Dec-2024 13:51:49 WARNING: An illegal reflective access operation has occurred error 06-Dec-2024 13:51:49 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 06-Dec-2024 13:51:49 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 06-Dec-2024 13:51:49 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 06-Dec-2024 13:51:49 WARNING: All illegal access operations will be denied in a future release build 06-Dec-2024 13:53:23 build 06-Dec-2024 13:53:23 > Task :testTask2 build 06-Dec-2024 13:53:23 Running tests WITH clover build 06-Dec-2024 13:53:26 build 06-Dec-2024 13:53:26 > Task :testTask3 build 06-Dec-2024 13:53:26 Running tests WITH clover error 06-Dec-2024 13:53:28 WARNING: An illegal reflective access operation has occurred error 06-Dec-2024 13:53:28 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 06-Dec-2024 13:53:28 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 06-Dec-2024 13:53:28 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 06-Dec-2024 13:53:28 WARNING: All illegal access operations will be denied in a future release build 06-Dec-2024 13:54:14 build 06-Dec-2024 13:54:14 > Task :test NO-SOURCE build 06-Dec-2024 13:54:14 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 06-Dec-2024 13:54:14 │jalview:testTask0 results: SUCCESS (1693 tests, 1693 successes, 0 failures, 0 skipped) in 3 minutes, 50.461 seconds │ build 06-Dec-2024 13:54:14 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/testTask0/index.html│ build 06-Dec-2024 13:54:14 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Dec-2024 13:54:14 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 35.685 seconds │ build 06-Dec-2024 13:54:14 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/testTask1/index.html│ build 06-Dec-2024 13:54:14 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Dec-2024 13:54:14 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.411 seconds │ build 06-Dec-2024 13:54:14 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/testTask2/index.html│ build 06-Dec-2024 13:54:14 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Dec-2024 13:54:14 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 49.015 seconds │ build 06-Dec-2024 13:54:14 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/testTask3/index.html│ build 06-Dec-2024 13:54:14 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Dec-2024 13:54:14 │OVERALL: results: SUCCESS (1768 tests, 1768 successes, 0 failures, 0 skipped) in 4 minutes, 138.572 seconds │ build 06-Dec-2024 13:54:14 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 06-Dec-2024 13:54:14 build 06-Dec-2024 13:54:14 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 06-Dec-2024 13:54:14 build 06-Dec-2024 13:54:14 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-Dec-2024 13:54:14 build 06-Dec-2024 13:54:14 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 06-Dec-2024 13:54:14 build 06-Dec-2024 13:54:14 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 06-Dec-2024 13:54:14 Please consult deprecation warnings for more details. build 06-Dec-2024 13:54:14 build 06-Dec-2024 13:54:14 BUILD SUCCESSFUL in 7m 13s build 06-Dec-2024 13:54:14 21 actionable tasks: 20 executed, 1 up-to-date simple 06-Dec-2024 13:54:14 Finished task 'Run tests with openclover under gradle' with result: Success simple 06-Dec-2024 13:54:14 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 06-Dec-2024 13:54:14 Bamboo Artifactory Plugin version: 2.6.2 command 06-Dec-2024 13:54:14 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #9 (JB-GDB633-JOB1-9)'\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-GDB633-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=39291a3fa3b81f3a82111b067ffd51c87b14fe8d\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB633-JOB1-9\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-GDB633-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB633-JOB1\nbamboo_shortPlanName=feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_46498136_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_repository_46498136_revision_number=39291a3fa3b81f3a82111b067ffd51c87b14fe8d\nbamboo_buildNumber=9\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-GDB633-JOB1-9\nbamboo_repository_46498136_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/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=GDB633\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=39291a3fa3b81f3a82111b067ffd51c87b14fe8d\nbamboo_buildTimeStamp=2024-12-06T13:47:00.413Z\nbamboo_repository_previous_revision_number=c8ec18cdaf58a232459fe4a2bc6fa2bb70678c32\nbamboo_planRepository_previousRevision=c8ec18cdaf58a232459fe4a2bc6fa2bb70678c32\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDB633-JOB1-9\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=39291a3fa3b81f3a82111b067ffd51c87b14fe8d\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\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_repository_46498136_previous_revision_number=c8ec18cdaf58a232459fe4a2bc6fa2bb70678c32\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=c8ec18cdaf58a232459fe4a2bc6fa2bb70678c32\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\nbamboo_repository_46498136_branch_name=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_46498136_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301871\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=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_repository_46498136_name=Jalview Git\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-GDB633-JOB1\nbamboo_planKey=JB-GDB633\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/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 06-Dec-2024 13:54:14 444 build 06-Dec-2024 13:54:21 build 06-Dec-2024 13:54:21 > Configure project : build 06-Dec-2024 13:54:21 Using properties from file './utils/channels/default/channel_gradle.properties' build 06-Dec-2024 13:54:21 JALVIEW_VERSION is set to '2.11.4.0' build 06-Dec-2024 13:54:21 HEADLESS BUILD build 06-Dec-2024 13:54:21 J2S ENABLED build 06-Dec-2024 13:54:21 Using a LOCAL profile. build 06-Dec-2024 13:54:22 eclipseDir exists build 06-Dec-2024 13:54:24 build 06-Dec-2024 13:54:24 > Task :cloverHtmlReport build 06-Dec-2024 13:54:24 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Dec-2024 13:54:25 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/clover' build 06-Dec-2024 13:55:03 Done. Processed 115 packages in 37700ms (327ms per package). build 06-Dec-2024 13:55:09 build 06-Dec-2024 13:55:09 > Task :cloverXmlReport build 06-Dec-2024 13:55:09 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Dec-2024 13:55:09 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/clover/clover.xml' build 06-Dec-2024 13:55:09 build 06-Dec-2024 13:55:09 > Task :cloverReport build 06-Dec-2024 13:55:09 build 06-Dec-2024 13:55:09 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 06-Dec-2024 13:55:09 build 06-Dec-2024 13:55:09 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-Dec-2024 13:55:09 build 06-Dec-2024 13:55:09 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 06-Dec-2024 13:55:09 build 06-Dec-2024 13:55:09 BUILD SUCCESSFUL in 55s build 06-Dec-2024 13:55:09 2 actionable tasks: 2 executed simple 06-Dec-2024 13:55:10 Finished task 'Clover Report' with result: Success simple 06-Dec-2024 13:55:10 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 06-Dec-2024 13:55:10 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1... simple 06-Dec-2024 13:55:10 Finished task 'TestNG Parser' with result: Success simple 06-Dec-2024 13:55:10 Running post build plugin 'NCover Results Collector' simple 06-Dec-2024 13:55:10 Running post build plugin 'Artifact Copier' simple 06-Dec-2024 13:55:10 Publishing an artifact: Clover Report (System) simple 06-Dec-2024 13:55:11 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.468 s simple 06-Dec-2024 13:55:11 Publishing an artifact: TestNG report error 06-Dec-2024 13:55:11 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/test does not exist. simple 06-Dec-2024 13:55:11 The artifact hasn't been successfully published after 1.339 ms simple 06-Dec-2024 13:55:11 Running post build plugin 'Artifactory Release Management Staging' simple 06-Dec-2024 13:55:11 Running post build plugin 'Artifactory Build Info Copier' simple 06-Dec-2024 13:55:11 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 06-Dec-2024 13:55:11 Running post build plugin 'npm Cache Cleanup' simple 06-Dec-2024 13:55:11 Running post build plugin 'Clover Results Collector' simple 06-Dec-2024 13:55:11 Running post build plugin 'Docker Container Cleanup' simple 06-Dec-2024 13:55:11 Finalising the build... simple 06-Dec-2024 13:55:11 Stopping timer. simple 06-Dec-2024 13:55:11 Build JB-GDB633-JOB1-9 completed. simple 06-Dec-2024 13:55:11 Running on server: post build plugin 'NCover Results Collector' simple 06-Dec-2024 13:55:11 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 06-Dec-2024 13:55:11 Running on server: post build plugin 'Clover Delta Calculator' simple 06-Dec-2024 13:55:11 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 06-Dec-2024 13:55:11 All post build plugins have finished simple 06-Dec-2024 13:55:11 Generating build results summary... simple 06-Dec-2024 13:55:11 Saving build results to disk... simple 06-Dec-2024 13:55:11 Logging substituted variables... simple 06-Dec-2024 13:55:11 Indexing build results... simple 06-Dec-2024 13:55:11 Finished building JB-GDB633-JOB1-9.