simple 18-Nov-2024 09:56:37 Build Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests #3 (JB-GDB647-JOB1-3) started building on agent Default Agent simple 18-Nov-2024 09:56:37 simple 18-Nov-2024 09:56:37 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1 simple 18-Nov-2024 09:56:37 Executing build Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests #3 (JB-GDB647-JOB1-3) simple 18-Nov-2024 09:56:37 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 18-Nov-2024 09:56:37 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1 simple 18-Nov-2024 09:56:37 Updating source code to revision: 5e8bd075739b756cac8f741a47a7de952c45f879 simple 18-Nov-2024 09:56:37 Fetching 'refs/heads/spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure' from 'http://source.jalview.org/git/jalview.git'. simple 18-Nov-2024 09:56:38 Checking out revision 5e8bd075739b756cac8f741a47a7de952c45f879. simple 18-Nov-2024 09:56:39 Already on 'spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure' simple 18-Nov-2024 09:56:39 Updated source code to revision: 5e8bd075739b756cac8f741a47a7de952c45f879 simple 18-Nov-2024 09:56:39 Finished task 'Checkout Default Repository' with result: Success simple 18-Nov-2024 09:56:39 Running pre-build action: VCS Version Collector simple 18-Nov-2024 09:56:39 Running pre-build action: Artifactory Release Staging simple 18-Nov-2024 09:56:39 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 18-Nov-2024 09:56:39 Bamboo Artifactory Plugin version: 2.6.2 command 18-Nov-2024 09:56:39 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests #3 (JB-GDB647-JOB1-3)'\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-GDB647-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_46498215_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB647-JOB1-3\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-GDB647-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB647-JOB1\nbamboo_shortPlanName=spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_46498215_name=Jalview Git\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=3\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-GDB647-JOB1-3\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_repository_46498215_git_username=\nbamboo_planName=Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_shortPlanKey=GDB647\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_buildTimeStamp=2024-11-18T09:56:37.727Z\nbamboo_repository_previous_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_planRepository_previousRevision=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_repository_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_buildResultKey=JB-GDB647-JOB1-3\nbamboo_repository_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_46498215_previous_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498215_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_planRepository_1_revision=5e8bd075739b756cac8f741a47a7de952c45f879\nSHLVL=1\nbamboo_repository_46498215_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\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/\nbamboo_dependenciesDisabled=false\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-4366_JAL-4386_JAL-4435_expandedmsafromstructure\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=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_repository_46498215_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302029\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_ManualBuildTriggerReason_userName=jprocter\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/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-GDB647-JOB1\nbamboo_planKey=JB-GDB647\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 18-Nov-2024 09:56:39 444 build 18-Nov-2024 09:56:40 build 18-Nov-2024 09:56:40 > Configure project : build 18-Nov-2024 09:56:40 Using properties from file './utils/channels/default/channel_gradle.properties' build 18-Nov-2024 09:56:40 JALVIEW_VERSION is set to '2.11.4.2' build 18-Nov-2024 09:56:40 HEADLESS BUILD build 18-Nov-2024 09:56:40 J2S ENABLED build 18-Nov-2024 09:56:40 Using a LOCAL profile. build 18-Nov-2024 09:56:40 eclipseDir exists build 18-Nov-2024 09:56:41 build 18-Nov-2024 09:56:41 > Task :clean build 18-Nov-2024 09:56:41 > Task :cleanClover build 18-Nov-2024 09:56:41 > Task :cleanTest UP-TO-DATE build 18-Nov-2024 09:56:43 build 18-Nov-2024 09:56:43 > Task :cloverInstrJava build 18-Nov-2024 09:56:43 Clover: About to instrument 1105 files build 18-Nov-2024 09:56:43 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 18-Nov-2024 09:56:43 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/clover/clover.db'. build 18-Nov-2024 09:56:43 Processing files at 1.9 source level. error 18-Nov-2024 09:56:46 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 18-Nov-2024 09:56:46 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 18-Nov-2024 09:56:46 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 18-Nov-2024 09:56:46 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 18-Nov-2024 09:56:46 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 18-Nov-2024 09:56:46 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 18-Nov-2024 09:56:46 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 18-Nov-2024 09:56:53 Clover all over. Instrumented 1105 files (112 packages). build 18-Nov-2024 09:56:55 build 18-Nov-2024 09:56:55 > Task :cloverInstrTests build 18-Nov-2024 09:56:55 Clover: About to instrument test files build 18-Nov-2024 09:56:55 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 18-Nov-2024 09:56:55 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/clover/clover.db'. build 18-Nov-2024 09:56:55 Processing files at 1.9 source level. build 18-Nov-2024 09:56:58 Clover all over. Instrumented 292 files (52 packages). build 18-Nov-2024 09:56:58 1600 test methods detected. build 18-Nov-2024 09:56:58 build 18-Nov-2024 09:56:58 > Task :cloverInstr build 18-Nov-2024 09:57:00 build 18-Nov-2024 09:57:00 > Task :compileCloverJava build 18-Nov-2024 09:57:00 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 18-Nov-2024 09:57:00 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:00 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:00 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:00 Setting target compatibility to 11 error 18-Nov-2024 09:57:14 Note: Some input files use or override a deprecated API. error 18-Nov-2024 09:57:14 Note: Recompile with -Xlint:deprecation for details. error 18-Nov-2024 09:57:14 Note: Some input files use unchecked or unsafe operations. error 18-Nov-2024 09:57:14 Note: Recompile with -Xlint:unchecked for details. build 18-Nov-2024 09:57:18 build 18-Nov-2024 09:57:18 > Task :processCloverResources NO-SOURCE build 18-Nov-2024 09:57:18 > Task :cloverClasses build 18-Nov-2024 09:57:18 > Task :copyHelp build 18-Nov-2024 09:57:19 > Task :buildIndices build 18-Nov-2024 09:57:19 > Task :copyResources build 18-Nov-2024 09:57:19 > Task :copyChannelResources build 18-Nov-2024 09:57:19 build 18-Nov-2024 09:57:19 > Task :createBuildProperties build 18-Nov-2024 09:57:19 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 18-Nov-2024 09:57:19 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:19 build 18-Nov-2024 09:57:19 > Task :buildResources build 18-Nov-2024 09:57:19 > Task :copyDocs build 18-Nov-2024 09:57:19 build 18-Nov-2024 09:57:19 > Task :convertMdFiles build 18-Nov-2024 09:57:19 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 18-Nov-2024 09:57:19 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/releaseprocess.html build 18-Nov-2024 09:57:19 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 18-Nov-2024 09:57:19 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/building.html build 18-Nov-2024 09:57:19 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/jalview-projects.html build 18-Nov-2024 09:57:19 build 18-Nov-2024 09:57:19 > Task :releasesTemplates build 18-Nov-2024 09:57:19 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 18-Nov-2024 09:57:19 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:19 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:19 Stripping rc/test/etc for TEST build 18-Nov-2024 09:57:19 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 18-Nov-2024 09:57:19 build 18-Nov-2024 09:57:19 > Task :prepare build 18-Nov-2024 09:57:21 build 18-Nov-2024 09:57:21 > Task :compileJava build 18-Nov-2024 09:57:21 Setting target compatibility to 11 error 18-Nov-2024 09:57:26 Note: Some input files use or override a deprecated API. error 18-Nov-2024 09:57:26 Note: Recompile with -Xlint:deprecation for details. error 18-Nov-2024 09:57:26 Note: Some input files use unchecked or unsafe operations. error 18-Nov-2024 09:57:26 Note: Recompile with -Xlint:unchecked for details. build 18-Nov-2024 09:57:29 build 18-Nov-2024 09:57:29 > Task :compileTestJava build 18-Nov-2024 09:57:29 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 18-Nov-2024 09:57:29 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:29 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:29 Setting target compatibility to 11 error 18-Nov-2024 09:57:33 Note: Some input files use or override a deprecated API. error 18-Nov-2024 09:57:33 Note: Recompile with -Xlint:deprecation for details. error 18-Nov-2024 09:57:33 Note: Some input files use unchecked or unsafe operations. error 18-Nov-2024 09:57:33 Note: Recompile with -Xlint:unchecked for details. build 18-Nov-2024 09:57:34 build 18-Nov-2024 09:57:34 > Task :processTestResources build 18-Nov-2024 09:57:34 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 18-Nov-2024 09:57:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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 18-Nov-2024 09:57:34 build 18-Nov-2024 09:57:34 > Task :testClasses build 18-Nov-2024 09:57:36 build 18-Nov-2024 09:57:36 > Task :testTask0 build 18-Nov-2024 09:57:36 Running tests WITH clover error 18-Nov-2024 09:57:38 WARNING: An illegal reflective access operation has occurred error 18-Nov-2024 09:57:38 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 18-Nov-2024 09:57:38 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 18-Nov-2024 09:57:38 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 18-Nov-2024 09:57:38 WARNING: All illegal access operations will be denied in a future release build 18-Nov-2024 10:01:25 build 18-Nov-2024 10:01:25 > Task :testTask1 build 18-Nov-2024 10:01:25 Running tests WITH clover error 18-Nov-2024 10:01:26 WARNING: An illegal reflective access operation has occurred error 18-Nov-2024 10:01:26 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 18-Nov-2024 10:01:26 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 18-Nov-2024 10:01:26 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 18-Nov-2024 10:01:26 WARNING: All illegal access operations will be denied in a future release build 18-Nov-2024 10:02:59 build 18-Nov-2024 10:02:59 > Task :testTask2 build 18-Nov-2024 10:02:59 Running tests WITH clover build 18-Nov-2024 10:03:03 build 18-Nov-2024 10:03:03 > Task :testTask3 build 18-Nov-2024 10:03:03 Running tests WITH clover error 18-Nov-2024 10:03:04 WARNING: An illegal reflective access operation has occurred error 18-Nov-2024 10:03:04 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 18-Nov-2024 10:03:04 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 18-Nov-2024 10:03:04 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 18-Nov-2024 10:03:04 WARNING: All illegal access operations will be denied in a future release build 18-Nov-2024 10:03:48 build 18-Nov-2024 10:03:48 > Task :test NO-SOURCE build 18-Nov-2024 10:03:48 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 18-Nov-2024 10:03:48 │jalview:testTask0 results: SUCCESS (1750 tests, 1750 successes, 0 failures, 0 skipped) in 3 minutes, 47.881 seconds │ build 18-Nov-2024 10:03:48 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/tests/testTask0/index.html│ build 18-Nov-2024 10:03:48 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 18-Nov-2024 10:03:48 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 34.102 seconds │ build 18-Nov-2024 10:03:48 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/tests/testTask1/index.html│ build 18-Nov-2024 10:03:48 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 18-Nov-2024 10:03:48 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.452 seconds │ build 18-Nov-2024 10:03:48 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/tests/testTask2/index.html│ build 18-Nov-2024 10:03:48 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 18-Nov-2024 10:03:48 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 47.143 seconds │ build 18-Nov-2024 10:03:48 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/tests/testTask3/index.html│ build 18-Nov-2024 10:03:48 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 18-Nov-2024 10:03:48 │OVERALL: results: SUCCESS (1825 tests, 1825 successes, 0 failures, 0 skipped) in 4 minutes, 132.578 seconds │ build 18-Nov-2024 10:03:48 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 18-Nov-2024 10:03:48 build 18-Nov-2024 10:03:48 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 18-Nov-2024 10:03:48 build 18-Nov-2024 10:03:48 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 18-Nov-2024 10:03:48 build 18-Nov-2024 10:03:48 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 18-Nov-2024 10:03:48 build 18-Nov-2024 10:03:48 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 18-Nov-2024 10:03:48 Please consult deprecation warnings for more details. build 18-Nov-2024 10:03:48 build 18-Nov-2024 10:03:48 BUILD SUCCESSFUL in 7m 8s build 18-Nov-2024 10:03:48 21 actionable tasks: 20 executed, 1 up-to-date simple 18-Nov-2024 10:03:48 Finished task 'Run tests with openclover under gradle' with result: Success simple 18-Nov-2024 10:03:48 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 18-Nov-2024 10:03:48 Bamboo Artifactory Plugin version: 2.6.2 command 18-Nov-2024 10:03:48 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests #3 (JB-GDB647-JOB1-3)'\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-GDB647-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_46498215_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB647-JOB1-3\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-GDB647-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB647-JOB1\nbamboo_shortPlanName=spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_46498215_name=Jalview Git\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=3\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-GDB647-JOB1-3\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_repository_46498215_git_username=\nbamboo_planName=Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_shortPlanKey=GDB647\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_buildTimeStamp=2024-11-18T09:56:37.727Z\nbamboo_repository_previous_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_planRepository_previousRevision=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_repository_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_buildResultKey=JB-GDB647-JOB1-3\nbamboo_repository_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_46498215_previous_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498215_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_planRepository_1_revision=5e8bd075739b756cac8f741a47a7de952c45f879\nSHLVL=1\nbamboo_repository_46498215_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\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/\nbamboo_dependenciesDisabled=false\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-4366_JAL-4386_JAL-4435_expandedmsafromstructure\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=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_repository_46498215_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302029\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_ManualBuildTriggerReason_userName=jprocter\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/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-GDB647-JOB1\nbamboo_planKey=JB-GDB647\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 18-Nov-2024 10:03:48 444 build 18-Nov-2024 10:04:00 build 18-Nov-2024 10:04:00 > Configure project : build 18-Nov-2024 10:04:00 Using properties from file './utils/channels/default/channel_gradle.properties' build 18-Nov-2024 10:04:00 JALVIEW_VERSION is set to '2.11.4.2' build 18-Nov-2024 10:04:00 HEADLESS BUILD build 18-Nov-2024 10:04:00 J2S ENABLED build 18-Nov-2024 10:04:00 Using a LOCAL profile. build 18-Nov-2024 10:04:01 eclipseDir exists build 18-Nov-2024 10:04:04 build 18-Nov-2024 10:04:04 > Task :cloverHtmlReport build 18-Nov-2024 10:04:04 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 18-Nov-2024 10:04:05 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/clover' build 18-Nov-2024 10:04:44 Done. Processed 116 packages in 39238ms (338ms per package). build 18-Nov-2024 10:04:49 build 18-Nov-2024 10:04:49 > Task :cloverXmlReport build 18-Nov-2024 10:04:49 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 18-Nov-2024 10:04:50 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/clover/clover.xml' build 18-Nov-2024 10:04:50 build 18-Nov-2024 10:04:50 > Task :cloverReport build 18-Nov-2024 10:04:50 build 18-Nov-2024 10:04:50 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 18-Nov-2024 10:04:50 build 18-Nov-2024 10:04:50 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 18-Nov-2024 10:04:50 build 18-Nov-2024 10:04:50 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 18-Nov-2024 10:04:50 build 18-Nov-2024 10:04:50 BUILD SUCCESSFUL in 1m 1s build 18-Nov-2024 10:04:50 2 actionable tasks: 2 executed simple 18-Nov-2024 10:04:50 Finished task 'Clover Report' with result: Success simple 18-Nov-2024 10:04:50 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 18-Nov-2024 10:04:50 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1... simple 18-Nov-2024 10:04:50 Finished task 'TestNG Parser' with result: Success simple 18-Nov-2024 10:04:50 Running post build plugin 'NCover Results Collector' simple 18-Nov-2024 10:04:50 Running post build plugin 'Artifact Copier' simple 18-Nov-2024 10:04:50 Publishing an artifact: Clover Report (System) simple 18-Nov-2024 10:04:51 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.386 s simple 18-Nov-2024 10:04:51 Publishing an artifact: TestNG report error 18-Nov-2024 10:04:51 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/tests/test does not exist. simple 18-Nov-2024 10:04:51 The artifact hasn't been successfully published after 1.302 ms simple 18-Nov-2024 10:04:51 Running post build plugin 'Artifactory Release Management Staging' simple 18-Nov-2024 10:04:51 Running post build plugin 'Artifactory Build Info Copier' simple 18-Nov-2024 10:04:51 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 18-Nov-2024 10:04:51 Running post build plugin 'npm Cache Cleanup' simple 18-Nov-2024 10:04:51 Running post build plugin 'Clover Results Collector' simple 18-Nov-2024 10:04:51 Running post build plugin 'Docker Container Cleanup' simple 18-Nov-2024 10:04:51 Finalising the build... simple 18-Nov-2024 10:04:51 Stopping timer. simple 18-Nov-2024 10:04:51 Build JB-GDB647-JOB1-3 completed. simple 18-Nov-2024 10:04:51 Running on server: post build plugin 'NCover Results Collector' simple 18-Nov-2024 10:04:51 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 18-Nov-2024 10:04:51 Running on server: post build plugin 'Clover Delta Calculator' simple 18-Nov-2024 10:04:51 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 18-Nov-2024 10:04:51 All post build plugins have finished simple 18-Nov-2024 10:04:51 Generating build results summary... simple 18-Nov-2024 10:04:52 Saving build results to disk... simple 18-Nov-2024 10:04:52 Logging substituted variables... simple 18-Nov-2024 10:04:52 Indexing build results... simple 18-Nov-2024 10:04:52 Finished building JB-GDB647-JOB1-3.