simple 15-Nov-2024 13:56:03 Build Jalview Builds - Gradle Develop Build - features-JAL-3914_modelqualityscores_v2115 - Clover and Tests #1 (JB-GDB646-JOB1-1) started building on agent Default Agent simple 15-Nov-2024 13:56:03 simple 15-Nov-2024 13:56:03 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1 simple 15-Nov-2024 13:56:03 Executing build Jalview Builds - Gradle Develop Build - features-JAL-3914_modelqualityscores_v2115 - Clover and Tests #1 (JB-GDB646-JOB1-1) simple 15-Nov-2024 13:56:03 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 15-Nov-2024 13:56:03 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1 simple 15-Nov-2024 13:56:03 Updating source code to revision: 8dbe9206561daac950b4154da519d7aad4cfeaee simple 15-Nov-2024 13:56:03 Fetching 'refs/heads/features/JAL-3914_modelqualityscores_v2115' from 'http://source.jalview.org/git/jalview.git'. simple 15-Nov-2024 13:56:03 Checking out revision 8dbe9206561daac950b4154da519d7aad4cfeaee. simple 15-Nov-2024 13:56:03 Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/.git'. simple 15-Nov-2024 13:56:03 Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1'... simple 15-Nov-2024 13:56:03 done. simple 15-Nov-2024 13:56:13 Switched to a new branch 'features/JAL-3914_modelqualityscores_v2115' simple 15-Nov-2024 13:56:13 Branch features/JAL-3914_modelqualityscores_v2115 set up to track remote branch features/JAL-3914_modelqualityscores_v2115 from origin. simple 15-Nov-2024 13:56:13 Updated source code to revision: 8dbe9206561daac950b4154da519d7aad4cfeaee simple 15-Nov-2024 13:56:13 Finished task 'Checkout Default Repository' with result: Success simple 15-Nov-2024 13:56:13 Running pre-build action: VCS Version Collector simple 15-Nov-2024 13:56:13 Running pre-build action: Artifactory Release Staging simple 15-Nov-2024 13:56:13 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 15-Nov-2024 13:56:13 Bamboo Artifactory Plugin version: 2.6.2 command 15-Nov-2024 13:56:13 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - features-JAL-3914_modelqualityscores_v2115 - Clover and Tests #1 (JB-GDB646-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-GDB646-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=features/JAL-3914_modelqualityscores_v2115\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=features/JAL-3914_modelqualityscores_v2115\nbamboo_repository_revision_number=8dbe9206561daac950b4154da519d7aad4cfeaee\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB646-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-GDB646-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB646-JOB1\nbamboo_shortPlanName=features-JAL-3914_modelqualityscores_v2115\nbamboo_planRepository_name=Jalview Git\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-GDB646-JOB1-1\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - features-JAL-3914_modelqualityscores_v2115\nbamboo_repository_46498209_branch_name=features/JAL-3914_modelqualityscores_v2115\nbamboo_shortPlanKey=GDB646\nbamboo_repository_46498209_name=Jalview Git\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=8dbe9206561daac950b4154da519d7aad4cfeaee\nbamboo_buildTimeStamp=2024-11-15T13:56:03.363Z\nbamboo_repository_git_branch=features/JAL-3914_modelqualityscores_v2115\nbamboo_buildResultKey=JB-GDB646-JOB1-1\nbamboo_repository_branch_name=features/JAL-3914_modelqualityscores_v2115\nbamboo_repository_46498209_git_branch=features/JAL-3914_modelqualityscores_v2115\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - features-JAL-3914_modelqualityscores_v2115 - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=8dbe9206561daac950b4154da519d7aad4cfeaee\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498209_git_username=\nbamboo_repository_name=Jalview Git\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=features/JAL-3914_modelqualityscores_v2115\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=features/JAL-3914_modelqualityscores_v2115\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=features/JAL-3914_modelqualityscores_v2115\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-46302017\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_repository_46498209_revision_number=8dbe9206561daac950b4154da519d7aad4cfeaee\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-GDB646-JOB1\nbamboo_repository_46498209_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planKey=JB-GDB646\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=features/JAL-3914_modelqualityscores_v2115\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 15-Nov-2024 13:56:13 444 build 15-Nov-2024 13:56:15 Starting a Gradle Daemon (subsequent builds will be faster) build 15-Nov-2024 13:56:30 build 15-Nov-2024 13:56:30 > Configure project : build 15-Nov-2024 13:56:30 Using properties from file './utils/channels/default/channel_gradle.properties' build 15-Nov-2024 13:56:30 JALVIEW_VERSION is set to '2.11.4.2' build 15-Nov-2024 13:56:30 HEADLESS BUILD build 15-Nov-2024 13:56:30 J2S ENABLED build 15-Nov-2024 13:56:31 Using a LOCAL profile. build 15-Nov-2024 13:56:31 eclipseDir exists build 15-Nov-2024 13:56:32 build 15-Nov-2024 13:56:32 > Task :clean build 15-Nov-2024 13:56:32 > Task :cleanClover build 15-Nov-2024 13:56:32 > Task :cleanTest UP-TO-DATE build 15-Nov-2024 13:56:34 build 15-Nov-2024 13:56:34 > Task :cloverInstrJava build 15-Nov-2024 13:56:34 Clover: About to instrument 1104 files build 15-Nov-2024 13:56:35 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 15-Nov-2024 13:56:35 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/clover/clover.db'. build 15-Nov-2024 13:56:35 Processing files at 1.9 source level. error 15-Nov-2024 13:56:39 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 15-Nov-2024 13:56:39 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 15-Nov-2024 13:56:39 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 15-Nov-2024 13:56:39 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 15-Nov-2024 13:56:39 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 15-Nov-2024 13:56:39 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 15-Nov-2024 13:56:39 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 15-Nov-2024 13:56:45 Clover all over. Instrumented 1104 files (112 packages). build 15-Nov-2024 13:56:48 build 15-Nov-2024 13:56:48 > Task :cloverInstrTests build 15-Nov-2024 13:56:48 Clover: About to instrument test files build 15-Nov-2024 13:56:48 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 15-Nov-2024 13:56:48 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/clover/clover.db'. build 15-Nov-2024 13:56:48 Processing files at 1.9 source level. build 15-Nov-2024 13:56:50 Clover all over. Instrumented 291 files (52 packages). build 15-Nov-2024 13:56:50 1598 test methods detected. build 15-Nov-2024 13:56:50 build 15-Nov-2024 13:56:50 > Task :cloverInstr build 15-Nov-2024 13:56:55 build 15-Nov-2024 13:56:55 > Task :compileCloverJava build 15-Nov-2024 13:56:55 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 15-Nov-2024 13:56:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:56:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:56:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:56:55 Setting target compatibility to 11 error 15-Nov-2024 13:57:18 Note: Some input files use or override a deprecated API. error 15-Nov-2024 13:57:18 Note: Recompile with -Xlint:deprecation for details. error 15-Nov-2024 13:57:18 Note: Some input files use unchecked or unsafe operations. error 15-Nov-2024 13:57:18 Note: Recompile with -Xlint:unchecked for details. build 15-Nov-2024 13:57:24 build 15-Nov-2024 13:57:24 > Task :processCloverResources NO-SOURCE build 15-Nov-2024 13:57:24 > Task :cloverClasses build 15-Nov-2024 13:57:24 > Task :copyHelp build 15-Nov-2024 13:57:25 > Task :buildIndices build 15-Nov-2024 13:57:25 > Task :copyResources build 15-Nov-2024 13:57:25 > Task :copyChannelResources build 15-Nov-2024 13:57:25 build 15-Nov-2024 13:57:25 > Task :createBuildProperties build 15-Nov-2024 13:57:25 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 15-Nov-2024 13:57:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:57:25 build 15-Nov-2024 13:57:25 > Task :buildResources build 15-Nov-2024 13:57:25 > Task :copyDocs build 15-Nov-2024 13:57:26 build 15-Nov-2024 13:57:26 > Task :convertMdFiles build 15-Nov-2024 13:57:26 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 15-Nov-2024 13:57:26 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/resources/doc_build/doc/releaseprocess.html build 15-Nov-2024 13:57:26 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 15-Nov-2024 13:57:26 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/resources/doc_build/doc/building.html build 15-Nov-2024 13:57:26 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/resources/doc_build/doc/jalview-projects.html build 15-Nov-2024 13:57:26 build 15-Nov-2024 13:57:26 > Task :releasesTemplates build 15-Nov-2024 13:57:26 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 15-Nov-2024 13:57:26 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:57:26 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:57:26 Stripping rc/test/etc for TEST build 15-Nov-2024 13:57:26 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 15-Nov-2024 13:57:26 build 15-Nov-2024 13:57:26 > Task :prepare build 15-Nov-2024 13:57:28 build 15-Nov-2024 13:57:28 > Task :compileJava build 15-Nov-2024 13:57:28 Setting target compatibility to 11 error 15-Nov-2024 13:57:35 Note: Some input files use or override a deprecated API. error 15-Nov-2024 13:57:35 Note: Recompile with -Xlint:deprecation for details. error 15-Nov-2024 13:57:35 Note: Some input files use unchecked or unsafe operations. error 15-Nov-2024 13:57:35 Note: Recompile with -Xlint:unchecked for details. build 15-Nov-2024 13:57:39 build 15-Nov-2024 13:57:39 > Task :compileTestJava build 15-Nov-2024 13:57:39 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 15-Nov-2024 13:57:39 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:57:39 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:57:39 Setting target compatibility to 11 error 15-Nov-2024 13:57:43 Note: Some input files use or override a deprecated API. error 15-Nov-2024 13:57:43 Note: Recompile with -Xlint:deprecation for details. error 15-Nov-2024 13:57:43 Note: Some input files use unchecked or unsafe operations. error 15-Nov-2024 13:57:43 Note: Recompile with -Xlint:unchecked for details. build 15-Nov-2024 13:57:44 build 15-Nov-2024 13:57:44 > Task :processTestResources build 15-Nov-2024 13:57:44 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 15-Nov-2024 13:57:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:57:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:57:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:57:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:57:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:57:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:57:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-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 15-Nov-2024 13:57:44 build 15-Nov-2024 13:57:44 > Task :testClasses build 15-Nov-2024 13:57:46 build 15-Nov-2024 13:57:46 > Task :testTask0 build 15-Nov-2024 13:57:46 Running tests WITH clover error 15-Nov-2024 13:57:49 WARNING: An illegal reflective access operation has occurred error 15-Nov-2024 13:57:49 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 15-Nov-2024 13:57:49 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 15-Nov-2024 13:57:49 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 15-Nov-2024 13:57:49 WARNING: All illegal access operations will be denied in a future release build 15-Nov-2024 14:01:41 build 15-Nov-2024 14:01:41 > Task :testTask1 build 15-Nov-2024 14:01:41 Running tests WITH clover error 15-Nov-2024 14:01:43 WARNING: An illegal reflective access operation has occurred error 15-Nov-2024 14:01:43 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 15-Nov-2024 14:01:43 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 15-Nov-2024 14:01:43 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 15-Nov-2024 14:01:43 WARNING: All illegal access operations will be denied in a future release build 15-Nov-2024 14:03:16 build 15-Nov-2024 14:03:16 > Task :testTask2 build 15-Nov-2024 14:03:16 Running tests WITH clover build 15-Nov-2024 14:03:20 build 15-Nov-2024 14:03:20 > Task :testTask3 build 15-Nov-2024 14:03:20 Running tests WITH clover error 15-Nov-2024 14:03:21 WARNING: An illegal reflective access operation has occurred error 15-Nov-2024 14:03:21 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 15-Nov-2024 14:03:21 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 15-Nov-2024 14:03:21 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 15-Nov-2024 14:03:21 WARNING: All illegal access operations will be denied in a future release build 15-Nov-2024 14:04:06 build 15-Nov-2024 14:04:06 > Task :test NO-SOURCE build 15-Nov-2024 14:04:06 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 15-Nov-2024 14:04:06 │jalview:testTask0 results: SUCCESS (1747 tests, 1747 successes, 0 failures, 0 skipped) in 3 minutes, 54.292 seconds │ build 15-Nov-2024 14:04:06 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/reports/tests/testTask0/index.html│ build 15-Nov-2024 14:04:06 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 15-Nov-2024 14:04:06 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 34.930 seconds │ build 15-Nov-2024 14:04:06 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/reports/tests/testTask1/index.html│ build 15-Nov-2024 14:04:06 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 15-Nov-2024 14:04:06 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.562 seconds │ build 15-Nov-2024 14:04:06 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/reports/tests/testTask2/index.html│ build 15-Nov-2024 14:04:06 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 15-Nov-2024 14:04:06 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 47.682 seconds │ build 15-Nov-2024 14:04:06 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/reports/tests/testTask3/index.html│ build 15-Nov-2024 14:04:06 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 15-Nov-2024 14:04:06 │OVERALL: results: SUCCESS (1822 tests, 1822 successes, 0 failures, 0 skipped) in 4 minutes, 140.466 seconds │ build 15-Nov-2024 14:04:06 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 15-Nov-2024 14:04:06 build 15-Nov-2024 14:04:06 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 15-Nov-2024 14:04:06 build 15-Nov-2024 14:04:06 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 15-Nov-2024 14:04:06 build 15-Nov-2024 14:04:06 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 15-Nov-2024 14:04:06 build 15-Nov-2024 14:04:06 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 15-Nov-2024 14:04:06 Please consult deprecation warnings for more details. build 15-Nov-2024 14:04:06 build 15-Nov-2024 14:04:06 BUILD SUCCESSFUL in 7m 52s build 15-Nov-2024 14:04:06 21 actionable tasks: 20 executed, 1 up-to-date simple 15-Nov-2024 14:04:06 Finished task 'Run tests with openclover under gradle' with result: Success simple 15-Nov-2024 14:04:06 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 15-Nov-2024 14:04:06 Bamboo Artifactory Plugin version: 2.6.2 command 15-Nov-2024 14:04:06 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - features-JAL-3914_modelqualityscores_v2115 - Clover and Tests #1 (JB-GDB646-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-GDB646-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=features/JAL-3914_modelqualityscores_v2115\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=features/JAL-3914_modelqualityscores_v2115\nbamboo_repository_revision_number=8dbe9206561daac950b4154da519d7aad4cfeaee\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB646-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-GDB646-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB646-JOB1\nbamboo_shortPlanName=features-JAL-3914_modelqualityscores_v2115\nbamboo_planRepository_name=Jalview Git\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-GDB646-JOB1-1\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - features-JAL-3914_modelqualityscores_v2115\nbamboo_repository_46498209_branch_name=features/JAL-3914_modelqualityscores_v2115\nbamboo_shortPlanKey=GDB646\nbamboo_repository_46498209_name=Jalview Git\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=8dbe9206561daac950b4154da519d7aad4cfeaee\nbamboo_buildTimeStamp=2024-11-15T13:56:03.363Z\nbamboo_repository_git_branch=features/JAL-3914_modelqualityscores_v2115\nbamboo_buildResultKey=JB-GDB646-JOB1-1\nbamboo_repository_branch_name=features/JAL-3914_modelqualityscores_v2115\nbamboo_repository_46498209_git_branch=features/JAL-3914_modelqualityscores_v2115\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - features-JAL-3914_modelqualityscores_v2115 - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=8dbe9206561daac950b4154da519d7aad4cfeaee\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498209_git_username=\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_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=features/JAL-3914_modelqualityscores_v2115\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_branchDisplayName=features/JAL-3914_modelqualityscores_v2115\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=features/JAL-3914_modelqualityscores_v2115\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-46302017\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_repository_46498209_revision_number=8dbe9206561daac950b4154da519d7aad4cfeaee\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-GDB646-JOB1\nbamboo_repository_46498209_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planKey=JB-GDB646\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=features/JAL-3914_modelqualityscores_v2115\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 15-Nov-2024 14:04:06 444 build 15-Nov-2024 14:04:17 build 15-Nov-2024 14:04:17 > Configure project : build 15-Nov-2024 14:04:17 Using properties from file './utils/channels/default/channel_gradle.properties' build 15-Nov-2024 14:04:17 JALVIEW_VERSION is set to '2.11.4.2' build 15-Nov-2024 14:04:17 HEADLESS BUILD build 15-Nov-2024 14:04:17 J2S ENABLED build 15-Nov-2024 14:04:17 Using a LOCAL profile. build 15-Nov-2024 14:04:18 eclipseDir exists build 15-Nov-2024 14:04:21 build 15-Nov-2024 14:04:21 > Task :cloverHtmlReport build 15-Nov-2024 14:04:21 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 15-Nov-2024 14:04:22 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/reports/clover' build 15-Nov-2024 14:05:00 Done. Processed 116 packages in 37764ms (325ms per package). build 15-Nov-2024 14:05:05 build 15-Nov-2024 14:05:05 > Task :cloverXmlReport build 15-Nov-2024 14:05:05 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 15-Nov-2024 14:05:05 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/reports/clover/clover.xml' build 15-Nov-2024 14:05:05 build 15-Nov-2024 14:05:05 > Task :cloverReport build 15-Nov-2024 14:05:05 build 15-Nov-2024 14:05:05 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 15-Nov-2024 14:05:05 build 15-Nov-2024 14:05:05 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 15-Nov-2024 14:05:05 build 15-Nov-2024 14:05:05 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 15-Nov-2024 14:05:05 build 15-Nov-2024 14:05:05 BUILD SUCCESSFUL in 58s build 15-Nov-2024 14:05:05 2 actionable tasks: 2 executed simple 15-Nov-2024 14:05:05 Finished task 'Clover Report' with result: Success simple 15-Nov-2024 14:05:05 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 15-Nov-2024 14:05:05 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1... simple 15-Nov-2024 14:05:05 Finished task 'TestNG Parser' with result: Success simple 15-Nov-2024 14:05:05 Running post build plugin 'NCover Results Collector' simple 15-Nov-2024 14:05:05 Running post build plugin 'Artifact Copier' simple 15-Nov-2024 14:05:05 Publishing an artifact: Clover Report (System) simple 15-Nov-2024 14:05:07 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.405 s simple 15-Nov-2024 14:05:07 Publishing an artifact: TestNG report error 15-Nov-2024 14:05:07 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB646-JOB1/build/reports/tests/test does not exist. simple 15-Nov-2024 14:05:07 The artifact hasn't been successfully published after 1.397 ms simple 15-Nov-2024 14:05:07 Running post build plugin 'Artifactory Release Management Staging' simple 15-Nov-2024 14:05:07 Running post build plugin 'Artifactory Build Info Copier' simple 15-Nov-2024 14:05:07 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 15-Nov-2024 14:05:07 Running post build plugin 'npm Cache Cleanup' simple 15-Nov-2024 14:05:07 Running post build plugin 'Clover Results Collector' simple 15-Nov-2024 14:05:07 Running post build plugin 'Docker Container Cleanup' simple 15-Nov-2024 14:05:07 Finalising the build... simple 15-Nov-2024 14:05:07 Stopping timer. simple 15-Nov-2024 14:05:07 Build JB-GDB646-JOB1-1 completed. simple 15-Nov-2024 14:05:07 Running on server: post build plugin 'NCover Results Collector' simple 15-Nov-2024 14:05:07 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 15-Nov-2024 14:05:07 Running on server: post build plugin 'Clover Delta Calculator' simple 15-Nov-2024 14:05:07 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 15-Nov-2024 14:05:07 All post build plugins have finished simple 15-Nov-2024 14:05:07 Generating build results summary... simple 15-Nov-2024 14:05:07 Saving build results to disk... simple 15-Nov-2024 14:05:07 Logging substituted variables... simple 15-Nov-2024 14:05:07 Indexing build results... simple 15-Nov-2024 14:05:07 Finished building JB-GDB646-JOB1-1.