simple 03-Sep-2024 12:17:00 Build Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_with_develop - Clover and Tests #2 (JB-GDB618-JOB1-2) started building on agent Default Agent simple 03-Sep-2024 12:17:00 simple 03-Sep-2024 12:17:00 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1 simple 03-Sep-2024 12:17:00 Executing build Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_with_develop - Clover and Tests #2 (JB-GDB618-JOB1-2) simple 03-Sep-2024 12:17:00 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 03-Sep-2024 12:17:00 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1 simple 03-Sep-2024 12:17:00 Updating source code to revision: 8f444ff1b9acc2753ed34bfdc2e2c46f4aaebe52 simple 03-Sep-2024 12:17:00 Fetching 'refs/heads/spike/JAL-4386_merge_with_develop' from 'http://source.jalview.org/git/jalview.git'. simple 03-Sep-2024 12:17:00 Checking out revision 8f444ff1b9acc2753ed34bfdc2e2c46f4aaebe52. simple 03-Sep-2024 12:17:00 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 03-Sep-2024 12:17:00 bd2650d..8f444ff spike/JAL-4386_merge_with_develop -> origin/spike/JAL-4386_merge_with_develop simple 03-Sep-2024 12:17:01 Your branch is behind 'origin/spike/JAL-4386_merge_with_develop' by 1 commit, and can be fast-forwarded. simple 03-Sep-2024 12:17:01 Already on 'spike/JAL-4386_merge_with_develop' simple 03-Sep-2024 12:17:01 (use "git pull" to update your local branch) simple 03-Sep-2024 12:17:01 HEAD is now at 8f444ff Correction in tests simple 03-Sep-2024 12:17:01 Updated source code to revision: 8f444ff1b9acc2753ed34bfdc2e2c46f4aaebe52 simple 03-Sep-2024 12:17:01 Finished task 'Checkout Default Repository' with result: Success simple 03-Sep-2024 12:17:01 Running pre-build action: VCS Version Collector simple 03-Sep-2024 12:17:01 Running pre-build action: Artifactory Release Staging simple 03-Sep-2024 12:17:01 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 03-Sep-2024 12:17:01 Bamboo Artifactory Plugin version: 2.6.2 command 03-Sep-2024 12:17:01 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_with_develop - Clover and Tests #2 (JB-GDB618-JOB1-2)'\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-GDB618-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=spike/JAL-4386_merge_with_develop\nbamboo_repository_46498069_name=Jalview Git\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=spike/JAL-4386_merge_with_develop\nbamboo_repository_revision_number=8f444ff1b9acc2753ed34bfdc2e2c46f4aaebe52\nbamboo_repository_46498069_git_username=\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB618-JOB1-2\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-GDB618-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB618-JOB1\nbamboo_shortPlanName=spike-JAL-4386_merge_with_develop\nbamboo_repository_46498069_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=2\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-GDB618-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_with_develop\nbamboo_shortPlanKey=GDB618\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=8f444ff1b9acc2753ed34bfdc2e2c46f4aaebe52\nbamboo_buildTimeStamp=2024-09-03T12:17:00.490+01:00\nbamboo_repository_previous_revision_number=bd2650d414b4687c32f580751fc0de7f65f8d1f3\nbamboo_repository_46498069_revision_number=8f444ff1b9acc2753ed34bfdc2e2c46f4aaebe52\nbamboo_planRepository_previousRevision=bd2650d414b4687c32f580751fc0de7f65f8d1f3\nbamboo_repository_git_branch=spike/JAL-4386_merge_with_develop\nbamboo_buildResultKey=JB-GDB618-JOB1-2\nbamboo_repository_branch_name=spike/JAL-4386_merge_with_develop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_with_develop - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=8f444ff1b9acc2753ed34bfdc2e2c46f4aaebe52\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_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=spike/JAL-4386_merge_with_develop\nbamboo_repository_46498069_git_branch=spike/JAL-4386_merge_with_develop\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=bd2650d414b4687c32f580751fc0de7f65f8d1f3\nbamboo_planRepository_branchDisplayName=spike/JAL-4386_merge_with_develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=spike/JAL-4386_merge_with_develop\nbamboo_repository_46498069_previous_revision_number=bd2650d414b4687c32f580751fc0de7f65f8d1f3\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_repository_46498069_branch_name=spike/JAL-4386_merge_with_develop\nbamboo_plan_storageTag=plan-46301737\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_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-GDB618-JOB1\nbamboo_planKey=JB-GDB618\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=spike/JAL-4386_merge_with_develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 03-Sep-2024 12:17:01 444 build 03-Sep-2024 12:17:02 build 03-Sep-2024 12:17:02 > Configure project : build 03-Sep-2024 12:17:02 Using properties from file './utils/channels/default/channel_gradle.properties' build 03-Sep-2024 12:17:02 JALVIEW_VERSION is set to '2.11.4.0' build 03-Sep-2024 12:17:02 HEADLESS BUILD build 03-Sep-2024 12:17:02 J2S ENABLED build 03-Sep-2024 12:17:02 Using a LOCAL profile. build 03-Sep-2024 12:17:02 eclipseDir exists build 03-Sep-2024 12:17:03 build 03-Sep-2024 12:17:03 > Task :clean build 03-Sep-2024 12:17:03 > Task :cleanClover build 03-Sep-2024 12:17:03 > Task :cleanTest UP-TO-DATE build 03-Sep-2024 12:17:05 build 03-Sep-2024 12:17:05 > Task :cloverInstrJava build 03-Sep-2024 12:17:05 Clover: About to instrument 1102 files build 03-Sep-2024 12:17:05 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Sep-2024 12:17:05 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/clover/clover.db'. build 03-Sep-2024 12:17:05 Processing files at 1.9 source level. error 03-Sep-2024 12:17:07 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 03-Sep-2024 12:17:07 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 03-Sep-2024 12:17:07 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 03-Sep-2024 12:17:07 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 03-Sep-2024 12:17:07 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 03-Sep-2024 12:17:07 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 03-Sep-2024 12:17:07 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 03-Sep-2024 12:17:14 Clover all over. Instrumented 1102 files (111 packages). build 03-Sep-2024 12:17:16 build 03-Sep-2024 12:17:16 > Task :cloverInstrTests build 03-Sep-2024 12:17:16 Clover: About to instrument test files build 03-Sep-2024 12:17:16 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Sep-2024 12:17:16 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/clover/clover.db'. build 03-Sep-2024 12:17:16 Processing files at 1.9 source level. build 03-Sep-2024 12:17:18 Clover all over. Instrumented 290 files (52 packages). build 03-Sep-2024 12:17:18 1592 test methods detected. build 03-Sep-2024 12:17:18 build 03-Sep-2024 12:17:18 > Task :cloverInstr build 03-Sep-2024 12:17:20 build 03-Sep-2024 12:17:20 > Task :compileCloverJava build 03-Sep-2024 12:17:20 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 03-Sep-2024 12:17:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:20 Setting target compatibility to 11 error 03-Sep-2024 12:17:34 Note: Some input files use or override a deprecated API. error 03-Sep-2024 12:17:34 Note: Recompile with -Xlint:deprecation for details. error 03-Sep-2024 12:17:34 Note: Some input files use unchecked or unsafe operations. error 03-Sep-2024 12:17:34 Note: Recompile with -Xlint:unchecked for details. build 03-Sep-2024 12:17:38 build 03-Sep-2024 12:17:38 > Task :processCloverResources NO-SOURCE build 03-Sep-2024 12:17:38 > Task :cloverClasses build 03-Sep-2024 12:17:38 > Task :copyHelp build 03-Sep-2024 12:17:39 > Task :buildIndices build 03-Sep-2024 12:17:39 > Task :copyResources build 03-Sep-2024 12:17:39 > Task :copyChannelResources build 03-Sep-2024 12:17:39 build 03-Sep-2024 12:17:39 > Task :createBuildProperties build 03-Sep-2024 12:17:39 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 03-Sep-2024 12:17:39 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:39 build 03-Sep-2024 12:17:39 > Task :buildResources build 03-Sep-2024 12:17:39 > Task :copyDocs build 03-Sep-2024 12:17:39 build 03-Sep-2024 12:17:39 > Task :convertMdFiles build 03-Sep-2024 12:17:39 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 03-Sep-2024 12:17:39 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/resources/doc_build/doc/releaseprocess.html build 03-Sep-2024 12:17:39 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 03-Sep-2024 12:17:39 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/resources/doc_build/doc/building.html build 03-Sep-2024 12:17:39 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/resources/doc_build/doc/jalview-projects.html build 03-Sep-2024 12:17:40 build 03-Sep-2024 12:17:40 > Task :releasesTemplates build 03-Sep-2024 12:17:40 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 03-Sep-2024 12:17:40 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:40 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:40 build 03-Sep-2024 12:17:40 > Task :prepare build 03-Sep-2024 12:17:42 build 03-Sep-2024 12:17:42 > Task :compileJava build 03-Sep-2024 12:17:42 Setting target compatibility to 11 error 03-Sep-2024 12:17:47 Note: Some input files use or override a deprecated API. error 03-Sep-2024 12:17:47 Note: Recompile with -Xlint:deprecation for details. error 03-Sep-2024 12:17:47 Note: Some input files use unchecked or unsafe operations. error 03-Sep-2024 12:17:47 Note: Recompile with -Xlint:unchecked for details. build 03-Sep-2024 12:17:49 build 03-Sep-2024 12:17:49 > Task :compileTestJava build 03-Sep-2024 12:17:49 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 03-Sep-2024 12:17:49 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:49 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:49 Setting target compatibility to 11 error 03-Sep-2024 12:17:54 Note: Some input files use or override a deprecated API. error 03-Sep-2024 12:17:54 Note: Recompile with -Xlint:deprecation for details. error 03-Sep-2024 12:17:54 Note: Some input files use unchecked or unsafe operations. error 03-Sep-2024 12:17:54 Note: Recompile with -Xlint:unchecked for details. build 03-Sep-2024 12:17:55 build 03-Sep-2024 12:17:55 > Task :processTestResources build 03-Sep-2024 12:17:55 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 03-Sep-2024 12:17:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-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 03-Sep-2024 12:17:55 build 03-Sep-2024 12:17:55 > Task :testClasses build 03-Sep-2024 12:17:57 build 03-Sep-2024 12:17:57 > Task :testTask0 build 03-Sep-2024 12:17:57 Running tests WITH clover error 03-Sep-2024 12:18:00 WARNING: An illegal reflective access operation has occurred error 03-Sep-2024 12:18:00 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 03-Sep-2024 12:18:00 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 03-Sep-2024 12:18:00 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 03-Sep-2024 12:18:00 WARNING: All illegal access operations will be denied in a future release build 03-Sep-2024 12:21:44 build 03-Sep-2024 12:21:44 > Task :testTask1 build 03-Sep-2024 12:21:44 Running tests WITH clover error 03-Sep-2024 12:21:46 WARNING: An illegal reflective access operation has occurred error 03-Sep-2024 12:21:46 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 03-Sep-2024 12:21:46 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 03-Sep-2024 12:21:46 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 03-Sep-2024 12:21:46 WARNING: All illegal access operations will be denied in a future release build 03-Sep-2024 12:23:19 build 03-Sep-2024 12:23:19 > Task :testTask2 build 03-Sep-2024 12:23:19 Running tests WITH clover build 03-Sep-2024 12:23:22 build 03-Sep-2024 12:23:22 > Task :testTask3 build 03-Sep-2024 12:23:22 Running tests WITH clover error 03-Sep-2024 12:23:24 WARNING: An illegal reflective access operation has occurred error 03-Sep-2024 12:23:24 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 03-Sep-2024 12:23:24 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 03-Sep-2024 12:23:24 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 03-Sep-2024 12:23:24 WARNING: All illegal access operations will be denied in a future release build 03-Sep-2024 12:24:08 build 03-Sep-2024 12:24:08 > Task :test NO-SOURCE build 03-Sep-2024 12:24:08 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 03-Sep-2024 12:24:08 │jalview:testTask0 results: SUCCESS (1693 tests, 1693 successes, 0 failures, 0 skipped) in 3 minutes, 46.753 seconds │ build 03-Sep-2024 12:24:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/reports/tests/testTask0/index.html│ build 03-Sep-2024 12:24:08 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Sep-2024 12:24:08 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 34.349 seconds │ build 03-Sep-2024 12:24:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/reports/tests/testTask1/index.html│ build 03-Sep-2024 12:24:08 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Sep-2024 12:24:08 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.516 seconds │ build 03-Sep-2024 12:24:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/reports/tests/testTask2/index.html│ build 03-Sep-2024 12:24:08 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Sep-2024 12:24:08 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 47.414 seconds │ build 03-Sep-2024 12:24:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/reports/tests/testTask3/index.html│ build 03-Sep-2024 12:24:08 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Sep-2024 12:24:08 │OVERALL: results: SUCCESS (1768 tests, 1768 successes, 0 failures, 0 skipped) in 4 minutes, 132.032 seconds │ build 03-Sep-2024 12:24:08 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 03-Sep-2024 12:24:08 build 03-Sep-2024 12:24:08 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 03-Sep-2024 12:24:08 build 03-Sep-2024 12:24:08 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 03-Sep-2024 12:24:08 build 03-Sep-2024 12:24:08 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 03-Sep-2024 12:24:08 build 03-Sep-2024 12:24:08 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 03-Sep-2024 12:24:08 Please consult deprecation warnings for more details. build 03-Sep-2024 12:24:08 build 03-Sep-2024 12:24:08 BUILD SUCCESSFUL in 7m 6s build 03-Sep-2024 12:24:08 21 actionable tasks: 20 executed, 1 up-to-date simple 03-Sep-2024 12:24:08 Finished task 'Run tests with openclover under gradle' with result: Success simple 03-Sep-2024 12:24:08 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 03-Sep-2024 12:24:08 Bamboo Artifactory Plugin version: 2.6.2 command 03-Sep-2024 12:24:08 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_with_develop - Clover and Tests #2 (JB-GDB618-JOB1-2)'\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-GDB618-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=spike/JAL-4386_merge_with_develop\nbamboo_repository_46498069_name=Jalview Git\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=spike/JAL-4386_merge_with_develop\nbamboo_repository_revision_number=8f444ff1b9acc2753ed34bfdc2e2c46f4aaebe52\nbamboo_repository_46498069_git_username=\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB618-JOB1-2\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-GDB618-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB618-JOB1\nbamboo_shortPlanName=spike-JAL-4386_merge_with_develop\nbamboo_repository_46498069_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=2\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-GDB618-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_with_develop\nbamboo_shortPlanKey=GDB618\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=8f444ff1b9acc2753ed34bfdc2e2c46f4aaebe52\nbamboo_buildTimeStamp=2024-09-03T12:17:00.490+01:00\nbamboo_repository_previous_revision_number=bd2650d414b4687c32f580751fc0de7f65f8d1f3\nbamboo_repository_46498069_revision_number=8f444ff1b9acc2753ed34bfdc2e2c46f4aaebe52\nbamboo_planRepository_previousRevision=bd2650d414b4687c32f580751fc0de7f65f8d1f3\nbamboo_repository_git_branch=spike/JAL-4386_merge_with_develop\nbamboo_buildResultKey=JB-GDB618-JOB1-2\nbamboo_repository_branch_name=spike/JAL-4386_merge_with_develop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-JAL-4386_merge_with_develop - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=8f444ff1b9acc2753ed34bfdc2e2c46f4aaebe52\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_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=spike/JAL-4386_merge_with_develop\nbamboo_repository_46498069_git_branch=spike/JAL-4386_merge_with_develop\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=bd2650d414b4687c32f580751fc0de7f65f8d1f3\nbamboo_planRepository_branchDisplayName=spike/JAL-4386_merge_with_develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=spike/JAL-4386_merge_with_develop\nbamboo_repository_46498069_previous_revision_number=bd2650d414b4687c32f580751fc0de7f65f8d1f3\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_repository_46498069_branch_name=spike/JAL-4386_merge_with_develop\nbamboo_plan_storageTag=plan-46301737\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_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-GDB618-JOB1\nbamboo_planKey=JB-GDB618\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=spike/JAL-4386_merge_with_develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 03-Sep-2024 12:24:08 444 build 03-Sep-2024 12:24:13 build 03-Sep-2024 12:24:13 > Configure project : build 03-Sep-2024 12:24:13 Using properties from file './utils/channels/default/channel_gradle.properties' build 03-Sep-2024 12:24:13 JALVIEW_VERSION is set to '2.11.4.0' build 03-Sep-2024 12:24:13 HEADLESS BUILD build 03-Sep-2024 12:24:13 J2S ENABLED build 03-Sep-2024 12:24:14 Using a LOCAL profile. build 03-Sep-2024 12:24:14 eclipseDir exists build 03-Sep-2024 12:24:17 build 03-Sep-2024 12:24:17 > Task :cloverHtmlReport build 03-Sep-2024 12:24:17 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Sep-2024 12:24:18 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/reports/clover' build 03-Sep-2024 12:24:56 Done. Processed 115 packages in 38314ms (333ms per package). build 03-Sep-2024 12:25:01 build 03-Sep-2024 12:25:01 > Task :cloverXmlReport build 03-Sep-2024 12:25:01 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Sep-2024 12:25:02 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/reports/clover/clover.xml' build 03-Sep-2024 12:25:02 build 03-Sep-2024 12:25:02 > Task :cloverReport build 03-Sep-2024 12:25:02 build 03-Sep-2024 12:25:02 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 03-Sep-2024 12:25:02 build 03-Sep-2024 12:25:02 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 03-Sep-2024 12:25:02 build 03-Sep-2024 12:25:02 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 03-Sep-2024 12:25:02 build 03-Sep-2024 12:25:02 BUILD SUCCESSFUL in 53s build 03-Sep-2024 12:25:02 2 actionable tasks: 2 executed simple 03-Sep-2024 12:25:02 Finished task 'Clover Report' with result: Success simple 03-Sep-2024 12:25:02 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 03-Sep-2024 12:25:02 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1... simple 03-Sep-2024 12:25:02 Finished task 'TestNG Parser' with result: Success simple 03-Sep-2024 12:25:02 Running post build plugin 'NCover Results Collector' simple 03-Sep-2024 12:25:02 Running post build plugin 'Artifact Copier' simple 03-Sep-2024 12:25:02 Publishing an artifact: Clover Report (System) simple 03-Sep-2024 12:25:04 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.455 s simple 03-Sep-2024 12:25:04 Publishing an artifact: TestNG report error 03-Sep-2024 12:25:04 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB618-JOB1/build/reports/tests/test does not exist. simple 03-Sep-2024 12:25:04 The artifact hasn't been successfully published after 1.289 ms simple 03-Sep-2024 12:25:04 Running post build plugin 'Artifactory Release Management Staging' simple 03-Sep-2024 12:25:04 Running post build plugin 'Artifactory Build Info Copier' simple 03-Sep-2024 12:25:04 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 03-Sep-2024 12:25:04 Running post build plugin 'npm Cache Cleanup' simple 03-Sep-2024 12:25:04 Running post build plugin 'Clover Results Collector' simple 03-Sep-2024 12:25:04 Running post build plugin 'Docker Container Cleanup' simple 03-Sep-2024 12:25:04 Finalising the build... simple 03-Sep-2024 12:25:04 Stopping timer. simple 03-Sep-2024 12:25:04 Build JB-GDB618-JOB1-2 completed. simple 03-Sep-2024 12:25:04 Running on server: post build plugin 'NCover Results Collector' simple 03-Sep-2024 12:25:04 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 03-Sep-2024 12:25:04 Running on server: post build plugin 'Clover Delta Calculator' simple 03-Sep-2024 12:25:04 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 03-Sep-2024 12:25:04 All post build plugins have finished simple 03-Sep-2024 12:25:04 Generating build results summary... simple 03-Sep-2024 12:25:04 Saving build results to disk... simple 03-Sep-2024 12:25:04 Logging substituted variables... simple 03-Sep-2024 12:25:04 Indexing build results... simple 03-Sep-2024 12:25:04 Finished building JB-GDB618-JOB1-2.