simple 17-Feb-2025 17:11:33 Build Jalview Builds - Gradle Develop Build - develop - Clover and Tests #3 (JB-GDB663-JOB1-3) started building on agent Default Agent simple 17-Feb-2025 17:11:33 simple 17-Feb-2025 17:11:33 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1 simple 17-Feb-2025 17:11:33 Executing build Jalview Builds - Gradle Develop Build - develop - Clover and Tests #3 (JB-GDB663-JOB1-3) simple 17-Feb-2025 17:11:33 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 17-Feb-2025 17:11:33 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1 simple 17-Feb-2025 17:11:33 Updating source code to revision: 2bd12a6bc5270ce38fce1e858e02ef060433aa0b simple 17-Feb-2025 17:11:33 Fetching 'refs/heads/develop' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 17-Feb-2025 17:11:34 From https://gitlab.jalview.org/jalview/jalview simple 17-Feb-2025 17:11:34 637f19e..2bd12a6 develop -> develop simple 17-Feb-2025 17:11:34 Checking out revision 2bd12a6bc5270ce38fce1e858e02ef060433aa0b. simple 17-Feb-2025 17:11:35 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 17-Feb-2025 17:11:35 637f19e..2bd12a6 develop -> origin/develop simple 17-Feb-2025 17:11:35 * [new branch] releases/Release_2_11_4_Branch -> origin/releases/Release_2_11_4_Branch simple 17-Feb-2025 17:11:35 Already on 'develop' simple 17-Feb-2025 17:11:35 Your branch is behind 'origin/develop' by 1 commit, and can be fast-forwarded. simple 17-Feb-2025 17:11:35 (use "git pull" to update your local branch) simple 17-Feb-2025 17:11:35 HEAD is now at 2bd12a6 JAL-4490 release notes for JAL-4511 simple 17-Feb-2025 17:11:35 Updated source code to revision: 2bd12a6bc5270ce38fce1e858e02ef060433aa0b simple 17-Feb-2025 17:11:35 Finished task 'Checkout Default Repository' with result: Success simple 17-Feb-2025 17:11:35 Running pre-build action: VCS Version Collector simple 17-Feb-2025 17:11:35 Running pre-build action: Artifactory Release Staging simple 17-Feb-2025 17:11:35 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 17-Feb-2025 17:11:35 Bamboo Artifactory Plugin version: 2.6.2 command 17-Feb-2025 17:11:35 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - develop - Clover and Tests #3 (JB-GDB663-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-GDB663-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nbamboo_repository_46498281_branch_name=develop\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB663-JOB1-3\nbamboo_repository_46498281_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\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-GDB663-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB663-JOB1\nbamboo_shortPlanName=develop\nbamboo_planRepository_name=Jalview Gitlab\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-GDB663-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - develop\nbamboo_shortPlanKey=GDB663\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nbamboo_buildTimeStamp=2025-02-17T17:04:20.198Z\nbamboo_repository_previous_revision_number=637f19e96cfb28244fe2adb13e36d0cbe16dbe6c\nbamboo_planRepository_previousRevision=637f19e96cfb28244fe2adb13e36d0cbe16dbe6c\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-GDB663-JOB1-3\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - develop - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498281_revision_number=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nbamboo_repository_46498281_git_branch=develop\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=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=637f19e96cfb28244fe2adb13e36d0cbe16dbe6c\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498281_previous_revision_number=637f19e96cfb28244fe2adb13e36d0cbe16dbe6c\nbamboo_repository_46498281_name=Jalview Gitlab\nbamboo_repository_46498281_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302147\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1\nbamboo_planKey=JB-GDB663\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 17-Feb-2025 17:11:35 444 build 17-Feb-2025 17:11:37 build 17-Feb-2025 17:11:37 > Configure project : build 17-Feb-2025 17:11:37 Using properties from file './utils/channels/default/channel_gradle.properties' build 17-Feb-2025 17:11:37 JALVIEW_VERSION is set to '2.11.4.2' build 17-Feb-2025 17:11:37 HEADLESS BUILD build 17-Feb-2025 17:11:37 J2S ENABLED build 17-Feb-2025 17:11:37 Using a LOCAL profile. build 17-Feb-2025 17:11:37 eclipseDir exists build 17-Feb-2025 17:11:37 build 17-Feb-2025 17:11:37 > Task :clean build 17-Feb-2025 17:11:37 > Task :cleanClover build 17-Feb-2025 17:11:37 > Task :cleanTest UP-TO-DATE build 17-Feb-2025 17:11:39 build 17-Feb-2025 17:11:39 > Task :cloverInstrJava build 17-Feb-2025 17:11:39 Clover: About to instrument 1103 files build 17-Feb-2025 17:11:39 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 17-Feb-2025 17:11:39 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/clover/clover.db'. build 17-Feb-2025 17:11:39 Processing files at 1.9 source level. error 17-Feb-2025 17:11:43 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 17-Feb-2025 17:11:43 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 17-Feb-2025 17:11:43 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 17-Feb-2025 17:11:43 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 17-Feb-2025 17:11:43 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 17-Feb-2025 17:11:43 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 17-Feb-2025 17:11:43 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 17-Feb-2025 17:11:51 Clover all over. Instrumented 1103 files (112 packages). build 17-Feb-2025 17:11:53 build 17-Feb-2025 17:11:53 > Task :cloverInstrTests build 17-Feb-2025 17:11:53 Clover: About to instrument test files build 17-Feb-2025 17:11:53 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 17-Feb-2025 17:11:53 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/clover/clover.db'. build 17-Feb-2025 17:11:53 Processing files at 1.9 source level. build 17-Feb-2025 17:11:56 Clover all over. Instrumented 291 files (52 packages). build 17-Feb-2025 17:11:56 1598 test methods detected. build 17-Feb-2025 17:11:57 build 17-Feb-2025 17:11:57 > Task :cloverInstr build 17-Feb-2025 17:11:59 build 17-Feb-2025 17:11:59 > Task :compileCloverJava build 17-Feb-2025 17:11:59 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 17-Feb-2025 17:11:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:11:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:11:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:11:59 Setting target compatibility to 11 error 17-Feb-2025 17:12:13 Note: Some input files use or override a deprecated API. error 17-Feb-2025 17:12:13 Note: Recompile with -Xlint:deprecation for details. error 17-Feb-2025 17:12:13 Note: Some input files use unchecked or unsafe operations. error 17-Feb-2025 17:12:13 Note: Recompile with -Xlint:unchecked for details. build 17-Feb-2025 17:12:17 build 17-Feb-2025 17:12:17 > Task :processCloverResources NO-SOURCE build 17-Feb-2025 17:12:17 > Task :cloverClasses build 17-Feb-2025 17:12:17 > Task :copyHelp build 17-Feb-2025 17:12:18 > Task :buildIndices build 17-Feb-2025 17:12:18 > Task :copyResources build 17-Feb-2025 17:12:18 > Task :copyChannelResources build 17-Feb-2025 17:12:18 build 17-Feb-2025 17:12:18 > Task :createBuildProperties build 17-Feb-2025 17:12:18 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 17-Feb-2025 17:12:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:12:18 build 17-Feb-2025 17:12:18 > Task :buildResources build 17-Feb-2025 17:12:18 > Task :copyDocs build 17-Feb-2025 17:12:18 build 17-Feb-2025 17:12:18 > Task :convertMdFiles build 17-Feb-2025 17:12:18 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 17-Feb-2025 17:12:18 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/resources/doc_build/doc/releaseprocess.html build 17-Feb-2025 17:12:18 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 17-Feb-2025 17:12:18 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/resources/doc_build/doc/building.html build 17-Feb-2025 17:12:18 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/resources/doc_build/doc/jalview-projects.html build 17-Feb-2025 17:12:18 build 17-Feb-2025 17:12:18 > Task :releasesTemplates build 17-Feb-2025 17:12:18 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 17-Feb-2025 17:12:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:12:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:12:18 Stripping rc/test/etc for TEST build 17-Feb-2025 17:12:18 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 17-Feb-2025 17:12:18 build 17-Feb-2025 17:12:18 > Task :prepare build 17-Feb-2025 17:12:20 build 17-Feb-2025 17:12:20 > Task :compileJava build 17-Feb-2025 17:12:20 Setting target compatibility to 11 error 17-Feb-2025 17:12:26 Note: Some input files use or override a deprecated API. error 17-Feb-2025 17:12:26 Note: Recompile with -Xlint:deprecation for details. error 17-Feb-2025 17:12:26 Note: Some input files use unchecked or unsafe operations. error 17-Feb-2025 17:12:26 Note: Recompile with -Xlint:unchecked for details. build 17-Feb-2025 17:12:28 build 17-Feb-2025 17:12:28 > Task :compileTestJava build 17-Feb-2025 17:12:28 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 17-Feb-2025 17:12:28 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:12:28 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:12:28 Setting target compatibility to 11 error 17-Feb-2025 17:12:33 Note: Some input files use or override a deprecated API. error 17-Feb-2025 17:12:33 Note: Recompile with -Xlint:deprecation for details. error 17-Feb-2025 17:12:33 Note: Some input files use unchecked or unsafe operations. error 17-Feb-2025 17:12:33 Note: Recompile with -Xlint:unchecked for details. build 17-Feb-2025 17:12:34 build 17-Feb-2025 17:12:34 > Task :processTestResources build 17-Feb-2025 17:12:34 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 17-Feb-2025 17:12:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:12:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:12:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:12:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:12:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:12:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:12:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:12:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-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 17-Feb-2025 17:12:34 build 17-Feb-2025 17:12:34 > Task :testClasses build 17-Feb-2025 17:12:36 build 17-Feb-2025 17:12:36 > Task :testTask0 build 17-Feb-2025 17:12:36 Running tests WITH clover error 17-Feb-2025 17:12:39 WARNING: An illegal reflective access operation has occurred error 17-Feb-2025 17:12:39 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 17-Feb-2025 17:12:39 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 17-Feb-2025 17:12:39 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 17-Feb-2025 17:12:39 WARNING: All illegal access operations will be denied in a future release build 17-Feb-2025 17:16:42 build 17-Feb-2025 17:16:42 > Task :testTask1 build 17-Feb-2025 17:16:42 Running tests WITH clover error 17-Feb-2025 17:16:44 WARNING: An illegal reflective access operation has occurred error 17-Feb-2025 17:16:44 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 17-Feb-2025 17:16:44 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 17-Feb-2025 17:16:44 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 17-Feb-2025 17:16:44 WARNING: All illegal access operations will be denied in a future release build 17-Feb-2025 17:18:26 build 17-Feb-2025 17:18:26 > Task :testTask2 build 17-Feb-2025 17:18:26 Running tests WITH clover build 17-Feb-2025 17:18:30 build 17-Feb-2025 17:18:30 > Task :testTask3 build 17-Feb-2025 17:18:30 Running tests WITH clover error 17-Feb-2025 17:18:32 WARNING: An illegal reflective access operation has occurred error 17-Feb-2025 17:18:32 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 17-Feb-2025 17:18:32 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 17-Feb-2025 17:18:32 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 17-Feb-2025 17:18:32 WARNING: All illegal access operations will be denied in a future release build 17-Feb-2025 17:19:23 build 17-Feb-2025 17:19:23 > Task :test NO-SOURCE build 17-Feb-2025 17:19:23 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 17-Feb-2025 17:19:23 │jalview:testTask0 results: [32mSUCCESS[0m (1746 tests, [32m1746[0m successes, 0 failures, 0 skipped) in 4 minutes, 5.950 seconds │ build 17-Feb-2025 17:19:23 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/reports/tests/testTask0/index.html│ build 17-Feb-2025 17:19:23 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 17-Feb-2025 17:19:23 │jalview:testTask1 results: [32mSUCCESS[0m (49 tests, [32m49[0m successes, 0 failures, 0 skipped) in 1 minutes, 44.029 seconds │ build 17-Feb-2025 17:19:23 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/reports/tests/testTask1/index.html│ build 17-Feb-2025 17:19:23 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 17-Feb-2025 17:19:23 │jalview:testTask2 results: [32mSUCCESS[0m (1 tests, [32m1[0m successes, 0 failures, 0 skipped) in 3.795 seconds │ build 17-Feb-2025 17:19:23 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/reports/tests/testTask2/index.html│ build 17-Feb-2025 17:19:23 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 17-Feb-2025 17:19:23 │jalview:testTask3 results: [32mSUCCESS[0m (25 tests, [32m25[0m successes, 0 failures, 0 skipped) in 54.384 seconds │ build 17-Feb-2025 17:19:23 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/reports/tests/testTask3/index.html│ build 17-Feb-2025 17:19:23 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 17-Feb-2025 17:19:23 │OVERALL: results: [32mSUCCESS[0m (1821 tests, [32m1821[0m successes, 0 failures, 0 skipped) in 5 minutes, 108.158 seconds │ build 17-Feb-2025 17:19:23 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 17-Feb-2025 17:19:23 build 17-Feb-2025 17:19:23 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 17-Feb-2025 17:19:23 build 17-Feb-2025 17:19:23 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 17-Feb-2025 17:19:23 build 17-Feb-2025 17:19:23 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 17-Feb-2025 17:19:23 build 17-Feb-2025 17:19:23 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 17-Feb-2025 17:19:23 Please consult deprecation warnings for more details. build 17-Feb-2025 17:19:23 build 17-Feb-2025 17:19:23 BUILD SUCCESSFUL in 7m 47s build 17-Feb-2025 17:19:23 21 actionable tasks: 20 executed, 1 up-to-date simple 17-Feb-2025 17:19:23 Finished task 'Run tests with openclover under gradle' with result: Success simple 17-Feb-2025 17:19:23 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 17-Feb-2025 17:19:23 Bamboo Artifactory Plugin version: 2.6.2 command 17-Feb-2025 17:19:23 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - develop - Clover and Tests #3 (JB-GDB663-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-GDB663-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nbamboo_repository_46498281_branch_name=develop\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB663-JOB1-3\nbamboo_repository_46498281_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\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-GDB663-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB663-JOB1\nbamboo_shortPlanName=develop\nbamboo_planRepository_name=Jalview Gitlab\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-GDB663-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - develop\nbamboo_shortPlanKey=GDB663\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nbamboo_buildTimeStamp=2025-02-17T17:04:20.198Z\nbamboo_repository_previous_revision_number=637f19e96cfb28244fe2adb13e36d0cbe16dbe6c\nbamboo_planRepository_previousRevision=637f19e96cfb28244fe2adb13e36d0cbe16dbe6c\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-GDB663-JOB1-3\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - develop - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498281_revision_number=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nbamboo_repository_46498281_git_branch=develop\nbamboo_repository_name=Jalview Gitlab\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=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=637f19e96cfb28244fe2adb13e36d0cbe16dbe6c\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498281_previous_revision_number=637f19e96cfb28244fe2adb13e36d0cbe16dbe6c\nbamboo_repository_46498281_name=Jalview Gitlab\nbamboo_repository_46498281_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302147\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1\nbamboo_planKey=JB-GDB663\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 17-Feb-2025 17:19:23 444 build 17-Feb-2025 17:19:34 build 17-Feb-2025 17:19:34 > Configure project : build 17-Feb-2025 17:19:34 Using properties from file './utils/channels/default/channel_gradle.properties' build 17-Feb-2025 17:19:34 JALVIEW_VERSION is set to '2.11.4.2' build 17-Feb-2025 17:19:34 HEADLESS BUILD build 17-Feb-2025 17:19:34 J2S ENABLED build 17-Feb-2025 17:19:35 Using a LOCAL profile. build 17-Feb-2025 17:19:36 eclipseDir exists build 17-Feb-2025 17:19:39 build 17-Feb-2025 17:19:39 > Task :cloverHtmlReport build 17-Feb-2025 17:19:39 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 17-Feb-2025 17:19:40 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/reports/clover' error 17-Feb-2025 17:20:16 ERROR: Invalid Java source found or Clover failed to parse it: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/src/jalview/schemes/ResidueProperties.java build 17-Feb-2025 17:20:20 Done. Processed 116 packages in 40102ms (345ms per package). build 17-Feb-2025 17:20:25 build 17-Feb-2025 17:20:25 > Task :cloverXmlReport build 17-Feb-2025 17:20:25 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 17-Feb-2025 17:20:26 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/reports/clover/clover.xml' build 17-Feb-2025 17:20:26 build 17-Feb-2025 17:20:26 > Task :cloverReport build 17-Feb-2025 17:20:26 build 17-Feb-2025 17:20:26 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 17-Feb-2025 17:20:26 build 17-Feb-2025 17:20:26 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 17-Feb-2025 17:20:26 build 17-Feb-2025 17:20:26 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 17-Feb-2025 17:20:26 build 17-Feb-2025 17:20:26 BUILD SUCCESSFUL in 1m 2s build 17-Feb-2025 17:20:26 2 actionable tasks: 2 executed simple 17-Feb-2025 17:20:26 Finished task 'Clover Report' with result: Success simple 17-Feb-2025 17:20:26 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 17-Feb-2025 17:20:26 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1... simple 17-Feb-2025 17:20:26 Finished task 'TestNG Parser' with result: Success simple 17-Feb-2025 17:20:26 Running post build plugin 'NCover Results Collector' simple 17-Feb-2025 17:20:26 Running post build plugin 'Artifact Copier' simple 17-Feb-2025 17:20:26 Publishing an artifact: Clover Report (System) simple 17-Feb-2025 17:20:28 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.408 s simple 17-Feb-2025 17:20:28 Publishing an artifact: TestNG report error 17-Feb-2025 17:20:28 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB663-JOB1/build/reports/tests/test does not exist. simple 17-Feb-2025 17:20:28 The artifact hasn't been successfully published after 129.4 μs simple 17-Feb-2025 17:20:28 Running post build plugin 'Artifactory Release Management Staging' simple 17-Feb-2025 17:20:28 Running post build plugin 'Artifactory Build Info Copier' simple 17-Feb-2025 17:20:28 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 17-Feb-2025 17:20:28 Running post build plugin 'npm Cache Cleanup' simple 17-Feb-2025 17:20:28 Running post build plugin 'Clover Results Collector' simple 17-Feb-2025 17:20:28 Running post build plugin 'Docker Container Cleanup' simple 17-Feb-2025 17:20:28 Finalising the build... simple 17-Feb-2025 17:20:28 Stopping timer. simple 17-Feb-2025 17:20:28 Build JB-GDB663-JOB1-3 completed. simple 17-Feb-2025 17:20:28 Running on server: post build plugin 'NCover Results Collector' simple 17-Feb-2025 17:20:28 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 17-Feb-2025 17:20:28 Running on server: post build plugin 'Clover Delta Calculator' simple 17-Feb-2025 17:20:28 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 17-Feb-2025 17:20:28 All post build plugins have finished simple 17-Feb-2025 17:20:28 Generating build results summary... simple 17-Feb-2025 17:20:28 Saving build results to disk... simple 17-Feb-2025 17:20:28 Logging substituted variables... simple 17-Feb-2025 17:20:28 Indexing build results... simple 17-Feb-2025 17:20:28 Finished building JB-GDB663-JOB1-3.