Build: #1 failed
Job: Clover and Tests failed
Build log
The build generated 280 lines of output. Download or view full build log
| 12-Dec-2025 14:18:15 | Build Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS - Clover and Tests #1 (JB-GDB737-JOB1-1) started building on agent Default Agent |
| 12-Dec-2025 14:18:15 | |
| 12-Dec-2025 14:18:15 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1 |
| 12-Dec-2025 14:18:15 | Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS - Clover and Tests #1 (JB-GDB737-JOB1-1) |
| 12-Dec-2025 14:18:15 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 12-Dec-2025 14:18:15 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1 |
| 12-Dec-2025 14:18:15 | Updating source code to revision: 3525096f6402fa9e390d4d0ee6718bda9344ac3f |
| 12-Dec-2025 14:18:15 | Fetching 'refs/heads/bug/JAL-4623_JAL-4624_PCA_for_SS' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 12-Dec-2025 14:18:15 | Checking out revision 3525096f6402fa9e390d4d0ee6718bda9344ac3f. |
| 12-Dec-2025 14:18:15 | Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/.git'. |
| 12-Dec-2025 14:18:15 | Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1'... |
| 12-Dec-2025 14:18:15 | done. |
| 12-Dec-2025 14:18:21 | Switched to a new branch 'bug/JAL-4623_JAL-4624_PCA_for_SS' |
| 12-Dec-2025 14:18:21 | Branch bug/JAL-4623_JAL-4624_PCA_for_SS set up to track remote branch bug/JAL-4623_JAL-4624_PCA_for_SS from origin. |
| 12-Dec-2025 14:18:21 | Updated source code to revision: 3525096f6402fa9e390d4d0ee6718bda9344ac3f |
| 12-Dec-2025 14:18:21 | Finished task 'Checkout Default Repository' with result: Success |
| 12-Dec-2025 14:18:21 | Running pre-build action: VCS Version Collector |
| 12-Dec-2025 14:18:21 | Running pre-build action: Artifactory Release Staging |
| 12-Dec-2025 14:18:21 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 12-Dec-2025 14:18:21 | Bamboo Artifactory Plugin version: 2.6.2 |
| 12-Dec-2025 14:18:21 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS - Clover and Tests #1 (JB-GDB737-JOB1-1)' ... running command line: /home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_repository_revision_number=3525096f6402fa9e390d4d0ee6718bda9344ac3f bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB737-JOB1-1 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1 bamboo_repository_48168968_git_username= bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB737-JOB1 bamboo_shortPlanName=bug-JAL-4623_JAL-4624_PCA_for_SS bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=1 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB737-JOB1-1 bamboo_repository_48168968_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS bamboo_shortPlanKey=GDB737 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=3525096f6402fa9e390d4d0ee6718bda9344ac3f bamboo_buildTimeStamp=2025-12-12T14:18:15.262Z bamboo_repository_48168968_git_branch=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_repository_git_branch=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_buildResultKey=JB-GDB737-JOB1-1 bamboo_repository_branch_name=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_repository_48168968_branch_name=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=3525096f6402fa9e390d4d0ee6718bda9344ac3f SHLVL=1 bamboo_repository_48168968_revision_number=3525096f6402fa9e390d4d0ee6718bda9344ac3f bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Gitlab JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ LANG=en_GB.UTF-8 bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_repository_48168968_name=Jalview Gitlab bamboo_planRepository_branchDisplayName=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=bug/JAL-4623_JAL-4624_PCA_for_SS _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr bamboo_plan_storageTag=plan-47972367 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1 bamboo_planKey=JB-GDB737 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=bug/JAL-4623_JAL-4624_PCA_for_SS PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 12-Dec-2025 14:18:21 | 2414 |
| 12-Dec-2025 14:18:22 | Starting a Gradle Daemon (subsequent builds will be faster) |
| 12-Dec-2025 14:18:28 | |
| 12-Dec-2025 14:18:28 | > Configure project : |
| 12-Dec-2025 14:18:28 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 12-Dec-2025 14:18:28 | JALVIEW_VERSION is set to '2.11.5.1' |
| 12-Dec-2025 14:18:28 | HEADLESS BUILD |
| 12-Dec-2025 14:18:28 | J2S ENABLED |
| 12-Dec-2025 14:18:28 | Using a LOCAL profile. |
| 12-Dec-2025 14:18:29 | eclipseDir exists |
| 12-Dec-2025 14:18:29 | |
| 12-Dec-2025 14:18:29 | > Task :clean |
| 12-Dec-2025 14:18:29 | > Task :cleanClover |
| 12-Dec-2025 14:18:29 | > Task :cleanTest UP-TO-DATE |
| 12-Dec-2025 14:18:32 | |
| 12-Dec-2025 14:18:32 | > Task :cloverInstrJava |
| 12-Dec-2025 14:18:32 | Clover: About to instrument 1109 files |
| 12-Dec-2025 14:18:32 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 12-Dec-2025 14:18:32 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/clover/clover.db'. |
| 12-Dec-2025 14:18:32 | Processing files at 1.9 source level. |
| 12-Dec-2025 14:18:35 | 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? |
| 12-Dec-2025 14:18:35 | 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? |
| 12-Dec-2025 14:18:35 | 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? |
| 12-Dec-2025 14:18:35 | 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? |
| 12-Dec-2025 14:18:35 | 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? |
| 12-Dec-2025 14:18:35 | 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? |
| 12-Dec-2025 14:18:35 | 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? |
| 12-Dec-2025 14:18:41 | Clover all over. Instrumented 1109 files (113 packages). |
| 12-Dec-2025 14:18:43 | |
| 12-Dec-2025 14:18:43 | > Task :cloverInstrTests |
| 12-Dec-2025 14:18:43 | Clover: About to instrument test files |
| 12-Dec-2025 14:18:43 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 12-Dec-2025 14:18:43 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/clover/clover.db'. |
| 12-Dec-2025 14:18:43 | Processing files at 1.9 source level. |
| 12-Dec-2025 14:18:45 | Clover all over. Instrumented 293 files (52 packages). |
| 12-Dec-2025 14:18:45 | 1627 test methods detected. |
| 12-Dec-2025 14:18:45 | |
| 12-Dec-2025 14:18:45 | > Task :cloverInstr |
| 12-Dec-2025 14:18:48 | |
| 12-Dec-2025 14:18:48 | > Task :compileCloverJava |
| 12-Dec-2025 14:18:48 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 12-Dec-2025 14:18:48 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:18:48 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:18:48 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:18:48 | Setting target compatibility to 11 |
| 12-Dec-2025 14:19:08 | Note: Some input files use or override a deprecated API. |
| 12-Dec-2025 14:19:08 | Note: Recompile with -Xlint:deprecation for details. |
| 12-Dec-2025 14:19:08 | Note: Some input files use unchecked or unsafe operations. |
| 12-Dec-2025 14:19:08 | Note: Recompile with -Xlint:unchecked for details. |
| 12-Dec-2025 14:19:14 | |
| 12-Dec-2025 14:19:14 | > Task :processCloverResources NO-SOURCE |
| 12-Dec-2025 14:19:14 | > Task :cloverClasses |
| 12-Dec-2025 14:19:14 | > Task :copyHelp |
| 12-Dec-2025 14:19:15 | > Task :buildIndices |
| 12-Dec-2025 14:19:15 | > Task :copyResources |
| 12-Dec-2025 14:19:15 | > Task :copyChannelResources |
| 12-Dec-2025 14:19:15 | |
| 12-Dec-2025 14:19:15 | > Task :createBuildProperties |
| 12-Dec-2025 14:19:15 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 12-Dec-2025 14:19:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:19:15 | |
| 12-Dec-2025 14:19:15 | > Task :buildResources |
| 12-Dec-2025 14:19:15 | > Task :copyDocs |
| 12-Dec-2025 14:19:15 | |
| 12-Dec-2025 14:19:15 | > Task :convertMdFiles |
| 12-Dec-2025 14:19:15 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 12-Dec-2025 14:19:15 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 12-Dec-2025 14:19:15 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 12-Dec-2025 14:19:15 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/resources/doc_build/doc/building.html |
| 12-Dec-2025 14:19:15 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 12-Dec-2025 14:19:16 | |
| 12-Dec-2025 14:19:16 | > Task :releasesTemplates |
| 12-Dec-2025 14:19:16 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 12-Dec-2025 14:19:16 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:19:16 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:19:16 | Stripping rc/test/etc for TEST |
| 12-Dec-2025 14:19:16 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/help/markdown/whatsnew/whatsnew-TEST.md |
| 12-Dec-2025 14:19:16 | |
| 12-Dec-2025 14:19:16 | > Task :prepare |
| 12-Dec-2025 14:19:18 | |
| 12-Dec-2025 14:19:18 | > Task :compileJava |
| 12-Dec-2025 14:19:18 | Setting target compatibility to 11 |
| 12-Dec-2025 14:19:22 | Note: Some input files use or override a deprecated API. |
| 12-Dec-2025 14:19:22 | Note: Recompile with -Xlint:deprecation for details. |
| 12-Dec-2025 14:19:22 | Note: Some input files use unchecked or unsafe operations. |
| 12-Dec-2025 14:19:22 | Note: Recompile with -Xlint:unchecked for details. |
| 12-Dec-2025 14:19:26 | |
| 12-Dec-2025 14:19:26 | > Task :compileTestJava |
| 12-Dec-2025 14:19:26 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
| 12-Dec-2025 14:19:26 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:19:26 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:19:26 | Setting target compatibility to 11 |
| 12-Dec-2025 14:19:30 | Note: Some input files use or override a deprecated API. |
| 12-Dec-2025 14:19:30 | Note: Recompile with -Xlint:deprecation for details. |
| 12-Dec-2025 14:19:30 | Note: Some input files use unchecked or unsafe operations. |
| 12-Dec-2025 14:19:30 | Note: Recompile with -Xlint:unchecked for details. |
| 12-Dec-2025 14:19:31 | |
| 12-Dec-2025 14:19:31 | > Task :processTestResources |
| 12-Dec-2025 14:19:31 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
| 12-Dec-2025 14:19:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:19:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:19:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:19:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:19:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:19:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:19:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-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. |
| 12-Dec-2025 14:19:31 | |
| 12-Dec-2025 14:19:31 | > Task :testClasses |
| 12-Dec-2025 14:19:33 | |
| 12-Dec-2025 14:19:33 | > Task :testTask0 |
| 12-Dec-2025 14:19:33 | Running tests WITH clover |
| 12-Dec-2025 14:19:35 | WARNING: An illegal reflective access operation has occurred |
| 12-Dec-2025 14:19:35 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 12-Dec-2025 14:19:35 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 12-Dec-2025 14:19:35 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 12-Dec-2025 14:19:35 | WARNING: All illegal access operations will be denied in a future release |
| 12-Dec-2025 14:20:34 | |
| 12-Dec-2025 14:20:34 | Gradle suite > Gradle test > jalview.gui.StructureChooserTest.fetchStructuresInfoMockedTest FAILED |
| 12-Dec-2025 14:20:34 | java.lang.ArrayIndexOutOfBoundsException: 0 >= 0 |
| 12-Dec-2025 14:20:34 | at java.base/java.util.Vector.removeElementAt(Vector.java:580) |
| 12-Dec-2025 14:20:34 | at java.desktop/javax.swing.table.DefaultTableColumnModel.removeColumn(DefaultTableColumnModel.java:152) |
| 12-Dec-2025 14:20:34 | at java.desktop/javax.swing.JTable.createDefaultColumnsFromModel(JTable.java:1293) |
| 12-Dec-2025 14:20:34 | at java.desktop/javax.swing.JTable.tableChanged(JTable.java:4391) |
| 12-Dec-2025 14:20:34 | at java.desktop/javax.swing.JTable.setModel(JTable.java:3693) |
| 12-Dec-2025 14:20:34 | at jalview.gui.StructureChooser.fetchStructuresMetaData(StructureChooser.java:548) |
| 12-Dec-2025 14:20:34 | at jalview.gui.StructureChooserTest.__CLR4_4_1gzvl9m3t5e(StructureChooserTest.java:233) |
| 12-Dec-2025 14:20:34 | at jalview.gui.StructureChooserTest.fetchStructuresInfoMockedTest(StructureChooserTest.java:226) |
| 12-Dec-2025 14:23:32 | |
| 12-Dec-2025 14:23:32 | 1835 tests completed, 1 failed |
| 12-Dec-2025 14:23:32 | There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/tests/testTask0/index.html |
| 12-Dec-2025 14:23:34 | |
| 12-Dec-2025 14:23:34 | > Task :testTask1 |
| 12-Dec-2025 14:23:34 | Running tests WITH clover |
| 12-Dec-2025 14:23:35 | WARNING: An illegal reflective access operation has occurred |
| 12-Dec-2025 14:23:35 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 12-Dec-2025 14:23:35 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 12-Dec-2025 14:23:35 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 12-Dec-2025 14:23:35 | WARNING: All illegal access operations will be denied in a future release |
| 12-Dec-2025 14:25:36 | |
| 12-Dec-2025 14:25:36 | > Task :testTask2 |
| 12-Dec-2025 14:25:36 | Running tests WITH clover |
| 12-Dec-2025 14:25:39 | |
| 12-Dec-2025 14:25:39 | > Task :testTask3 |
| 12-Dec-2025 14:25:39 | Running tests WITH clover |
| 12-Dec-2025 14:25:40 | WARNING: An illegal reflective access operation has occurred |
| 12-Dec-2025 14:25:40 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 12-Dec-2025 14:25:40 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 12-Dec-2025 14:25:40 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 12-Dec-2025 14:25:40 | WARNING: All illegal access operations will be denied in a future release |
| 12-Dec-2025 14:26:25 | |
| 12-Dec-2025 14:26:25 | > Task :test NO-SOURCE |
| 12-Dec-2025 14:26:25 | ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ |
| 12-Dec-2025 14:26:25 | │jalview:testTask0 results: FAILURE (1835 tests, 1834 successes, 1 failures, 0 skipped) in 4 minutes, 0.498 seconds │ |
| 12-Dec-2025 14:26:25 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/tests/testTask0/index.html│ |
| 12-Dec-2025 14:26:25 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 12-Dec-2025 14:26:25 | │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 1.690 seconds │ |
| 12-Dec-2025 14:26:25 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/tests/testTask1/index.html│ |
| 12-Dec-2025 14:26:25 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 12-Dec-2025 14:26:25 | │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 2.933 seconds │ |
| 12-Dec-2025 14:26:25 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/tests/testTask2/index.html│ |
| 12-Dec-2025 14:26:25 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 12-Dec-2025 14:26:25 | │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 47.533 seconds │ |
| 12-Dec-2025 14:26:25 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/tests/testTask3/index.html│ |
| 12-Dec-2025 14:26:25 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 12-Dec-2025 14:26:25 | │OVERALL: results: FAILURE (1923 tests, 1922 successes, 1 failures, 0 skipped) in 6 minutes, 52.654 seconds │ |
| 12-Dec-2025 14:26:25 | └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ |
| 12-Dec-2025 14:26:25 | |
| 12-Dec-2025 14:26:25 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 12-Dec-2025 14:26:25 | |
| 12-Dec-2025 14:26:25 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 12-Dec-2025 14:26:25 | |
| 12-Dec-2025 14:26:25 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 12-Dec-2025 14:26:25 | |
| 12-Dec-2025 14:26:25 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 12-Dec-2025 14:26:25 | Please consult deprecation warnings for more details. |
| 12-Dec-2025 14:26:25 | 21 actionable tasks: 20 executed, 1 up-to-date |
| 12-Dec-2025 14:26:25 | |
| 12-Dec-2025 14:26:25 | FAILURE: Build failed with an exception. |
| 12-Dec-2025 14:26:25 | |
| 12-Dec-2025 14:26:25 | * Where: |
| 12-Dec-2025 14:26:25 | Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build.gradle' line: 1967 |
| 12-Dec-2025 14:26:25 | |
| 12-Dec-2025 14:26:25 | * What went wrong: |
| 12-Dec-2025 14:26:25 | Failed tests! |
| 12-Dec-2025 14:26:25 | |
| 12-Dec-2025 14:26:25 | * Try: |
| 12-Dec-2025 14:26:25 | > Run with --stacktrace option to get the stack trace. |
| 12-Dec-2025 14:26:25 | > Run with --info or --debug option to get more log output. |
| 12-Dec-2025 14:26:25 | > Run with --scan to get full insights. |
| 12-Dec-2025 14:26:25 | |
| 12-Dec-2025 14:26:25 | * Get more help at https://help.gradle.org |
| 12-Dec-2025 14:26:25 | |
| 12-Dec-2025 14:26:25 | BUILD FAILED in 8m 3s |
| 12-Dec-2025 14:26:25 | |
| 12-Dec-2025 14:26:25 | Failing task since return code of [/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test] was 1 while expected 0 |
| 12-Dec-2025 14:26:25 | Finished task 'Run tests with openclover under gradle' with result: Failed |
| 12-Dec-2025 14:26:25 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 12-Dec-2025 14:26:25 | Bamboo Artifactory Plugin version: 2.6.2 |
| 12-Dec-2025 14:26:25 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS - Clover and Tests #1 (JB-GDB737-JOB1-1)' ... running command line: /home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_repository_revision_number=3525096f6402fa9e390d4d0ee6718bda9344ac3f bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB737-JOB1-1 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1 bamboo_repository_48168968_git_username= bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB737-JOB1 bamboo_shortPlanName=bug-JAL-4623_JAL-4624_PCA_for_SS bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=1 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB737-JOB1-1 bamboo_repository_48168968_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS bamboo_shortPlanKey=GDB737 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=3525096f6402fa9e390d4d0ee6718bda9344ac3f bamboo_buildTimeStamp=2025-12-12T14:18:15.262Z bamboo_repository_48168968_git_branch=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_repository_git_branch=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_buildResultKey=JB-GDB737-JOB1-1 bamboo_repository_branch_name=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_repository_48168968_branch_name=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4623_JAL-4624_PCA_for_SS - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=3525096f6402fa9e390d4d0ee6718bda9344ac3f SHLVL=1 bamboo_repository_48168968_revision_number=3525096f6402fa9e390d4d0ee6718bda9344ac3f bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Gitlab bamboo_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 JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ LANG=en_GB.UTF-8 bamboo_buildFailed=true bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_jobFailed=true bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_repository_48168968_name=Jalview Gitlab bamboo_planRepository_branchDisplayName=bug/JAL-4623_JAL-4624_PCA_for_SS bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=bug/JAL-4623_JAL-4624_PCA_for_SS _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr bamboo_plan_storageTag=plan-47972367 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1 bamboo_planKey=JB-GDB737 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=bug/JAL-4623_JAL-4624_PCA_for_SS PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 12-Dec-2025 14:26:25 | 2414 |
| 12-Dec-2025 14:26:30 | |
| 12-Dec-2025 14:26:30 | > Configure project : |
| 12-Dec-2025 14:26:30 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 12-Dec-2025 14:26:30 | JALVIEW_VERSION is set to '2.11.5.1' |
| 12-Dec-2025 14:26:30 | HEADLESS BUILD |
| 12-Dec-2025 14:26:30 | J2S ENABLED |
| 12-Dec-2025 14:26:30 | Using a LOCAL profile. |
| 12-Dec-2025 14:26:31 | eclipseDir exists |
| 12-Dec-2025 14:26:33 | |
| 12-Dec-2025 14:26:33 | > Task :cloverHtmlReport |
| 12-Dec-2025 14:26:33 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 12-Dec-2025 14:26:34 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/clover' |
| 12-Dec-2025 14:27:18 | Done. Processed 117 packages in 44528ms (380ms per package). |
| 12-Dec-2025 14:27:23 | |
| 12-Dec-2025 14:27:23 | > Task :cloverXmlReport |
| 12-Dec-2025 14:27:23 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 12-Dec-2025 14:27:24 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/clover/clover.xml' |
| 12-Dec-2025 14:27:24 | |
| 12-Dec-2025 14:27:24 | > Task :cloverReport |
| 12-Dec-2025 14:27:24 | |
| 12-Dec-2025 14:27:24 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 12-Dec-2025 14:27:24 | |
| 12-Dec-2025 14:27:24 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 12-Dec-2025 14:27:24 | |
| 12-Dec-2025 14:27:24 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 12-Dec-2025 14:27:24 | |
| 12-Dec-2025 14:27:24 | BUILD SUCCESSFUL in 58s |
| 12-Dec-2025 14:27:24 | 2 actionable tasks: 2 executed |
| 12-Dec-2025 14:27:24 | Finished task 'Clover Report' with result: Success |
| 12-Dec-2025 14:27:24 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 12-Dec-2025 14:27:24 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1... |
| 12-Dec-2025 14:27:24 | Failing task since 1 failing test cases were found. |
| 12-Dec-2025 14:27:24 | Finished task 'TestNG Parser' with result: Failed |
| 12-Dec-2025 14:27:24 | Running post build plugin 'NCover Results Collector' |
| 12-Dec-2025 14:27:24 | Running post build plugin 'Artifact Copier' |
| 12-Dec-2025 14:27:24 | Publishing an artifact: Clover Report (System) |
| 12-Dec-2025 14:27:27 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.430 s |
| 12-Dec-2025 14:27:27 | Publishing an artifact: TestNG report |
| 12-Dec-2025 14:27:27 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB737-JOB1/build/reports/tests/test does not exist. |
| 12-Dec-2025 14:27:27 | The artifact hasn't been successfully published after 1.332 ms |
| 12-Dec-2025 14:27:27 | Running post build plugin 'Artifactory Release Management Staging' |
| 12-Dec-2025 14:27:27 | Running post build plugin 'Artifactory Build Info Copier' |
| 12-Dec-2025 14:27:27 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 12-Dec-2025 14:27:27 | Running post build plugin 'npm Cache Cleanup' |
| 12-Dec-2025 14:27:27 | Running post build plugin 'Clover Results Collector' |
| 12-Dec-2025 14:27:27 | Running post build plugin 'Docker Container Cleanup' |
| 12-Dec-2025 14:27:27 | Finalising the build... |
| 12-Dec-2025 14:27:27 | Stopping timer. |
| 12-Dec-2025 14:27:27 | Build JB-GDB737-JOB1-1 completed. |
| 12-Dec-2025 14:27:27 | Running on server: post build plugin 'NCover Results Collector' |
| 12-Dec-2025 14:27:27 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 12-Dec-2025 14:27:27 | Running on server: post build plugin 'Clover Delta Calculator' |
| 12-Dec-2025 14:27:27 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 12-Dec-2025 14:27:27 | All post build plugins have finished |
| 12-Dec-2025 14:27:27 | Generating build results summary... |
| 12-Dec-2025 14:27:27 | Saving build results to disk... |
| 12-Dec-2025 14:27:27 | Logging substituted variables... |
| 12-Dec-2025 14:27:27 | Indexing build results... |
| 12-Dec-2025 14:27:27 | Finished building JB-GDB737-JOB1-1. |