Build: #1 was successful
Job: Clover and Tests was successful
Build log
The build generated 508 lines of output. Download or view full build log
| 25-Mar-2026 16:53:02 | Build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-JOB1-1) started building on agent Default Agent |
| 25-Mar-2026 16:53:02 | |
| 25-Mar-2026 16:53:02 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1 |
| 25-Mar-2026 16:53:02 | Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-JOB1-1) |
| 25-Mar-2026 16:53:02 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 25-Mar-2026 16:53:02 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1 |
| 25-Mar-2026 16:53:02 | Updating source code to revision: 570cfd128c945bc7593ad75c31b9761ff81f5fee |
| 25-Mar-2026 16:53:02 | Fetching 'refs/heads/patch/JAL-4410_multimers_from_3dbeacons' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 25-Mar-2026 16:53:03 | Checking out revision 570cfd128c945bc7593ad75c31b9761ff81f5fee. |
| 25-Mar-2026 16:53:03 | Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/.git'. |
| 25-Mar-2026 16:53:03 | Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1'... |
| 25-Mar-2026 16:53:03 | done. |
| 25-Mar-2026 16:53:09 | Switched to a new branch 'patch/JAL-4410_multimers_from_3dbeacons' |
| 25-Mar-2026 16:53:09 | Branch patch/JAL-4410_multimers_from_3dbeacons set up to track remote branch patch/JAL-4410_multimers_from_3dbeacons from origin. |
| 25-Mar-2026 16:53:09 | Updated source code to revision: 570cfd128c945bc7593ad75c31b9761ff81f5fee |
| 25-Mar-2026 16:53:09 | Finished task 'Checkout Default Repository' with result: Success |
| 25-Mar-2026 16:53:09 | Running pre-build action: VCS Version Collector |
| 25-Mar-2026 16:53:09 | Running pre-build action: Artifactory Release Staging |
| 25-Mar-2026 16:53:09 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 25-Mar-2026 16:53:09 | Bamboo Artifactory Plugin version: 2.6.2 |
| 25-Mar-2026 16:53:09 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-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-GDB749-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons bamboo_repository_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-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-GDB749-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB749-JOB1 bamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons 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_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-1 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons bamboo_shortPlanKey=GDB749 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee bamboo_buildTimeStamp=2026-03-25T16:53:02.888Z bamboo_repository_48169043_name=Jalview Gitlab bamboo_repository_git_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_buildResultKey=JB-GDB749-JOB1-1 bamboo_repository_branch_name=patch/JAL-4410_multimers_from_3dbeacons bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee SHLVL=1 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=patch/JAL-4410_multimers_from_3dbeacons bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_48169043_git_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_repository_git_username= bamboo_planRepository_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=patch/JAL-4410_multimers_from_3dbeacons _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_repository_48169043_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee bamboo_capability_system_builderivy_Ivy=/usr bamboo_repository_48169043_git_username= bamboo_plan_storageTag=plan-47972517 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-GDB749-JOB1 bamboo_planKey=JB-GDB749 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=patch/JAL-4410_multimers_from_3dbeacons PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 25-Mar-2026 16:53:09 | 2414 |
| 25-Mar-2026 16:53:10 | Starting a Gradle Daemon (subsequent builds will be faster) |
| 25-Mar-2026 16:53:20 | |
| 25-Mar-2026 16:53:20 | > Configure project : |
| 25-Mar-2026 16:53:20 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 25-Mar-2026 16:53:20 | JALVIEW_VERSION is set to '2.11.5.1' |
| 25-Mar-2026 16:53:20 | HEADLESS BUILD |
| 25-Mar-2026 16:53:20 | J2S ENABLED |
| 25-Mar-2026 16:53:20 | Using a LOCAL profile. |
| 25-Mar-2026 16:53:21 | eclipseDir exists |
| 25-Mar-2026 16:53:21 | |
| 25-Mar-2026 16:53:21 | > Task :clean |
| 25-Mar-2026 16:53:21 | > Task :cleanClover |
| 25-Mar-2026 16:53:21 | > Task :cleanTest UP-TO-DATE |
| 25-Mar-2026 16:53:23 | |
| 25-Mar-2026 16:53:23 | > Task :cloverInstrJava |
| 25-Mar-2026 16:53:23 | Clover: About to instrument 1110 files |
| 25-Mar-2026 16:53:24 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 25-Mar-2026 16:53:24 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'. |
| 25-Mar-2026 16:53:24 | Processing files at 1.9 source level. |
| 25-Mar-2026 16:53:27 | 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? |
| 25-Mar-2026 16:53:27 | 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? |
| 25-Mar-2026 16:53:27 | 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? |
| 25-Mar-2026 16:53:27 | 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? |
| 25-Mar-2026 16:53:27 | 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? |
| 25-Mar-2026 16:53:27 | 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? |
| 25-Mar-2026 16:53:27 | 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? |
| 25-Mar-2026 16:53:33 | Clover all over. Instrumented 1110 files (113 packages). |
| 25-Mar-2026 16:53:35 | |
| 25-Mar-2026 16:53:35 | > Task :cloverInstrTests |
| 25-Mar-2026 16:53:35 | Clover: About to instrument test files |
| 25-Mar-2026 16:53:35 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 25-Mar-2026 16:53:35 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'. |
| 25-Mar-2026 16:53:35 | Processing files at 1.9 source level. |
| 25-Mar-2026 16:53:37 | Clover all over. Instrumented 293 files (52 packages). |
| 25-Mar-2026 16:53:37 | 1627 test methods detected. |
| 25-Mar-2026 16:53:37 | |
| 25-Mar-2026 16:53:37 | > Task :cloverInstr |
| 25-Mar-2026 16:53:41 | |
| 25-Mar-2026 16:53:41 | > Task :compileCloverJava |
| 25-Mar-2026 16:53:41 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 25-Mar-2026 16:53:41 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:53:41 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:53:41 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:53:41 | Setting target compatibility to 11 |
| 25-Mar-2026 16:54:01 | Note: Some input files use or override a deprecated API. |
| 25-Mar-2026 16:54:01 | Note: Recompile with -Xlint:deprecation for details. |
| 25-Mar-2026 16:54:01 | Note: Some input files use unchecked or unsafe operations. |
| 25-Mar-2026 16:54:01 | Note: Recompile with -Xlint:unchecked for details. |
| 25-Mar-2026 16:54:08 | |
| 25-Mar-2026 16:54:08 | > Task :processCloverResources NO-SOURCE |
| 25-Mar-2026 16:54:08 | > Task :cloverClasses |
| 25-Mar-2026 16:54:09 | > Task :copyHelp |
| 25-Mar-2026 16:54:10 | > Task :buildIndices |
| 25-Mar-2026 16:54:10 | > Task :copyResources |
| 25-Mar-2026 16:54:10 | > Task :copyChannelResources |
| 25-Mar-2026 16:54:10 | |
| 25-Mar-2026 16:54:10 | > Task :createBuildProperties |
| 25-Mar-2026 16:54:10 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 25-Mar-2026 16:54:10 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:54:10 | |
| 25-Mar-2026 16:54:10 | > Task :buildResources |
| 25-Mar-2026 16:54:10 | > Task :copyDocs |
| 25-Mar-2026 16:54:10 | |
| 25-Mar-2026 16:54:10 | > Task :convertMdFiles |
| 25-Mar-2026 16:54:10 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 25-Mar-2026 16:54:10 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 25-Mar-2026 16:54:10 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 25-Mar-2026 16:54:10 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/building.html |
| 25-Mar-2026 16:54:10 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 25-Mar-2026 16:54:11 | |
| 25-Mar-2026 16:54:11 | > Task :releasesTemplates |
| 25-Mar-2026 16:54:11 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 25-Mar-2026 16:54:11 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:54:11 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:54:11 | Stripping rc/test/etc for TEST |
| 25-Mar-2026 16:54:11 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/help/markdown/whatsnew/whatsnew-TEST.md |
| 25-Mar-2026 16:54:11 | |
| 25-Mar-2026 16:54:11 | > Task :prepare |
| 25-Mar-2026 16:54:13 | |
| 25-Mar-2026 16:54:13 | > Task :compileJava |
| 25-Mar-2026 16:54:13 | Setting target compatibility to 11 |
| 25-Mar-2026 16:54:18 | Note: Some input files use or override a deprecated API. |
| 25-Mar-2026 16:54:18 | Note: Recompile with -Xlint:deprecation for details. |
| 25-Mar-2026 16:54:18 | Note: Some input files use unchecked or unsafe operations. |
| 25-Mar-2026 16:54:18 | Note: Recompile with -Xlint:unchecked for details. |
| 25-Mar-2026 16:54:23 | |
| 25-Mar-2026 16:54:23 | > Task :compileTestJava |
| 25-Mar-2026 16:54:23 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
| 25-Mar-2026 16:54:23 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:54:23 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:54:23 | Setting target compatibility to 11 |
| 25-Mar-2026 16:54:26 | Note: Some input files use or override a deprecated API. |
| 25-Mar-2026 16:54:26 | Note: Recompile with -Xlint:deprecation for details. |
| 25-Mar-2026 16:54:26 | Note: Some input files use unchecked or unsafe operations. |
| 25-Mar-2026 16:54:26 | Note: Recompile with -Xlint:unchecked for details. |
| 25-Mar-2026 16:54:28 | |
| 25-Mar-2026 16:54:28 | > Task :processTestResources |
| 25-Mar-2026 16:54:28 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
| 25-Mar-2026 16:54:28 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:54:28 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:54:28 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:54:28 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:54:28 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:54:28 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:54:28 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 25-Mar-2026 16:54:28 | |
| 25-Mar-2026 16:54:28 | > Task :testClasses |
| 25-Mar-2026 16:54:30 | |
| 25-Mar-2026 16:54:30 | > Task :testTask0 |
| 25-Mar-2026 16:54:30 | Running tests WITH clover |
| 25-Mar-2026 16:54:32 | WARNING: An illegal reflective access operation has occurred |
| 25-Mar-2026 16:54:32 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 25-Mar-2026 16:54:32 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 25-Mar-2026 16:54:32 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 25-Mar-2026 16:54:32 | WARNING: All illegal access operations will be denied in a future release |
| 25-Mar-2026 16:55:25 | |
| 25-Mar-2026 16:55:25 | Gradle suite > Gradle test > jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy FAILED |
| 25-Mar-2026 16:55:25 | java.lang.AssertionError: Expected occupancy to be non-null in column 5 expected object to not be null |
| 25-Mar-2026 16:55:25 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Mar-2026 16:55:25 | at org.testng.Assert.assertNotNull(Assert.java:406) |
| 25-Mar-2026 16:55:25 | at jalview.gui.AlignViewportTest.__CLR4_4_1lfq8443uvh(AlignViewportTest.java:478) |
| 25-Mar-2026 16:55:25 | at jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy(AlignViewportTest.java:446) |
| 25-Mar-2026 17:09:28 | Requesting stop of task ':testTask0' as it has exceeded its configured timeout of 15m. |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | > Task :testTask0 FAILED |
| 25-Mar-2026 17:09:28 | ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ |
| 25-Mar-2026 17:09:28 | │jalview:testTask0 results: FAILURE (975 tests, 973 successes, 1 failures, 1 skipped) in 14 minutes, 59.937 seconds │ |
| 25-Mar-2026 17:09:28 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask0/index.html│ |
| 25-Mar-2026 17:09:28 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 25-Mar-2026 17:09:28 | │OVERALL: results: FAILURE (975 tests, 973 successes, 1 failures, 1 skipped) in 14 minutes, 59.937 seconds │ |
| 25-Mar-2026 17:09:28 | └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 25-Mar-2026 17:09:28 | Please consult deprecation warnings for more details. |
| 25-Mar-2026 17:09:28 | 18 actionable tasks: 17 executed, 1 up-to-date |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | 975 tests completed, 1 failed, 1 skipped |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | FAILURE: Build completed with 2 failures. |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | 1: Task failed with an exception. |
| 25-Mar-2026 17:09:28 | ----------- |
| 25-Mar-2026 17:09:28 | * What went wrong: |
| 25-Mar-2026 17:09:28 | Execution failed for task ':testTask0'. |
| 25-Mar-2026 17:09:28 | > Timeout has been exceeded |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | * Try: |
| 25-Mar-2026 17:09:28 | > Run with --stacktrace option to get the stack trace. |
| 25-Mar-2026 17:09:28 | > Run with --info or --debug option to get more log output. |
| 25-Mar-2026 17:09:28 | > Run with --scan to get full insights. |
| 25-Mar-2026 17:09:28 | ============================================================================== |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | 2: Task failed with an exception. |
| 25-Mar-2026 17:09:28 | ----------- |
| 25-Mar-2026 17:09:28 | * Where: |
| 25-Mar-2026 17:09:28 | Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build.gradle' line: 1967 |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | * What went wrong: |
| 25-Mar-2026 17:09:28 | Failed tests! |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | * Try: |
| 25-Mar-2026 17:09:28 | > Run with --stacktrace option to get the stack trace. |
| 25-Mar-2026 17:09:28 | > Run with --info or --debug option to get more log output. |
| 25-Mar-2026 17:09:28 | > Run with --scan to get full insights. |
| 25-Mar-2026 17:09:28 | ============================================================================== |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | * Get more help at https://help.gradle.org |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | BUILD FAILED in 16m 18s |
| 25-Mar-2026 17:09:28 | |
| 25-Mar-2026 17:09:28 | 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 |
| 25-Mar-2026 17:09:28 | Finished task 'Run tests with openclover under gradle' with result: Failed |
| 25-Mar-2026 17:09:28 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 25-Mar-2026 17:09:28 | Bamboo Artifactory Plugin version: 2.6.2 |
| 25-Mar-2026 17:09:28 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-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-GDB749-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons bamboo_repository_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-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-GDB749-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB749-JOB1 bamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons 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_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-1 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons bamboo_shortPlanKey=GDB749 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee bamboo_buildTimeStamp=2026-03-25T16:53:02.888Z bamboo_repository_48169043_name=Jalview Gitlab bamboo_repository_git_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_buildResultKey=JB-GDB749-JOB1-1 bamboo_repository_branch_name=patch/JAL-4410_multimers_from_3dbeacons bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee SHLVL=1 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=patch/JAL-4410_multimers_from_3dbeacons bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_jobFailed=true bamboo_capability_system_git_executable=/bin/git bamboo_repository_48169043_git_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_repository_git_username= bamboo_planRepository_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=patch/JAL-4410_multimers_from_3dbeacons _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_repository_48169043_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee bamboo_capability_system_builderivy_Ivy=/usr bamboo_repository_48169043_git_username= bamboo_plan_storageTag=plan-47972517 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-GDB749-JOB1 bamboo_planKey=JB-GDB749 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=patch/JAL-4410_multimers_from_3dbeacons PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 25-Mar-2026 17:09:28 | 2414 |
| 25-Mar-2026 17:09:33 | |
| 25-Mar-2026 17:09:33 | > Configure project : |
| 25-Mar-2026 17:09:33 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 25-Mar-2026 17:09:33 | JALVIEW_VERSION is set to '2.11.5.1' |
| 25-Mar-2026 17:09:33 | HEADLESS BUILD |
| 25-Mar-2026 17:09:33 | J2S ENABLED |
| 25-Mar-2026 17:09:34 | Using a LOCAL profile. |
| 25-Mar-2026 17:09:34 | eclipseDir exists |
| 25-Mar-2026 17:09:37 | |
| 25-Mar-2026 17:09:37 | > Task :cloverHtmlReport |
| 25-Mar-2026 17:09:37 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 25-Mar-2026 17:09:37 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/clover' |
| 25-Mar-2026 17:10:05 | Done. Processed 117 packages in 27582ms (235ms per package). |
| 25-Mar-2026 17:10:09 | |
| 25-Mar-2026 17:10:09 | > Task :cloverXmlReport |
| 25-Mar-2026 17:10:09 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 25-Mar-2026 17:10:10 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/clover/clover.xml' |
| 25-Mar-2026 17:10:10 | |
| 25-Mar-2026 17:10:10 | > Task :cloverReport |
| 25-Mar-2026 17:10:10 | |
| 25-Mar-2026 17:10:10 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 25-Mar-2026 17:10:10 | |
| 25-Mar-2026 17:10:10 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 25-Mar-2026 17:10:10 | |
| 25-Mar-2026 17:10:10 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 25-Mar-2026 17:10:10 | |
| 25-Mar-2026 17:10:10 | BUILD SUCCESSFUL in 41s |
| 25-Mar-2026 17:10:10 | 2 actionable tasks: 2 executed |
| 25-Mar-2026 17:10:10 | Finished task 'Clover Report' with result: Success |
| 25-Mar-2026 17:10:10 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 25-Mar-2026 17:10:10 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1... |
| 25-Mar-2026 17:10:10 | Failing task since test cases were expected but none were found. |
| 25-Mar-2026 17:10:10 | Finished task 'TestNG Parser' with result: Failed |
| 25-Mar-2026 17:10:10 | Running post build plugin 'NCover Results Collector' |
| 25-Mar-2026 17:10:10 | Running post build plugin 'Artifact Copier' |
| 25-Mar-2026 17:10:10 | Publishing an artifact: Clover Report (System) |
| 25-Mar-2026 17:10:11 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.421 s |
| 25-Mar-2026 17:10:11 | Publishing an artifact: TestNG report |
| 25-Mar-2026 17:10:11 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/test does not exist. |
| 25-Mar-2026 17:10:11 | The artifact hasn't been successfully published after 2.510 ms |
| 25-Mar-2026 17:10:11 | Running post build plugin 'Artifactory Release Management Staging' |
| 25-Mar-2026 17:10:11 | Running post build plugin 'Artifactory Build Info Copier' |
| 25-Mar-2026 17:10:11 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 25-Mar-2026 17:10:11 | Running post build plugin 'npm Cache Cleanup' |
| 25-Mar-2026 17:10:11 | Running post build plugin 'Clover Results Collector' |
| 25-Mar-2026 17:10:11 | Running post build plugin 'Docker Container Cleanup' |
| 25-Mar-2026 17:10:11 | Finalising the build... |
| 25-Mar-2026 17:10:11 | Stopping timer. |
| 25-Mar-2026 17:10:11 | Build JB-GDB749-JOB1-1 completed. |
| 25-Mar-2026 17:10:11 | Running on server: post build plugin 'NCover Results Collector' |
| 25-Mar-2026 17:10:11 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 25-Mar-2026 17:10:11 | Running on server: post build plugin 'Clover Delta Calculator' |
| 25-Mar-2026 17:10:11 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 25-Mar-2026 17:10:11 | All post build plugins have finished |
| 25-Mar-2026 17:10:11 | Generating build results summary... |
| 25-Mar-2026 17:10:11 | Saving build results to disk... |
| 25-Mar-2026 17:10:11 | Logging substituted variables... |
| 25-Mar-2026 17:10:11 | Indexing build results... |
| 25-Mar-2026 17:10:11 | Finished building JB-GDB749-JOB1-1. |
| 26-Mar-2026 08:01:21 | Build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-JOB1-1) started building on agent Default Agent |
| 26-Mar-2026 08:01:21 | |
| 26-Mar-2026 08:01:21 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1 |
| 26-Mar-2026 08:01:21 | Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-JOB1-1) |
| 26-Mar-2026 08:01:21 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 26-Mar-2026 08:01:21 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1 |
| 26-Mar-2026 08:01:21 | Updating source code to revision: 570cfd128c945bc7593ad75c31b9761ff81f5fee |
| 26-Mar-2026 08:01:21 | Fetching 'refs/heads/patch/JAL-4410_multimers_from_3dbeacons' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 26-Mar-2026 08:01:22 | Checking out revision 570cfd128c945bc7593ad75c31b9761ff81f5fee. |
| 26-Mar-2026 08:01:23 | Already on 'patch/JAL-4410_multimers_from_3dbeacons' |
| 26-Mar-2026 08:01:23 | Updated source code to revision: 570cfd128c945bc7593ad75c31b9761ff81f5fee |
| 26-Mar-2026 08:01:23 | Finished task 'Checkout Default Repository' with result: Success |
| 26-Mar-2026 08:01:23 | Running pre-build action: VCS Version Collector |
| 26-Mar-2026 08:01:23 | Running pre-build action: Artifactory Release Staging |
| 26-Mar-2026 08:01:23 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 26-Mar-2026 08:01:23 | Bamboo Artifactory Plugin version: 2.6.2 |
| 26-Mar-2026 08:01:23 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-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-GDB749-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons bamboo_repository_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee bamboo_CLOVER_ELEMENTS=171386 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-1 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_CLOVER_BUILD_COVERAGE=29.3 bamboo_CLOVER_CLASSES=1419 bamboo_CLOVER_METHODS=16228 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB749-JOB1 bamboo_CLOVER_COVERED_STATEMENTS=33560 bamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons bamboo_planRepository_name=Jalview Gitlab bamboo_CLOVER_COVERED_CONDITIONALS=11321 LOGNAME=bamboo bamboo_buildNumber=1 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-1 bamboo_CLOVER_STATEMENTS=112778 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_ManualBuildTriggerReason_stageName=Default Stage bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons bamboo_shortPlanKey=GDB749 bamboo_shortJobKey=JOB1 bamboo_CLOVER_NCLOC=269847 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee bamboo_buildTimeStamp=2026-03-26T08:01:21.888Z bamboo_repository_48169043_name=Jalview Gitlab bamboo_CLOVER_COVERED_METHODS=5339 bamboo_CLOVER_CONDITIONALS=42380 bamboo_repository_git_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_buildResultKey=JB-GDB749-JOB1-1 bamboo_repository_branch_name=patch/JAL-4410_multimers_from_3dbeacons bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_4=/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport 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/ bamboo_CLOVER_PACKAGES=115 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=patch/JAL-4410_multimers_from_3dbeacons bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_48169043_git_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_repository_git_username= bamboo_planRepository_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=patch/JAL-4410_multimers_from_3dbeacons _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_repository_48169043_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee bamboo_capability_system_builderivy_Ivy=/usr bamboo_repository_48169043_git_username= bamboo_plan_storageTag=plan-47972517 bamboo_CLOVER_LOC=427989 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_CLOVER_FILES=1123 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_ManualBuildTriggerReason_userName=jprocter bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_CLOVER_COVERED_ELEMENTS=50220 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-GDB749-JOB1 bamboo_planKey=JB-GDB749 bamboo_RerunBuildTriggerReason_noOfRetries=1 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=patch/JAL-4410_multimers_from_3dbeacons PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 26-Mar-2026 08:01:23 | 2414 |
| 26-Mar-2026 08:01:24 | Starting a Gradle Daemon (subsequent builds will be faster) |
| 26-Mar-2026 08:01:30 | |
| 26-Mar-2026 08:01:30 | > Configure project : |
| 26-Mar-2026 08:01:30 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 26-Mar-2026 08:01:30 | JALVIEW_VERSION is set to '2.11.5.1' |
| 26-Mar-2026 08:01:30 | HEADLESS BUILD |
| 26-Mar-2026 08:01:30 | J2S ENABLED |
| 26-Mar-2026 08:01:30 | Using a LOCAL profile. |
| 26-Mar-2026 08:01:31 | eclipseDir exists |
| 26-Mar-2026 08:01:32 | |
| 26-Mar-2026 08:01:32 | > Task :clean |
| 26-Mar-2026 08:01:32 | > Task :cleanClover |
| 26-Mar-2026 08:01:32 | > Task :cleanTest UP-TO-DATE |
| 26-Mar-2026 08:01:34 | |
| 26-Mar-2026 08:01:34 | > Task :cloverInstrJava |
| 26-Mar-2026 08:01:34 | Clover: About to instrument 1110 files |
| 26-Mar-2026 08:01:34 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 26-Mar-2026 08:01:34 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'. |
| 26-Mar-2026 08:01:34 | Processing files at 1.9 source level. |
| 26-Mar-2026 08:01:36 | 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? |
| 26-Mar-2026 08:01:36 | 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? |
| 26-Mar-2026 08:01:36 | 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? |
| 26-Mar-2026 08:01:36 | 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? |
| 26-Mar-2026 08:01:36 | 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? |
| 26-Mar-2026 08:01:36 | 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? |
| 26-Mar-2026 08:01:36 | 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? |
| 26-Mar-2026 08:01:42 | Clover all over. Instrumented 1110 files (113 packages). |
| 26-Mar-2026 08:01:45 | |
| 26-Mar-2026 08:01:45 | > Task :cloverInstrTests |
| 26-Mar-2026 08:01:45 | Clover: About to instrument test files |
| 26-Mar-2026 08:01:45 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 26-Mar-2026 08:01:45 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'. |
| 26-Mar-2026 08:01:45 | Processing files at 1.9 source level. |
| 26-Mar-2026 08:01:47 | Clover all over. Instrumented 293 files (52 packages). |
| 26-Mar-2026 08:01:47 | 1627 test methods detected. |
| 26-Mar-2026 08:01:47 | |
| 26-Mar-2026 08:01:47 | > Task :cloverInstr |
| 26-Mar-2026 08:01:49 | |
| 26-Mar-2026 08:01:49 | > Task :compileCloverJava |
| 26-Mar-2026 08:01:49 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 26-Mar-2026 08:01:49 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:01:49 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:01:49 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:01:49 | Setting target compatibility to 11 |
| 26-Mar-2026 08:02:10 | Note: Some input files use or override a deprecated API. |
| 26-Mar-2026 08:02:10 | Note: Recompile with -Xlint:deprecation for details. |
| 26-Mar-2026 08:02:10 | Note: Some input files use unchecked or unsafe operations. |
| 26-Mar-2026 08:02:10 | Note: Recompile with -Xlint:unchecked for details. |
| 26-Mar-2026 08:02:16 | |
| 26-Mar-2026 08:02:16 | > Task :processCloverResources NO-SOURCE |
| 26-Mar-2026 08:02:16 | > Task :cloverClasses |
| 26-Mar-2026 08:02:17 | > Task :copyHelp |
| 26-Mar-2026 08:02:18 | > Task :buildIndices |
| 26-Mar-2026 08:02:18 | > Task :copyResources |
| 26-Mar-2026 08:02:18 | > Task :copyChannelResources |
| 26-Mar-2026 08:02:18 | |
| 26-Mar-2026 08:02:18 | > Task :createBuildProperties |
| 26-Mar-2026 08:02:18 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 26-Mar-2026 08:02:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:02:18 | |
| 26-Mar-2026 08:02:18 | > Task :buildResources |
| 26-Mar-2026 08:02:18 | > Task :copyDocs |
| 26-Mar-2026 08:02:18 | |
| 26-Mar-2026 08:02:18 | > Task :convertMdFiles |
| 26-Mar-2026 08:02:18 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 26-Mar-2026 08:02:18 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 26-Mar-2026 08:02:18 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 26-Mar-2026 08:02:18 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/building.html |
| 26-Mar-2026 08:02:18 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 26-Mar-2026 08:02:19 | |
| 26-Mar-2026 08:02:19 | > Task :releasesTemplates |
| 26-Mar-2026 08:02:19 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 26-Mar-2026 08:02:19 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:02:19 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:02:19 | Stripping rc/test/etc for TEST |
| 26-Mar-2026 08:02:19 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/help/markdown/whatsnew/whatsnew-TEST.md |
| 26-Mar-2026 08:02:19 | |
| 26-Mar-2026 08:02:19 | > Task :prepare |
| 26-Mar-2026 08:02:21 | |
| 26-Mar-2026 08:02:21 | > Task :compileJava |
| 26-Mar-2026 08:02:21 | Setting target compatibility to 11 |
| 26-Mar-2026 08:02:26 | Note: Some input files use or override a deprecated API. |
| 26-Mar-2026 08:02:26 | Note: Recompile with -Xlint:deprecation for details. |
| 26-Mar-2026 08:02:26 | Note: Some input files use unchecked or unsafe operations. |
| 26-Mar-2026 08:02:26 | Note: Recompile with -Xlint:unchecked for details. |
| 26-Mar-2026 08:02:30 | |
| 26-Mar-2026 08:02:30 | > Task :compileTestJava |
| 26-Mar-2026 08:02:30 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
| 26-Mar-2026 08:02:30 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:02:30 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:02:30 | Setting target compatibility to 11 |
| 26-Mar-2026 08:02:34 | Note: Some input files use or override a deprecated API. |
| 26-Mar-2026 08:02:34 | Note: Recompile with -Xlint:deprecation for details. |
| 26-Mar-2026 08:02:34 | Note: Some input files use unchecked or unsafe operations. |
| 26-Mar-2026 08:02:34 | Note: Recompile with -Xlint:unchecked for details. |
| 26-Mar-2026 08:02:35 | |
| 26-Mar-2026 08:02:35 | > Task :processTestResources |
| 26-Mar-2026 08:02:35 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
| 26-Mar-2026 08:02:35 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:02:35 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:02:35 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:02:35 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:02:35 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:02:35 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:02:35 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:02:35 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 26-Mar-2026 08:02:35 | |
| 26-Mar-2026 08:02:35 | > Task :testClasses |
| 26-Mar-2026 08:02:37 | |
| 26-Mar-2026 08:02:37 | > Task :testTask0 |
| 26-Mar-2026 08:02:37 | Running tests WITH clover |
| 26-Mar-2026 08:02:39 | WARNING: An illegal reflective access operation has occurred |
| 26-Mar-2026 08:02:39 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 26-Mar-2026 08:02:39 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 26-Mar-2026 08:02:39 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 26-Mar-2026 08:02:39 | WARNING: All illegal access operations will be denied in a future release |
| 26-Mar-2026 08:06:56 | |
| 26-Mar-2026 08:06:56 | > Task :testTask1 |
| 26-Mar-2026 08:06:56 | Running tests WITH clover |
| 26-Mar-2026 08:06:57 | WARNING: An illegal reflective access operation has occurred |
| 26-Mar-2026 08:06:57 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 26-Mar-2026 08:06:57 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 26-Mar-2026 08:06:57 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 26-Mar-2026 08:06:57 | WARNING: All illegal access operations will be denied in a future release |
| 26-Mar-2026 08:09:15 | |
| 26-Mar-2026 08:09:15 | > Task :testTask2 |
| 26-Mar-2026 08:09:15 | Running tests WITH clover |
| 26-Mar-2026 08:09:18 | |
| 26-Mar-2026 08:09:18 | > Task :testTask3 |
| 26-Mar-2026 08:09:18 | Running tests WITH clover |
| 26-Mar-2026 08:09:19 | WARNING: An illegal reflective access operation has occurred |
| 26-Mar-2026 08:09:19 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 26-Mar-2026 08:09:19 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 26-Mar-2026 08:09:19 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 26-Mar-2026 08:09:19 | WARNING: All illegal access operations will be denied in a future release |
| 26-Mar-2026 08:10:07 | |
| 26-Mar-2026 08:10:07 | > Task :test NO-SOURCE |
| 26-Mar-2026 08:10:07 | ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ |
| 26-Mar-2026 08:10:07 | │jalview:testTask0 results: SUCCESS (1835 tests, 1835 successes, 0 failures, 0 skipped) in 4 minutes, 17.393 seconds │ |
| 26-Mar-2026 08:10:07 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask0/index.html│ |
| 26-Mar-2026 08:10:07 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 26-Mar-2026 08:10:07 | │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 19.016 seconds │ |
| 26-Mar-2026 08:10:07 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask1/index.html│ |
| 26-Mar-2026 08:10:07 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 26-Mar-2026 08:10:07 | │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.120 seconds │ |
| 26-Mar-2026 08:10:07 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask2/index.html│ |
| 26-Mar-2026 08:10:07 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 26-Mar-2026 08:10:07 | │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 50.678 seconds │ |
| 26-Mar-2026 08:10:07 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask3/index.html│ |
| 26-Mar-2026 08:10:07 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 26-Mar-2026 08:10:07 | │OVERALL: results: SUCCESS (1923 tests, 1923 successes, 0 failures, 0 skipped) in 6 minutes, 90.207 seconds │ |
| 26-Mar-2026 08:10:07 | └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ |
| 26-Mar-2026 08:10:07 | |
| 26-Mar-2026 08:10:07 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 26-Mar-2026 08:10:07 | |
| 26-Mar-2026 08:10:07 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 26-Mar-2026 08:10:07 | |
| 26-Mar-2026 08:10:07 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 26-Mar-2026 08:10:07 | |
| 26-Mar-2026 08:10:07 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 26-Mar-2026 08:10:07 | Please consult deprecation warnings for more details. |
| 26-Mar-2026 08:10:07 | |
| 26-Mar-2026 08:10:07 | BUILD SUCCESSFUL in 8m 43s |
| 26-Mar-2026 08:10:07 | 21 actionable tasks: 20 executed, 1 up-to-date |
| 26-Mar-2026 08:10:07 | Finished task 'Run tests with openclover under gradle' with result: Success |
| 26-Mar-2026 08:10:07 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 26-Mar-2026 08:10:07 | Bamboo Artifactory Plugin version: 2.6.2 |
| 26-Mar-2026 08:10:07 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #1 (JB-GDB749-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-GDB749-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons bamboo_repository_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee bamboo_CLOVER_ELEMENTS=171386 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-1 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_CLOVER_BUILD_COVERAGE=29.3 bamboo_CLOVER_CLASSES=1419 bamboo_CLOVER_METHODS=16228 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB749-JOB1 bamboo_CLOVER_COVERED_STATEMENTS=33560 bamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons bamboo_planRepository_name=Jalview Gitlab bamboo_CLOVER_COVERED_CONDITIONALS=11321 LOGNAME=bamboo bamboo_buildNumber=1 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-1 bamboo_CLOVER_STATEMENTS=112778 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_ManualBuildTriggerReason_stageName=Default Stage bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons bamboo_shortPlanKey=GDB749 bamboo_shortJobKey=JOB1 bamboo_CLOVER_NCLOC=269847 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee bamboo_buildTimeStamp=2026-03-26T08:01:21.888Z bamboo_repository_48169043_name=Jalview Gitlab bamboo_CLOVER_COVERED_METHODS=5339 bamboo_CLOVER_CONDITIONALS=42380 bamboo_repository_git_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_buildResultKey=JB-GDB749-JOB1-1 bamboo_repository_branch_name=patch/JAL-4410_multimers_from_3dbeacons bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=570cfd128c945bc7593ad75c31b9761ff81f5fee SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_4=/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport 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/ bamboo_CLOVER_PACKAGES=115 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=patch/JAL-4410_multimers_from_3dbeacons bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_jobFailed=false bamboo_capability_system_git_executable=/bin/git bamboo_repository_48169043_git_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_repository_git_username= bamboo_planRepository_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=patch/JAL-4410_multimers_from_3dbeacons _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_repository_48169043_revision_number=570cfd128c945bc7593ad75c31b9761ff81f5fee bamboo_capability_system_builderivy_Ivy=/usr bamboo_repository_48169043_git_username= bamboo_plan_storageTag=plan-47972517 bamboo_CLOVER_LOC=427989 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_CLOVER_FILES=1123 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_ManualBuildTriggerReason_userName=jprocter bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_CLOVER_COVERED_ELEMENTS=50220 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-GDB749-JOB1 bamboo_planKey=JB-GDB749 bamboo_RerunBuildTriggerReason_noOfRetries=1 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=patch/JAL-4410_multimers_from_3dbeacons PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 26-Mar-2026 08:10:07 | 2414 |
| 26-Mar-2026 08:10:13 | |
| 26-Mar-2026 08:10:13 | > Configure project : |
| 26-Mar-2026 08:10:13 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 26-Mar-2026 08:10:13 | JALVIEW_VERSION is set to '2.11.5.1' |
| 26-Mar-2026 08:10:13 | HEADLESS BUILD |
| 26-Mar-2026 08:10:13 | J2S ENABLED |
| 26-Mar-2026 08:10:13 | Using a LOCAL profile. |
| 26-Mar-2026 08:10:14 | eclipseDir exists |
| 26-Mar-2026 08:10:16 | |
| 26-Mar-2026 08:10:16 | > Task :cloverHtmlReport |
| 26-Mar-2026 08:10:16 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 26-Mar-2026 08:10:17 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/clover' |
| 26-Mar-2026 08:11:02 | Done. Processed 117 packages in 45267ms (386ms per package). |
| 26-Mar-2026 08:11:07 | |
| 26-Mar-2026 08:11:07 | > Task :cloverXmlReport |
| 26-Mar-2026 08:11:07 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 26-Mar-2026 08:11:09 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/clover/clover.xml' |
| 26-Mar-2026 08:11:09 | |
| 26-Mar-2026 08:11:09 | > Task :cloverReport |
| 26-Mar-2026 08:11:09 | |
| 26-Mar-2026 08:11:09 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 26-Mar-2026 08:11:09 | |
| 26-Mar-2026 08:11:09 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 26-Mar-2026 08:11:09 | |
| 26-Mar-2026 08:11:09 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 26-Mar-2026 08:11:09 | |
| 26-Mar-2026 08:11:09 | BUILD SUCCESSFUL in 1m 1s |
| 26-Mar-2026 08:11:09 | 2 actionable tasks: 2 executed |
| 26-Mar-2026 08:11:09 | Finished task 'Clover Report' with result: Success |
| 26-Mar-2026 08:11:09 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 26-Mar-2026 08:11:09 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1... |
| 26-Mar-2026 08:11:10 | Finished task 'TestNG Parser' with result: Success |
| 26-Mar-2026 08:11:10 | Running post build plugin 'NCover Results Collector' |
| 26-Mar-2026 08:11:10 | Running post build plugin 'Artifact Copier' |
| 26-Mar-2026 08:11:10 | Publishing an artifact: Clover Report (System) |
| 26-Mar-2026 08:11:11 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.685 s |
| 26-Mar-2026 08:11:11 | Publishing an artifact: TestNG report |
| 26-Mar-2026 08:11:11 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/test does not exist. |
| 26-Mar-2026 08:11:11 | The artifact hasn't been successfully published after 2.428 ms |
| 26-Mar-2026 08:11:11 | Running post build plugin 'Artifactory Release Management Staging' |
| 26-Mar-2026 08:11:11 | Running post build plugin 'Artifactory Build Info Copier' |
| 26-Mar-2026 08:11:11 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 26-Mar-2026 08:11:11 | Running post build plugin 'npm Cache Cleanup' |
| 26-Mar-2026 08:11:11 | Running post build plugin 'Clover Results Collector' |
| 26-Mar-2026 08:11:11 | Running post build plugin 'Docker Container Cleanup' |
| 26-Mar-2026 08:11:11 | Finalising the build... |
| 26-Mar-2026 08:11:11 | Stopping timer. |
| 26-Mar-2026 08:11:11 | Build JB-GDB749-JOB1-1 completed. |
| 26-Mar-2026 08:11:11 | Running on server: post build plugin 'NCover Results Collector' |
| 26-Mar-2026 08:11:11 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 26-Mar-2026 08:11:11 | Running on server: post build plugin 'Clover Delta Calculator' |
| 26-Mar-2026 08:11:11 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 26-Mar-2026 08:11:11 | All post build plugins have finished |
| 26-Mar-2026 08:11:11 | Generating build results summary... |
| 26-Mar-2026 08:11:12 | Saving build results to disk... |
| 26-Mar-2026 08:11:12 | Logging substituted variables... |
| 26-Mar-2026 08:11:12 | Indexing build results... |
| 26-Mar-2026 08:11:12 | Finished building JB-GDB749-JOB1-1. |