Build and run tests under Java 11
Build: #3 was successful
Job: Clover and Tests was successful
Build log
The build generated 249 lines of output. Download or view full build log
| 03-Jul-2026 13:27:38 | Build Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #3 (JB-GDB761-JOB1-3) started building on agent Default Agent |
| 03-Jul-2026 13:27:38 | |
| 03-Jul-2026 13:27:38 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1 |
| 03-Jul-2026 13:27:38 | Executing build Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #3 (JB-GDB761-JOB1-3) |
| 03-Jul-2026 13:27:38 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 03-Jul-2026 13:27:38 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1 |
| 03-Jul-2026 13:27:38 | Updating source code to revision: 2a40a889270803a56cfcf63b8fa3c767662d0a06 |
| 03-Jul-2026 13:27:38 | Fetching 'refs/heads/development/Release_2_11_5_Branch' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 03-Jul-2026 13:27:38 | Checking out revision 2a40a889270803a56cfcf63b8fa3c767662d0a06. |
| 03-Jul-2026 13:27:38 | From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 |
| 03-Jul-2026 13:27:38 | fd8d288..2a40a88 development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch |
| 03-Jul-2026 13:27:38 | Already on 'development/Release_2_11_5_Branch' |
| 03-Jul-2026 13:27:38 | Your branch is behind 'origin/development/Release_2_11_5_Branch' by 1 commit, and can be fast-forwarded. |
| 03-Jul-2026 13:27:38 | (use "git pull" to update your local branch) |
| 03-Jul-2026 13:27:38 | HEAD is now at 2a40a88 JAL-4672 format release notes |
| 03-Jul-2026 13:27:38 | Updated source code to revision: 2a40a889270803a56cfcf63b8fa3c767662d0a06 |
| 03-Jul-2026 13:27:38 | Finished task 'Checkout Default Repository' with result: Success |
| 03-Jul-2026 13:27:38 | Running pre-build action: VCS Version Collector |
| 03-Jul-2026 13:27:38 | Running pre-build action: Artifactory Release Staging |
| 03-Jul-2026 13:27:38 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 03-Jul-2026 13:27:38 | Bamboo Artifactory Plugin version: 2.6.2 |
| 03-Jul-2026 13:27:38 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #3 (JB-GDB761-JOB1-3)' ... 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-GDB761-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=development/Release_2_11_5_Branch bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=development/Release_2_11_5_Branch bamboo_repository_revision_number=2a40a889270803a56cfcf63b8fa3c767662d0a06 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB761-JOB1-3 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-GDB761-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB761-JOB1 bamboo_shortPlanName=development-Release_2_11_5_Branch bamboo_repository_48169107_name=Jalview Gitlab bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=3 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-GDB761-JOB1-3 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - 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| 03-Jul-2026 13:27:38 | 2477 |
| 03-Jul-2026 13:27:39 | |
| 03-Jul-2026 13:27:39 | > Configure project : |
| 03-Jul-2026 13:27:39 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 03-Jul-2026 13:27:39 | JALVIEW_VERSION is set to '2.11.5.2' |
| 03-Jul-2026 13:27:39 | HEADLESS BUILD |
| 03-Jul-2026 13:27:39 | J2S ENABLED |
| 03-Jul-2026 13:27:39 | Using a LOCAL profile. |
| 03-Jul-2026 13:27:39 | eclipseDir exists |
| 03-Jul-2026 13:27:40 | |
| 03-Jul-2026 13:27:40 | > Task :clean |
| 03-Jul-2026 13:27:40 | > Task :cleanClover |
| 03-Jul-2026 13:27:40 | > Task :cleanTest UP-TO-DATE |
| 03-Jul-2026 13:27:42 | |
| 03-Jul-2026 13:27:42 | > Task :cloverInstrJava |
| 03-Jul-2026 13:27:42 | Clover: About to instrument 1109 files |
| 03-Jul-2026 13:27:42 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 03-Jul-2026 13:27:42 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/clover/clover.db'. |
| 03-Jul-2026 13:27:42 | Processing files at 1.9 source level. |
| 03-Jul-2026 13:27:45 | 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? |
| 03-Jul-2026 13:27:45 | 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? |
| 03-Jul-2026 13:27:45 | 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? |
| 03-Jul-2026 13:27:45 | 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? |
| 03-Jul-2026 13:27:45 | 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? |
| 03-Jul-2026 13:27:45 | 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? |
| 03-Jul-2026 13:27:45 | 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? |
| 03-Jul-2026 13:27:51 | Clover all over. Instrumented 1109 files (113 packages). |
| 03-Jul-2026 13:27:53 | |
| 03-Jul-2026 13:27:53 | > Task :cloverInstrTests |
| 03-Jul-2026 13:27:53 | Clover: About to instrument test files |
| 03-Jul-2026 13:27:53 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 03-Jul-2026 13:27:53 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/clover/clover.db'. |
| 03-Jul-2026 13:27:53 | Processing files at 1.9 source level. |
| 03-Jul-2026 13:27:56 | Clover all over. Instrumented 293 files (52 packages). |
| 03-Jul-2026 13:27:56 | 1627 test methods detected. |
| 03-Jul-2026 13:27:56 | |
| 03-Jul-2026 13:27:56 | > Task :cloverInstr |
| 03-Jul-2026 13:27:58 | |
| 03-Jul-2026 13:27:58 | > Task :compileCloverJava |
| 03-Jul-2026 13:27:58 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 03-Jul-2026 13:27:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:27:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:27:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:27:58 | Setting target compatibility to 11 |
| 03-Jul-2026 13:28:09 | Note: Some input files use or override a deprecated API. |
| 03-Jul-2026 13:28:09 | Note: Recompile with -Xlint:deprecation for details. |
| 03-Jul-2026 13:28:09 | Note: Some input files use unchecked or unsafe operations. |
| 03-Jul-2026 13:28:09 | Note: Recompile with -Xlint:unchecked for details. |
| 03-Jul-2026 13:28:13 | |
| 03-Jul-2026 13:28:13 | > Task :processCloverResources NO-SOURCE |
| 03-Jul-2026 13:28:13 | > Task :cloverClasses |
| 03-Jul-2026 13:28:14 | > Task :copyHelp |
| 03-Jul-2026 13:28:14 | > Task :buildIndices |
| 03-Jul-2026 13:28:15 | > Task :copyResources |
| 03-Jul-2026 13:28:15 | > Task :copyChannelResources |
| 03-Jul-2026 13:28:15 | |
| 03-Jul-2026 13:28:15 | > Task :createBuildProperties |
| 03-Jul-2026 13:28:15 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 03-Jul-2026 13:28:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:28:15 | |
| 03-Jul-2026 13:28:15 | > Task :buildResources |
| 03-Jul-2026 13:28:15 | > Task :copyDocs |
| 03-Jul-2026 13:28:15 | |
| 03-Jul-2026 13:28:15 | > Task :convertMdFiles |
| 03-Jul-2026 13:28:15 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 03-Jul-2026 13:28:15 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 03-Jul-2026 13:28:15 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 03-Jul-2026 13:28:15 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/resources/doc_build/doc/building.html |
| 03-Jul-2026 13:28:15 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 03-Jul-2026 13:28:15 | |
| 03-Jul-2026 13:28:15 | > Task :releasesTemplates |
| 03-Jul-2026 13:28:15 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 03-Jul-2026 13:28:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:28:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:28:15 | Stripping rc/test/etc for TEST |
| 03-Jul-2026 13:28:15 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/help/markdown/whatsnew/whatsnew-TEST.md |
| 03-Jul-2026 13:28:15 | |
| 03-Jul-2026 13:28:15 | > Task :prepare |
| 03-Jul-2026 13:28:17 | |
| 03-Jul-2026 13:28:17 | > Task :compileJava |
| 03-Jul-2026 13:28:17 | Setting target compatibility to 11 |
| 03-Jul-2026 13:28:21 | Note: Some input files use or override a deprecated API. |
| 03-Jul-2026 13:28:21 | Note: Recompile with -Xlint:deprecation for details. |
| 03-Jul-2026 13:28:21 | Note: Some input files use unchecked or unsafe operations. |
| 03-Jul-2026 13:28:21 | Note: Recompile with -Xlint:unchecked for details. |
| 03-Jul-2026 13:28:23 | |
| 03-Jul-2026 13:28:23 | > Task :compileTestJava |
| 03-Jul-2026 13:28:23 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
| 03-Jul-2026 13:28:23 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:28:23 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:28:23 | Setting target compatibility to 11 |
| 03-Jul-2026 13:28:26 | Note: Some input files use or override a deprecated API. |
| 03-Jul-2026 13:28:26 | Note: Recompile with -Xlint:deprecation for details. |
| 03-Jul-2026 13:28:26 | Note: Some input files use unchecked or unsafe operations. |
| 03-Jul-2026 13:28:26 | Note: Recompile with -Xlint:unchecked for details. |
| 03-Jul-2026 13:28:27 | |
| 03-Jul-2026 13:28:27 | > Task :processTestResources |
| 03-Jul-2026 13:28:27 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
| 03-Jul-2026 13:28:27 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:28:27 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:28:27 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:28:27 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:28:27 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:28:27 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:28:27 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:28:27 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-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. |
| 03-Jul-2026 13:28:27 | |
| 03-Jul-2026 13:28:27 | > Task :testClasses |
| 03-Jul-2026 13:28:29 | |
| 03-Jul-2026 13:28:29 | > Task :testTask0 |
| 03-Jul-2026 13:28:29 | Running tests WITH clover |
| 03-Jul-2026 13:28:31 | WARNING: An illegal reflective access operation has occurred |
| 03-Jul-2026 13:28:31 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 03-Jul-2026 13:28:31 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 03-Jul-2026 13:28:31 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 03-Jul-2026 13:28:31 | WARNING: All illegal access operations will be denied in a future release |
| 03-Jul-2026 13:32:49 | |
| 03-Jul-2026 13:32:49 | > Task :testTask1 |
| 03-Jul-2026 13:32:49 | Running tests WITH clover |
| 03-Jul-2026 13:32:50 | WARNING: An illegal reflective access operation has occurred |
| 03-Jul-2026 13:32:50 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 03-Jul-2026 13:32:50 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 03-Jul-2026 13:32:50 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 03-Jul-2026 13:32:50 | WARNING: All illegal access operations will be denied in a future release |
| 03-Jul-2026 13:35:00 | |
| 03-Jul-2026 13:35:00 | > Task :testTask2 |
| 03-Jul-2026 13:35:00 | Running tests WITH clover |
| 03-Jul-2026 13:35:03 | |
| 03-Jul-2026 13:35:03 | > Task :testTask3 |
| 03-Jul-2026 13:35:03 | Running tests WITH clover |
| 03-Jul-2026 13:35:04 | WARNING: An illegal reflective access operation has occurred |
| 03-Jul-2026 13:35:04 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 03-Jul-2026 13:35:04 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 03-Jul-2026 13:35:04 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 03-Jul-2026 13:35:04 | WARNING: All illegal access operations will be denied in a future release |
| 03-Jul-2026 13:35:51 | |
| 03-Jul-2026 13:35:51 | > Task :test NO-SOURCE |
| 03-Jul-2026 13:35:51 | ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ |
| 03-Jul-2026 13:35:51 | │jalview:testTask0 results: SUCCESS (1836 tests, 1836 successes, 0 failures, 0 skipped) in 4 minutes, 19.358 seconds │ |
| 03-Jul-2026 13:35:51 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/reports/tests/testTask0/index.html│ |
| 03-Jul-2026 13:35:51 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 03-Jul-2026 13:35:51 | │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 10.374 seconds │ |
| 03-Jul-2026 13:35:51 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/reports/tests/testTask1/index.html│ |
| 03-Jul-2026 13:35:51 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 03-Jul-2026 13:35:51 | │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.169 seconds │ |
| 03-Jul-2026 13:35:51 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/reports/tests/testTask2/index.html│ |
| 03-Jul-2026 13:35:51 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 03-Jul-2026 13:35:51 | │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 50.173 seconds │ |
| 03-Jul-2026 13:35:51 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/reports/tests/testTask3/index.html│ |
| 03-Jul-2026 13:35:51 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 03-Jul-2026 13:35:51 | │OVERALL: results: SUCCESS (1924 tests, 1924 successes, 0 failures, 0 skipped) in 6 minutes, 83.074 seconds │ |
| 03-Jul-2026 13:35:51 | └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ |
| 03-Jul-2026 13:35:51 | |
| 03-Jul-2026 13:35:51 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 03-Jul-2026 13:35:51 | |
| 03-Jul-2026 13:35:51 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 03-Jul-2026 13:35:51 | |
| 03-Jul-2026 13:35:51 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 03-Jul-2026 13:35:51 | |
| 03-Jul-2026 13:35:51 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 03-Jul-2026 13:35:51 | Please consult deprecation warnings for more details. |
| 03-Jul-2026 13:35:51 | |
| 03-Jul-2026 13:35:51 | BUILD SUCCESSFUL in 8m 12s |
| 03-Jul-2026 13:35:51 | 21 actionable tasks: 20 executed, 1 up-to-date |
| 03-Jul-2026 13:35:51 | Finished task 'Run tests with openclover under gradle' with result: Success |
| 03-Jul-2026 13:35:51 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 03-Jul-2026 13:35:51 | Bamboo Artifactory Plugin version: 2.6.2 |
| 03-Jul-2026 13:35:51 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #3 (JB-GDB761-JOB1-3)' ... 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-GDB761-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=development/Release_2_11_5_Branch bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=development/Release_2_11_5_Branch bamboo_repository_revision_number=2a40a889270803a56cfcf63b8fa3c767662d0a06 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB761-JOB1-3 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-GDB761-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB761-JOB1 bamboo_shortPlanName=development-Release_2_11_5_Branch bamboo_repository_48169107_name=Jalview Gitlab bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=3 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-GDB761-JOB1-3 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch bamboo_shortPlanKey=GDB761 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=2a40a889270803a56cfcf63b8fa3c767662d0a06 bamboo_buildTimeStamp=2026-07-03T13:27:38.206+01:00 bamboo_repository_previous_revision_number=fd8d28895d1f0f2d449706b858b3f2d04f2fb351 bamboo_planRepository_previousRevision=fd8d28895d1f0f2d449706b858b3f2d04f2fb351 bamboo_repository_48169107_git_branch=development/Release_2_11_5_Branch bamboo_repository_git_branch=development/Release_2_11_5_Branch bamboo_buildResultKey=JB-GDB761-JOB1-3 bamboo_repository_branch_name=development/Release_2_11_5_Branch bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=2a40a889270803a56cfcf63b8fa3c767662d0a06 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=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_repository_48169107_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_branch=development/Release_2_11_5_Branch bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_jobFailed=false bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=fd8d28895d1f0f2d449706b858b3f2d04f2fb351 bamboo_planRepository_branchDisplayName=development/Release_2_11_5_Branch bamboo_repository_48169107_branch_name=development/Release_2_11_5_Branch bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=development/Release_2_11_5_Branch bamboo_repository_48169107_revision_number=2a40a889270803a56cfcf63b8fa3c767662d0a06 _=/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-47972645 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_repository_48169107_git_username= 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-GDB761-JOB1 bamboo_planKey=JB-GDB761 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= bamboo_repository_48169107_previous_revision_number=fd8d28895d1f0f2d449706b858b3f2d04f2fb351 HOME=/home/bamboo bamboo_planRepository_1_branchName=development/Release_2_11_5_Branch PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 03-Jul-2026 13:35:51 | 2477 |
| 03-Jul-2026 13:35:57 | |
| 03-Jul-2026 13:35:57 | > Configure project : |
| 03-Jul-2026 13:35:57 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 03-Jul-2026 13:35:57 | JALVIEW_VERSION is set to '2.11.5.2' |
| 03-Jul-2026 13:35:57 | HEADLESS BUILD |
| 03-Jul-2026 13:35:57 | J2S ENABLED |
| 03-Jul-2026 13:35:57 | Using a LOCAL profile. |
| 03-Jul-2026 13:35:58 | eclipseDir exists |
| 03-Jul-2026 13:36:01 | |
| 03-Jul-2026 13:36:01 | > Task :cloverHtmlReport |
| 03-Jul-2026 13:36:01 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 03-Jul-2026 13:36:02 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/reports/clover' |
| 03-Jul-2026 13:36:47 | Done. Processed 117 packages in 45468ms (388ms per package). |
| 03-Jul-2026 13:36:53 | |
| 03-Jul-2026 13:36:53 | > Task :cloverXmlReport |
| 03-Jul-2026 13:36:53 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 03-Jul-2026 13:36:54 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/reports/clover/clover.xml' |
| 03-Jul-2026 13:36:54 | |
| 03-Jul-2026 13:36:54 | > Task :cloverReport |
| 03-Jul-2026 13:36:54 | |
| 03-Jul-2026 13:36:54 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 03-Jul-2026 13:36:54 | |
| 03-Jul-2026 13:36:54 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 03-Jul-2026 13:36:54 | |
| 03-Jul-2026 13:36:54 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 03-Jul-2026 13:36:54 | |
| 03-Jul-2026 13:36:54 | BUILD SUCCESSFUL in 1m 2s |
| 03-Jul-2026 13:36:54 | 2 actionable tasks: 2 executed |
| 03-Jul-2026 13:36:54 | Finished task 'Clover Report' with result: Success |
| 03-Jul-2026 13:36:54 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 03-Jul-2026 13:36:54 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1... |
| 03-Jul-2026 13:36:54 | Finished task 'TestNG Parser' with result: Success |
| 03-Jul-2026 13:36:54 | Running post build plugin 'NCover Results Collector' |
| 03-Jul-2026 13:36:54 | Running post build plugin 'Artifact Copier' |
| 03-Jul-2026 13:36:54 | Publishing an artifact: Clover Report (System) |
| 03-Jul-2026 13:36:56 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.701 s |
| 03-Jul-2026 13:36:56 | Publishing an artifact: TestNG report |
| 03-Jul-2026 13:36:56 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB761-JOB1/build/reports/tests/test does not exist. |
| 03-Jul-2026 13:36:56 | The artifact hasn't been successfully published after 936.8 μs |
| 03-Jul-2026 13:36:56 | Running post build plugin 'Artifactory Release Management Staging' |
| 03-Jul-2026 13:36:56 | Running post build plugin 'Artifactory Build Info Copier' |
| 03-Jul-2026 13:36:56 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 03-Jul-2026 13:36:56 | Running post build plugin 'npm Cache Cleanup' |
| 03-Jul-2026 13:36:56 | Running post build plugin 'Clover Results Collector' |
| 03-Jul-2026 13:36:56 | Running post build plugin 'Docker Container Cleanup' |
| 03-Jul-2026 13:36:56 | Finalising the build... |
| 03-Jul-2026 13:36:56 | Stopping timer. |
| 03-Jul-2026 13:36:56 | Build JB-GDB761-JOB1-3 completed. |
| 03-Jul-2026 13:36:56 | Running on server: post build plugin 'NCover Results Collector' |
| 03-Jul-2026 13:36:56 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 03-Jul-2026 13:36:56 | Running on server: post build plugin 'Clover Delta Calculator' |
| 03-Jul-2026 13:36:56 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 03-Jul-2026 13:36:56 | All post build plugins have finished |
| 03-Jul-2026 13:36:56 | Generating build results summary... |
| 03-Jul-2026 13:36:56 | Saving build results to disk... |
| 03-Jul-2026 13:36:56 | Logging substituted variables... |
| 03-Jul-2026 13:36:56 | Indexing build results... |
| 03-Jul-2026 13:36:56 | Finished building JB-GDB761-JOB1-3. |