Build #4

Build and run tests under Java 11

Build: #4 was successful

Job: Clover and Tests was successful

Stages & jobs

  1. Default Stage

Build log

The build generated 316 lines of output. Download or view full build log

04-Dec-2025 14:42:58 Build Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests #4 (JB-GDB732-JOB1-4) started building on agent Default Agent
04-Dec-2025 14:42:58
04-Dec-2025 14:42:58 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1
04-Dec-2025 14:42:58 Executing build Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests #4 (JB-GDB732-JOB1-4)
04-Dec-2025 14:42:58 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
04-Dec-2025 14:42:58 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1
04-Dec-2025 14:42:58 Updating source code to revision: ef35c026c41b6d9fc6d3a1b11d89676881680686
04-Dec-2025 14:42:58 Fetching 'refs/heads/development/Release_2_12_Branch' from 'https://gitlab.jalview.org/jalview/jalview.git'.
04-Dec-2025 14:42:59 Checking out revision ef35c026c41b6d9fc6d3a1b11d89676881680686.
04-Dec-2025 14:42:59 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
04-Dec-2025 14:42:59    7d35e28..ef35c02  development/Release_2_12_Branch -> origin/development/Release_2_12_Branch
04-Dec-2025 14:42:59 Already on 'development/Release_2_12_Branch'
04-Dec-2025 14:42:59 Your branch is behind 'origin/development/Release_2_12_Branch' by 1 commit, and can be fast-forwarded.
04-Dec-2025 14:42:59   (use "git pull" to update your local branch)
04-Dec-2025 14:42:59 HEAD is now at ef35c02 JAL-4107 fixing some broken @j2s code
04-Dec-2025 14:42:59 Updated source code to revision: ef35c026c41b6d9fc6d3a1b11d89676881680686
04-Dec-2025 14:42:59 Finished task 'Checkout Default Repository' with result: Success
04-Dec-2025 14:42:59 Running pre-build action: VCS Version Collector
04-Dec-2025 14:42:59 Running pre-build action: Artifactory Release Staging
04-Dec-2025 14:42:59 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
04-Dec-2025 14:42:59 Bamboo Artifactory Plugin version: 2.6.2
04-Dec-2025 14:42:59
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests #4 (JB-GDB732-JOB1-4)'
... 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-GDB732-JOB1
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04-Dec-2025 14:42:59 444
04-Dec-2025 14:43:00 Starting a Gradle Daemon (subsequent builds will be faster)
04-Dec-2025 14:43:07
04-Dec-2025 14:43:07 > Configure project :
04-Dec-2025 14:43:07 Using properties from file './utils/channels/default/channel_gradle.properties'
04-Dec-2025 14:43:07 JALVIEW_VERSION is set to '2.12.0'
04-Dec-2025 14:43:07 HEADLESS BUILD
04-Dec-2025 14:43:07 J2S ENABLED
04-Dec-2025 14:43:08 Using a LOCAL profile.
04-Dec-2025 14:43:09 eclipseDir exists
04-Dec-2025 14:43:11
04-Dec-2025 14:43:11 > Task :clean
04-Dec-2025 14:43:11 > Task :cleanClover
04-Dec-2025 14:43:11 > Task :cleanTest UP-TO-DATE
04-Dec-2025 14:43:13
04-Dec-2025 14:43:13 > Task :cloverInstrJava
04-Dec-2025 14:43:13 Clover: About to instrument 1253 files
04-Dec-2025 14:43:13 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
04-Dec-2025 14:43:13 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover.db'.
04-Dec-2025 14:43:13 Processing files at 1.9 source level.
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:16 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?
04-Dec-2025 14:43:17 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?
04-Dec-2025 14:43:17 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?
04-Dec-2025 14:43:17 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?
04-Dec-2025 14:43:17 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?
04-Dec-2025 14:43:17 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?
04-Dec-2025 14:43:17 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?
04-Dec-2025 14:43:17 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?
04-Dec-2025 14:43:17 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?
04-Dec-2025 14:43:17 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?
04-Dec-2025 14:43:17 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?
04-Dec-2025 14:43:17 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?
04-Dec-2025 14:43:17 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?
04-Dec-2025 14:43:24 Clover all over. Instrumented 1253 files (133 packages).
04-Dec-2025 14:43:26
04-Dec-2025 14:43:26 > Task :cloverInstrTests
04-Dec-2025 14:43:26 Clover: About to instrument test files
04-Dec-2025 14:43:26 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
04-Dec-2025 14:43:26 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover.db'.
04-Dec-2025 14:43:26 Processing files at 1.9 source level.
04-Dec-2025 14:43:31 Clover all over. Instrumented 315 files (58 packages).
04-Dec-2025 14:43:31 1770 test methods detected.
04-Dec-2025 14:43:31
04-Dec-2025 14:43:31 > Task :cloverInstr
04-Dec-2025 14:43:33
04-Dec-2025 14:43:33 > Task :compileCloverJava
04-Dec-2025 14:43:33 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
04-Dec-2025 14:43:33   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:43:33   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:43:33   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:43:33 Setting target compatibility to 11
04-Dec-2025 14:43:59 Note: Some input files use or override a deprecated API.
04-Dec-2025 14:43:59 Note: Recompile with -Xlint:deprecation for details.
04-Dec-2025 14:43:59 Note: Some input files use unchecked or unsafe operations.
04-Dec-2025 14:43:59 Note: Recompile with -Xlint:unchecked for details.
04-Dec-2025 14:44:07
04-Dec-2025 14:44:07 > Task :processCloverResources NO-SOURCE
04-Dec-2025 14:44:07 > Task :cloverClasses
04-Dec-2025 14:44:08 > Task :copyHelp
04-Dec-2025 14:44:09 > Task :buildIndices
04-Dec-2025 14:44:09 > Task :copyResources
04-Dec-2025 14:44:09 > Task :copyChannelResources
04-Dec-2025 14:44:09
04-Dec-2025 14:44:09 > Task :createBuildProperties
04-Dec-2025 14:44:09 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
04-Dec-2025 14:44:09   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:44:09
04-Dec-2025 14:44:09 > Task :buildResources
04-Dec-2025 14:44:09 > Task :copyDocs
04-Dec-2025 14:44:10
04-Dec-2025 14:44:10 > Task :convertMdFiles
04-Dec-2025 14:44:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
04-Dec-2025 14:44:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/releaseprocess.html
04-Dec-2025 14:44:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
04-Dec-2025 14:44:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
04-Dec-2025 14:44:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/building.html
04-Dec-2025 14:44:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/addingWebClient.html
04-Dec-2025 14:44:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/jalview-projects.html
04-Dec-2025 14:44:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
04-Dec-2025 14:44:10
04-Dec-2025 14:44:10 > Task :releasesTemplates
04-Dec-2025 14:44:10 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
04-Dec-2025 14:44:10   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:44:10   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:44:10 Stripping rc/test/etc for TEST
04-Dec-2025 14:44:10 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
04-Dec-2025 14:44:10
04-Dec-2025 14:44:10 > Task :prepare
04-Dec-2025 14:44:12
04-Dec-2025 14:44:12 > Task :compileJava
04-Dec-2025 14:44:12 Setting target compatibility to 11
04-Dec-2025 14:44:20 Note: Some input files use or override a deprecated API.
04-Dec-2025 14:44:20 Note: Recompile with -Xlint:deprecation for details.
04-Dec-2025 14:44:20 Note: Some input files use unchecked or unsafe operations.
04-Dec-2025 14:44:20 Note: Recompile with -Xlint:unchecked for details.
04-Dec-2025 14:44:25
04-Dec-2025 14:44:25 > Task :compileTestJava
04-Dec-2025 14:44:25 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
04-Dec-2025 14:44:25   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:44:25   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:44:25 Setting target compatibility to 11
04-Dec-2025 14:44:34 Note: Some input files use or override a deprecated API.
04-Dec-2025 14:44:34 Note: Recompile with -Xlint:deprecation for details.
04-Dec-2025 14:44:34 Note: Some input files use unchecked or unsafe operations.
04-Dec-2025 14:44:34 Note: Recompile with -Xlint:unchecked for details.
04-Dec-2025 14:44:35
04-Dec-2025 14:44:35 > Task :processTestResources
04-Dec-2025 14:44:35 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
04-Dec-2025 14:44:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:44:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:44:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:44:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:44:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:44:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:44:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:44:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-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.
04-Dec-2025 14:44:35
04-Dec-2025 14:44:35 > Task :testClasses
04-Dec-2025 14:44:37
04-Dec-2025 14:44:37 > Task :testTask0
04-Dec-2025 14:44:37 Running tests WITH clover
04-Dec-2025 14:44:40 WARNING: An illegal reflective access operation has occurred
04-Dec-2025 14:44:40 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
04-Dec-2025 14:44:40 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
04-Dec-2025 14:44:40 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
04-Dec-2025 14:44:40 WARNING: All illegal access operations will be denied in a future release
04-Dec-2025 14:50:04
04-Dec-2025 14:50:04 > Task :testTask1
04-Dec-2025 14:50:04 Running tests WITH clover
04-Dec-2025 14:50:07 WARNING: An illegal reflective access operation has occurred
04-Dec-2025 14:50:07 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
04-Dec-2025 14:50:07 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
04-Dec-2025 14:50:07 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
04-Dec-2025 14:50:07 WARNING: All illegal access operations will be denied in a future release
04-Dec-2025 14:52:44
04-Dec-2025 14:52:44 > Task :testTask2
04-Dec-2025 14:52:44 Running tests WITH clover
04-Dec-2025 14:52:45 WARNING: An illegal reflective access operation has occurred
04-Dec-2025 14:52:45 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
04-Dec-2025 14:52:45 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
04-Dec-2025 14:52:45 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
04-Dec-2025 14:52:45 WARNING: All illegal access operations will be denied in a future release
04-Dec-2025 14:52:50
04-Dec-2025 14:52:50 > Task :testTask3
04-Dec-2025 14:52:50 Running tests WITH clover
04-Dec-2025 14:52:52 WARNING: An illegal reflective access operation has occurred
04-Dec-2025 14:52:52 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
04-Dec-2025 14:52:52 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
04-Dec-2025 14:52:52 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
04-Dec-2025 14:52:52 WARNING: All illegal access operations will be denied in a future release
04-Dec-2025 14:53:15
04-Dec-2025 14:53:15 > Task :test NO-SOURCE
04-Dec-2025 14:53:15 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
04-Dec-2025 14:53:15 │jalview:testTask0 results: SUCCESS (2102 tests, 2102 successes, 0 failures, 0 skipped) in 5 minutes, 25.971 seconds   │
04-Dec-2025 14:53:15 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/testTask0/index.html│
04-Dec-2025 14:53:15 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
04-Dec-2025 14:53:15 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 39.741 seconds       │
04-Dec-2025 14:53:15 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/testTask1/index.html│
04-Dec-2025 14:53:15 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
04-Dec-2025 14:53:15 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 5.923 seconds                     │
04-Dec-2025 14:53:15 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/testTask2/index.html│
04-Dec-2025 14:53:15 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
04-Dec-2025 14:53:15 │jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 26.946 seconds                  │
04-Dec-2025 14:53:15 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/testTask3/index.html│
04-Dec-2025 14:53:15 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
04-Dec-2025 14:53:15 │OVERALL: results: SUCCESS (2179 tests, 2178 successes, 0 failures, 1 skipped) in 7 minutes, 98.581 seconds            │
04-Dec-2025 14:53:15 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
04-Dec-2025 14:53:15
04-Dec-2025 14:53:15 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
04-Dec-2025 14:53:15
04-Dec-2025 14:53:15 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
04-Dec-2025 14:53:15
04-Dec-2025 14:53:15 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
04-Dec-2025 14:53:15
04-Dec-2025 14:53:15 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
04-Dec-2025 14:53:15 Please consult deprecation warnings for more details.
04-Dec-2025 14:53:15
04-Dec-2025 14:53:15 BUILD SUCCESSFUL in 10m 15s
04-Dec-2025 14:53:15 21 actionable tasks: 20 executed, 1 up-to-date
04-Dec-2025 14:53:15 Finished task 'Run tests with openclover under gradle' with result: Success
04-Dec-2025 14:53:15 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
04-Dec-2025 14:53:15 Bamboo Artifactory Plugin version: 2.6.2
04-Dec-2025 14:53:15
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests #4 (JB-GDB732-JOB1-4)'
... 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-GDB732-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=development/Release_2_12_Branch
bamboo_repository_46498611_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=development/Release_2_12_Branch
bamboo_repository_revision_number=ef35c026c41b6d9fc6d3a1b11d89676881680686
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB732-JOB1-4
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-GDB732-JOB1
bamboo_planRepository_1_name=Jalview Gitlab
bamboo_buildKey=JB-GDB732-JOB1
bamboo_shortPlanName=development-Release_2_12_Branch
bamboo_planRepository_name=Jalview Gitlab
LOGNAME=bamboo
bamboo_buildNumber=4
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-GDB732-JOB1-4
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_12_Branch
bamboo_shortPlanKey=GDB732
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=ef35c026c41b6d9fc6d3a1b11d89676881680686
bamboo_buildTimeStamp=2025-12-04T14:42:58.928Z
bamboo_repository_previous_revision_number=7d35e28797636155c3de86cbdb1030eaf9110ecc
bamboo_planRepository_previousRevision=7d35e28797636155c3de86cbdb1030eaf9110ecc
bamboo_repository_git_branch=development/Release_2_12_Branch
bamboo_buildResultKey=JB-GDB732-JOB1-4
bamboo_repository_branch_name=development/Release_2_12_Branch
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - development-Release_2_12_Branch - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=ef35c026c41b6d9fc6d3a1b11d89676881680686
SHLVL=1
bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant
bamboo_repository_46498611_revision_number=ef35c026c41b6d9fc6d3a1b11d89676881680686
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_46498611_git_branch=development/Release_2_12_Branch
bamboo_planRepository_branch=development/Release_2_12_Branch
bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609
bamboo_jobFailed=false
bamboo_repository_46498611_git_username=
bamboo_capability_system_git_executable=/bin/git
bamboo_repository_git_username=
bamboo_planRepository_1_previousRevision=7d35e28797636155c3de86cbdb1030eaf9110ecc
bamboo_repository_46498611_name=Jalview Gitlab
bamboo_repository_46498611_previous_revision_number=7d35e28797636155c3de86cbdb1030eaf9110ecc
bamboo_planRepository_branchDisplayName=development/Release_2_12_Branch
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=development/Release_2_12_Branch
bamboo_repository_46498611_branch_name=development/Release_2_12_Branch
_=/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-46302793
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-GDB732-JOB1
bamboo_planKey=JB-GDB732
bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_planRepository_username=
HOME=/home/bamboo
bamboo_planRepository_1_branchName=development/Release_2_12_Branch
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
04-Dec-2025 14:53:15 444
04-Dec-2025 14:53:22
04-Dec-2025 14:53:22 > Configure project :
04-Dec-2025 14:53:22 Using properties from file './utils/channels/default/channel_gradle.properties'
04-Dec-2025 14:53:22 JALVIEW_VERSION is set to '2.12.0'
04-Dec-2025 14:53:22 HEADLESS BUILD
04-Dec-2025 14:53:22 J2S ENABLED
04-Dec-2025 14:53:22 Using a LOCAL profile.
04-Dec-2025 14:53:23 eclipseDir exists
04-Dec-2025 14:53:26
04-Dec-2025 14:53:26 > Task :cloverHtmlReport
04-Dec-2025 14:53:26 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
04-Dec-2025 14:53:29 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/clover'
04-Dec-2025 14:54:32 Done. Processed 137 packages in 63131ms (460ms per package).
04-Dec-2025 14:54:39
04-Dec-2025 14:54:39 > Task :cloverXmlReport
04-Dec-2025 14:54:39 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
04-Dec-2025 14:54:40 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/clover/clover.xml'
04-Dec-2025 14:54:40
04-Dec-2025 14:54:40 > Task :cloverReport
04-Dec-2025 14:54:40
04-Dec-2025 14:54:40 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
04-Dec-2025 14:54:40
04-Dec-2025 14:54:40 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
04-Dec-2025 14:54:40
04-Dec-2025 14:54:40 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
04-Dec-2025 14:54:40
04-Dec-2025 14:54:40 BUILD SUCCESSFUL in 1m 24s
04-Dec-2025 14:54:40 2 actionable tasks: 2 executed
04-Dec-2025 14:54:41 Finished task 'Clover Report' with result: Success
04-Dec-2025 14:54:41 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
04-Dec-2025 14:54:41 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1...
04-Dec-2025 14:54:41 Finished task 'TestNG Parser' with result: Success
04-Dec-2025 14:54:41 Running post build plugin 'NCover Results Collector'
04-Dec-2025 14:54:41 Running post build plugin 'Artifact Copier'
04-Dec-2025 14:54:41 Publishing an artifact: Clover Report (System)
04-Dec-2025 14:54:47 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 6.163 s
04-Dec-2025 14:54:47 Publishing an artifact: TestNG report
04-Dec-2025 14:54:47 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB732-JOB1/build/reports/tests/test does not exist.
04-Dec-2025 14:54:47 The artifact hasn't been successfully published after 3.924 ms
04-Dec-2025 14:54:47 Running post build plugin 'Artifactory Release Management Staging'
04-Dec-2025 14:54:47 Running post build plugin 'Artifactory Build Info Copier'
04-Dec-2025 14:54:47 Running post build plugin 'Artifactory Gradle Properties Info Copier'
04-Dec-2025 14:54:47 Running post build plugin 'npm Cache Cleanup'
04-Dec-2025 14:54:47 Running post build plugin 'Clover Results Collector'
04-Dec-2025 14:54:47 Running post build plugin 'Docker Container Cleanup'
04-Dec-2025 14:54:47 Finalising the build...
04-Dec-2025 14:54:47 Stopping timer.
04-Dec-2025 14:54:47 Build JB-GDB732-JOB1-4 completed.
04-Dec-2025 14:54:47 Running on server: post build plugin 'NCover Results Collector'
04-Dec-2025 14:54:47 Running on server: post build plugin 'Build Hanging Detection Configuration'
04-Dec-2025 14:54:47 Running on server: post build plugin 'Clover Delta Calculator'
04-Dec-2025 14:54:47 Running on server: post build plugin 'Maven Dependencies Postprocessor'
04-Dec-2025 14:54:47 All post build plugins have finished
04-Dec-2025 14:54:47 Generating build results summary...
04-Dec-2025 14:54:48 Saving build results to disk...
04-Dec-2025 14:54:48 Logging substituted variables...
04-Dec-2025 14:54:48 Indexing build results...
04-Dec-2025 14:54:48 Finished building JB-GDB732-JOB1-4.