Build #4

Build: #4 failed

Job: Clover and Tests failed

Stages & jobs

  1. Default Stage

Build log

The build generated 348 lines of output. Download or view full build log

11-Dec-2025 10:57:22 Build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #4 (JB-GDB734-JOB1-4) started building on agent Default Agent
11-Dec-2025 10:57:22
11-Dec-2025 10:57:22 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1
11-Dec-2025 10:57:22 Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #4 (JB-GDB734-JOB1-4)
11-Dec-2025 10:57:22 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
11-Dec-2025 10:57:22 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1
11-Dec-2025 10:57:22 Updating source code to revision: 5857fe763e55a89397fc3bb157f282726c22b1a7
11-Dec-2025 10:57:22 Fetching 'refs/heads/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' from 'https://gitlab.jalview.org/jalview/jalview.git'.
11-Dec-2025 10:57:23 Checking out revision 5857fe763e55a89397fc3bb157f282726c22b1a7.
11-Dec-2025 10:57:23 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
11-Dec-2025 10:57:23    b80719b..5857fe7  bug/JAL-4107_jalviewjs_fixes_on_2_12_branch -> origin/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch
11-Dec-2025 10:57:23 Already on 'bug/JAL-4107_jalviewjs_fixes_on_2_12_branch'
11-Dec-2025 10:57:23 Your branch is behind 'origin/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' by 1 commit, and can be fast-forwarded.
11-Dec-2025 10:57:23   (use "git pull" to update your local branch)
11-Dec-2025 10:57:23 HEAD is now at 5857fe7 JAL-4107 Use Jalview.instanceExsits() in the test too
11-Dec-2025 10:57:23 Updated source code to revision: 5857fe763e55a89397fc3bb157f282726c22b1a7
11-Dec-2025 10:57:23 Finished task 'Checkout Default Repository' with result: Success
11-Dec-2025 10:57:23 Running pre-build action: VCS Version Collector
11-Dec-2025 10:57:23 Running pre-build action: Artifactory Release Staging
11-Dec-2025 10:57:23 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
11-Dec-2025 10:57:23 Bamboo Artifactory Plugin version: 2.6.2
11-Dec-2025 10:57:23
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #4 (JB-GDB734-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-GDB734-JOB1
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11-Dec-2025 10:57:23 2414
11-Dec-2025 10:57:24 Starting a Gradle Daemon (subsequent builds will be faster)
11-Dec-2025 10:57:29
11-Dec-2025 10:57:29 > Configure project :
11-Dec-2025 10:57:29 Using properties from file './utils/channels/default/channel_gradle.properties'
11-Dec-2025 10:57:30 JALVIEW_VERSION is set to '2.12.0'
11-Dec-2025 10:57:30 HEADLESS BUILD
11-Dec-2025 10:57:30 J2S ENABLED
11-Dec-2025 10:57:30 Using a LOCAL profile.
11-Dec-2025 10:57:31 eclipseDir exists
11-Dec-2025 10:57:32
11-Dec-2025 10:57:32 > Task :clean
11-Dec-2025 10:57:32 > Task :cleanClover
11-Dec-2025 10:57:32 > Task :cleanTest UP-TO-DATE
11-Dec-2025 10:57:34
11-Dec-2025 10:57:34 > Task :cloverInstrJava
11-Dec-2025 10:57:34 Clover: About to instrument 1253 files
11-Dec-2025 10:57:34 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Dec-2025 10:57:34 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'.
11-Dec-2025 10:57:34 Processing files at 1.9 source level.
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:36 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?
11-Dec-2025 10:57:37 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?
11-Dec-2025 10:57:37 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?
11-Dec-2025 10:57:37 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?
11-Dec-2025 10:57:37 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?
11-Dec-2025 10:57:37 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?
11-Dec-2025 10:57:37 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?
11-Dec-2025 10:57:37 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?
11-Dec-2025 10:57:37 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?
11-Dec-2025 10:57:37 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?
11-Dec-2025 10:57:37 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?
11-Dec-2025 10:57:37 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?
11-Dec-2025 10:57:37 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?
11-Dec-2025 10:57:43 Clover all over. Instrumented 1253 files (133 packages).
11-Dec-2025 10:57:45
11-Dec-2025 10:57:45 > Task :cloverInstrTests
11-Dec-2025 10:57:45 Clover: About to instrument test files
11-Dec-2025 10:57:45 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Dec-2025 10:57:45 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'.
11-Dec-2025 10:57:45 Processing files at 1.9 source level.
11-Dec-2025 10:57:48 Clover all over. Instrumented 315 files (58 packages).
11-Dec-2025 10:57:48 1770 test methods detected.
11-Dec-2025 10:57:48
11-Dec-2025 10:57:48 > Task :cloverInstr
11-Dec-2025 10:57:50
11-Dec-2025 10:57:50 > Task :compileCloverJava
11-Dec-2025 10:57:50 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
11-Dec-2025 10:57:50   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:57:50   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:57:50   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:57:50 Setting target compatibility to 11
11-Dec-2025 10:58:12 Note: Some input files use or override a deprecated API.
11-Dec-2025 10:58:12 Note: Recompile with -Xlint:deprecation for details.
11-Dec-2025 10:58:12 Note: Some input files use unchecked or unsafe operations.
11-Dec-2025 10:58:12 Note: Recompile with -Xlint:unchecked for details.
11-Dec-2025 10:58:19
11-Dec-2025 10:58:19 > Task :processCloverResources NO-SOURCE
11-Dec-2025 10:58:19 > Task :cloverClasses
11-Dec-2025 10:58:20 > Task :copyHelp
11-Dec-2025 10:58:21 > Task :buildIndices
11-Dec-2025 10:58:21 > Task :copyResources
11-Dec-2025 10:58:21 > Task :copyChannelResources
11-Dec-2025 10:58:21
11-Dec-2025 10:58:21 > Task :createBuildProperties
11-Dec-2025 10:58:21 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
11-Dec-2025 10:58:21   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:58:21
11-Dec-2025 10:58:21 > Task :buildResources
11-Dec-2025 10:58:21 > Task :copyDocs
11-Dec-2025 10:58:21
11-Dec-2025 10:58:21 > Task :convertMdFiles
11-Dec-2025 10:58:21 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
11-Dec-2025 10:58:21 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/releaseprocess.html
11-Dec-2025 10:58:21 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
11-Dec-2025 10:58:21 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
11-Dec-2025 10:58:21 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/building.html
11-Dec-2025 10:58:21 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/addingWebClient.html
11-Dec-2025 10:58:21 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/jalview-projects.html
11-Dec-2025 10:58:21 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
11-Dec-2025 10:58:22
11-Dec-2025 10:58:22 > Task :releasesTemplates
11-Dec-2025 10:58:22 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
11-Dec-2025 10:58:22   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:58:22   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:58:22 Stripping rc/test/etc for TEST
11-Dec-2025 10:58:22 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
11-Dec-2025 10:58:22
11-Dec-2025 10:58:22 > Task :prepare
11-Dec-2025 10:58:24
11-Dec-2025 10:58:24 > Task :compileJava
11-Dec-2025 10:58:24 Setting target compatibility to 11
11-Dec-2025 10:58:29 Note: Some input files use or override a deprecated API.
11-Dec-2025 10:58:29 Note: Recompile with -Xlint:deprecation for details.
11-Dec-2025 10:58:29 Note: Some input files use unchecked or unsafe operations.
11-Dec-2025 10:58:29 Note: Recompile with -Xlint:unchecked for details.
11-Dec-2025 10:58:34
11-Dec-2025 10:58:34 > Task :compileTestJava
11-Dec-2025 10:58:34 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
11-Dec-2025 10:58:34   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:58:34   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:58:34 Setting target compatibility to 11
11-Dec-2025 10:58:40 Note: Some input files use or override a deprecated API.
11-Dec-2025 10:58:40 Note: Recompile with -Xlint:deprecation for details.
11-Dec-2025 10:58:40 Note: Some input files use unchecked or unsafe operations.
11-Dec-2025 10:58:40 Note: Recompile with -Xlint:unchecked for details.
11-Dec-2025 10:58:41
11-Dec-2025 10:58:41 > Task :processTestResources
11-Dec-2025 10:58:41 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
11-Dec-2025 10:58:41   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:58:41   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:58:41   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:58:41   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:58:41   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:58:41   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:58:41   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:58:41   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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.
11-Dec-2025 10:58:41
11-Dec-2025 10:58:41 > Task :testClasses
11-Dec-2025 10:58:43
11-Dec-2025 10:58:43 > Task :testTask0
11-Dec-2025 10:58:43 Running tests WITH clover
11-Dec-2025 10:58:45 WARNING: An illegal reflective access operation has occurred
11-Dec-2025 10:58:45 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
11-Dec-2025 10:58:45 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
11-Dec-2025 10:58:45 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
11-Dec-2025 10:58:45 WARNING: All illegal access operations will be denied in a future release
11-Dec-2025 11:01:06 [144.096s][warning][gc,alloc] AWT-EventQueue-0: Retried waiting for GCLocker too often allocating 135080516 words
11-Dec-2025 11:01:16
11-Dec-2025 11:01:16 Gradle suite > Gradle test > jalview.project.Jalview2xmlTests > noDuplicatePdbMappingsMade FAILED
11-Dec-2025 11:01:16     java.lang.AssertionError: Expected only two mappings for 1A70 expected [2] but found [0]
11-Dec-2025 11:01:16         at org.testng.Assert.fail(Assert.java:110)
11-Dec-2025 11:01:16         at org.testng.Assert.failNotEquals(Assert.java:1413)
11-Dec-2025 11:01:16         at org.testng.Assert.assertEqualsImpl(Assert.java:149)
11-Dec-2025 11:01:16         at org.testng.Assert.assertEquals(Assert.java:131)
11-Dec-2025 11:01:16         at org.testng.Assert.assertEquals(Assert.java:1240)
11-Dec-2025 11:01:16         at jalview.project.Jalview2xmlTests.__CLR4_4_11umpz94jwy(Jalview2xmlTests.java:355)
11-Dec-2025 11:01:16         at jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade(Jalview2xmlTests.java:331)
11-Dec-2025 11:03:12
11-Dec-2025 11:03:12 2102 tests completed, 1 failed
11-Dec-2025 11:03:12 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask0/index.html
11-Dec-2025 11:03:14
11-Dec-2025 11:03:14 > Task :testTask1
11-Dec-2025 11:03:14 Running tests WITH clover
11-Dec-2025 11:03:15 WARNING: An illegal reflective access operation has occurred
11-Dec-2025 11:03:15 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
11-Dec-2025 11:03:15 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
11-Dec-2025 11:03:15 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
11-Dec-2025 11:03:15 WARNING: All illegal access operations will be denied in a future release
11-Dec-2025 11:05:23
11-Dec-2025 11:05:23 > Task :testTask2
11-Dec-2025 11:05:23 Running tests WITH clover
11-Dec-2025 11:05:24 WARNING: An illegal reflective access operation has occurred
11-Dec-2025 11:05:24 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
11-Dec-2025 11:05:24 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
11-Dec-2025 11:05:24 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
11-Dec-2025 11:05:24 WARNING: All illegal access operations will be denied in a future release
11-Dec-2025 11:05:28
11-Dec-2025 11:05:28 > Task :testTask3
11-Dec-2025 11:05:28 Running tests WITH clover
11-Dec-2025 11:05:29 WARNING: An illegal reflective access operation has occurred
11-Dec-2025 11:05:29 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
11-Dec-2025 11:05:29 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
11-Dec-2025 11:05:29 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
11-Dec-2025 11:05:29 WARNING: All illegal access operations will be denied in a future release
11-Dec-2025 11:05:47
11-Dec-2025 11:05:47 > Task :test NO-SOURCE
11-Dec-2025 11:05:47 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
11-Dec-2025 11:05:47 │jalview:testTask0 results: FAILURE (2102 tests, 2101 successes, 1 failures, 0 skipped) in 4 minutes, 30.295 seconds   │
11-Dec-2025 11:05:47 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask0/index.html│
11-Dec-2025 11:05:47 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Dec-2025 11:05:47 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 8.881 seconds        │
11-Dec-2025 11:05:47 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask1/index.html│
11-Dec-2025 11:05:47 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Dec-2025 11:05:47 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.996 seconds                     │
11-Dec-2025 11:05:47 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask2/index.html│
11-Dec-2025 11:05:47 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Dec-2025 11:05:47 │jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 20.938 seconds                  │
11-Dec-2025 11:05:47 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask3/index.html│
11-Dec-2025 11:05:47 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Dec-2025 11:05:47 │OVERALL: results: FAILURE (2179 tests, 2177 successes, 1 failures, 1 skipped) in 6 minutes, 65.110 seconds            │
11-Dec-2025 11:05:47 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
11-Dec-2025 11:05:47
11-Dec-2025 11:05:47 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
11-Dec-2025 11:05:47
11-Dec-2025 11:05:47 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
11-Dec-2025 11:05:47
11-Dec-2025 11:05:47 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
11-Dec-2025 11:05:47
11-Dec-2025 11:05:47 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
11-Dec-2025 11:05:47 Please consult deprecation warnings for more details.
11-Dec-2025 11:05:47 21 actionable tasks: 20 executed, 1 up-to-date
11-Dec-2025 11:05:47
11-Dec-2025 11:05:47 FAILURE: Build failed with an exception.
11-Dec-2025 11:05:47
11-Dec-2025 11:05:47 * Where:
11-Dec-2025 11:05:47 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build.gradle' line: 1964
11-Dec-2025 11:05:47
11-Dec-2025 11:05:47 * What went wrong:
11-Dec-2025 11:05:47 Failed tests!
11-Dec-2025 11:05:47
11-Dec-2025 11:05:47 * Try:
11-Dec-2025 11:05:47 > Run with --stacktrace option to get the stack trace.
11-Dec-2025 11:05:47 > Run with --info or --debug option to get more log output.
11-Dec-2025 11:05:47 > Run with --scan to get full insights.
11-Dec-2025 11:05:47
11-Dec-2025 11:05:47 * Get more help at https://help.gradle.org
11-Dec-2025 11:05:47
11-Dec-2025 11:05:47 BUILD FAILED in 8m 24s
11-Dec-2025 11:05:48
11-Dec-2025 11:05:48 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
11-Dec-2025 11:05:48 Finished task 'Run tests with openclover under gradle' with result: Failed
11-Dec-2025 11:05:48 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
11-Dec-2025 11:05:48 Bamboo Artifactory Plugin version: 2.6.2
11-Dec-2025 11:05:48
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #4 (JB-GDB734-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-GDB734-JOB1
... using extra environment variables:
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bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1
bamboo_planKey=JB-GDB734
bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_planRepository_username=
bamboo_repository_46498616_git_username=
bamboo_repository_46498616_previous_revision_number=b80719bcafaf18f88875dd6956bb3bd47ff21bed
bamboo_repository_46498616_name=Jalview Gitlab
HOME=/home/bamboo
bamboo_planRepository_1_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch
bamboo_repository_46498616_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
11-Dec-2025 11:05:48 2414
11-Dec-2025 11:05:53
11-Dec-2025 11:05:53 > Configure project :
11-Dec-2025 11:05:53 Using properties from file './utils/channels/default/channel_gradle.properties'
11-Dec-2025 11:05:53 JALVIEW_VERSION is set to '2.12.0'
11-Dec-2025 11:05:53 HEADLESS BUILD
11-Dec-2025 11:05:53 J2S ENABLED
11-Dec-2025 11:05:53 Using a LOCAL profile.
11-Dec-2025 11:05:54 eclipseDir exists
11-Dec-2025 11:05:57
11-Dec-2025 11:05:57 > Task :cloverHtmlReport
11-Dec-2025 11:05:57 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Dec-2025 11:05:58 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover'
11-Dec-2025 11:06:51 Done. Processed 137 packages in 52684ms (384ms per package).
11-Dec-2025 11:06:56
11-Dec-2025 11:06:56 > Task :cloverXmlReport
11-Dec-2025 11:06:56 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Dec-2025 11:06:57 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover/clover.xml'
11-Dec-2025 11:06:57
11-Dec-2025 11:06:57 > Task :cloverReport
11-Dec-2025 11:06:57
11-Dec-2025 11:06:57 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
11-Dec-2025 11:06:57
11-Dec-2025 11:06:57 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
11-Dec-2025 11:06:57
11-Dec-2025 11:06:57 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
11-Dec-2025 11:06:57
11-Dec-2025 11:06:57 BUILD SUCCESSFUL in 1m 8s
11-Dec-2025 11:06:57 2 actionable tasks: 2 executed
11-Dec-2025 11:06:57 Finished task 'Clover Report' with result: Success
11-Dec-2025 11:06:57 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
11-Dec-2025 11:06:57 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1...
11-Dec-2025 11:06:57 Failing task since 1 failing test cases were found.
11-Dec-2025 11:06:57 Finished task 'TestNG Parser' with result: Failed
11-Dec-2025 11:06:57 Running post build plugin 'NCover Results Collector'
11-Dec-2025 11:06:57 Running post build plugin 'Artifact Copier'
11-Dec-2025 11:06:57 Publishing an artifact: Clover Report (System)
11-Dec-2025 11:06:59 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.152 s
11-Dec-2025 11:06:59 Publishing an artifact: TestNG report
11-Dec-2025 11:06:59 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/test does not exist.
11-Dec-2025 11:06:59 The artifact hasn't been successfully published after 1.361 ms
11-Dec-2025 11:06:59 Running post build plugin 'Artifactory Release Management Staging'
11-Dec-2025 11:06:59 Running post build plugin 'Artifactory Build Info Copier'
11-Dec-2025 11:06:59 Running post build plugin 'Artifactory Gradle Properties Info Copier'
11-Dec-2025 11:06:59 Running post build plugin 'npm Cache Cleanup'
11-Dec-2025 11:06:59 Running post build plugin 'Clover Results Collector'
11-Dec-2025 11:06:59 Running post build plugin 'Docker Container Cleanup'
11-Dec-2025 11:06:59 Finalising the build...
11-Dec-2025 11:06:59 Stopping timer.
11-Dec-2025 11:06:59 Build JB-GDB734-JOB1-4 completed.
11-Dec-2025 11:06:59 Running on server: post build plugin 'NCover Results Collector'
11-Dec-2025 11:06:59 Running on server: post build plugin 'Build Hanging Detection Configuration'
11-Dec-2025 11:06:59 Running on server: post build plugin 'Clover Delta Calculator'
11-Dec-2025 11:06:59 Running on server: post build plugin 'Maven Dependencies Postprocessor'
11-Dec-2025 11:06:59 All post build plugins have finished
11-Dec-2025 11:06:59 Generating build results summary...
11-Dec-2025 11:07:00 Saving build results to disk...
11-Dec-2025 11:07:00 Logging substituted variables...
11-Dec-2025 11:07:00 Indexing build results...
11-Dec-2025 11:07:00 Finished building JB-GDB734-JOB1-4.