Build #3

Build: #3 was successful

Job: Clover and Tests was successful

Stages & jobs

  1. Default Stage

Build log

The build generated 317 lines of output. Download or view full build log

28-May-2026 15:40:23 Build Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #3 (JB-GDB747-JOB1-3) started building on agent Default Agent
28-May-2026 15:40:23
28-May-2026 15:40:23 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1
28-May-2026 15:40:23 Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #3 (JB-GDB747-JOB1-3)
28-May-2026 15:40:23 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
28-May-2026 15:40:23 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1
28-May-2026 15:40:23 Updating source code to revision: 6a7235f462b663d348cdbc6a03f0b3016af28fd3
28-May-2026 15:40:23 Fetching 'refs/heads/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts' from 'https://gitlab.jalview.org/jalview/jalview.git'.
28-May-2026 15:40:24 Checking out revision 6a7235f462b663d348cdbc6a03f0b3016af28fd3.
28-May-2026 15:40:24 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
28-May-2026 15:40:24    378b2a6..6a7235f  patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts -> origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
28-May-2026 15:40:24 * [new branch]      patch/JAL-4478_r212_initialpatch -> origin/patch/JAL-4478_r212_initialpatch
28-May-2026 15:40:24 * [new branch]      spike/na_hack_JAL-4673 -> origin/spike/na_hack_JAL-4673
28-May-2026 15:40:24 Already on 'patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts'
28-May-2026 15:40:24 Your branch is behind 'origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts' by 1 commit, and can be fast-forwarded.
28-May-2026 15:40:24   (use "git pull" to update your local branch)
28-May-2026 15:40:24 HEAD is now at 6a7235f JAL-4658 fix up failing test due to the annotation score model
28-May-2026 15:40:24 Updated source code to revision: 6a7235f462b663d348cdbc6a03f0b3016af28fd3
28-May-2026 15:40:24 Finished task 'Checkout Default Repository' with result: Success
28-May-2026 15:40:24 Running pre-build action: VCS Version Collector
28-May-2026 15:40:24 Running pre-build action: Artifactory Release Staging
28-May-2026 15:40:24 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
28-May-2026 15:40:24 Bamboo Artifactory Plugin version: 2.6.2
28-May-2026 15:40:24
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #3 (JB-GDB747-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-GDB747-JOB1
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28-May-2026 15:40:24 2414
28-May-2026 15:40:26
28-May-2026 15:40:26 > Configure project :
28-May-2026 15:40:26 Using properties from file './utils/channels/default/channel_gradle.properties'
28-May-2026 15:40:26 JALVIEW_VERSION is set to '2.12.0'
28-May-2026 15:40:26 HEADLESS BUILD
28-May-2026 15:40:26 J2S ENABLED
28-May-2026 15:40:26 Using a LOCAL profile.
28-May-2026 15:40:26 eclipseDir exists
28-May-2026 15:40:27
28-May-2026 15:40:27 > Task :clean
28-May-2026 15:40:27 > Task :cleanClover
28-May-2026 15:40:27 > Task :cleanTest UP-TO-DATE
28-May-2026 15:40:29
28-May-2026 15:40:29 > Task :cloverInstrJava
28-May-2026 15:40:29 Clover: About to instrument 1256 files
28-May-2026 15:40:29 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
28-May-2026 15:40:29 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover.db'.
28-May-2026 15:40:29 Processing files at 1.9 source level.
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:32 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?
28-May-2026 15:40:33 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?
28-May-2026 15:40:33 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?
28-May-2026 15:40:33 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?
28-May-2026 15:40:33 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?
28-May-2026 15:40:33 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?
28-May-2026 15:40:33 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?
28-May-2026 15:40:33 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?
28-May-2026 15:40:33 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?
28-May-2026 15:40:33 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?
28-May-2026 15:40:33 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?
28-May-2026 15:40:33 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?
28-May-2026 15:40:33 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?
28-May-2026 15:40:39 Clover all over. Instrumented 1256 files (133 packages).
28-May-2026 15:40:41
28-May-2026 15:40:41 > Task :cloverInstrTests
28-May-2026 15:40:41 Clover: About to instrument test files
28-May-2026 15:40:41 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
28-May-2026 15:40:41 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover.db'.
28-May-2026 15:40:41 Processing files at 1.9 source level.
28-May-2026 15:40:44 Clover all over. Instrumented 315 files (58 packages).
28-May-2026 15:40:44 1771 test methods detected.
28-May-2026 15:40:44
28-May-2026 15:40:44 > Task :cloverInstr
28-May-2026 15:40:46
28-May-2026 15:40:46 > Task :compileCloverJava
28-May-2026 15:40:46 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
28-May-2026 15:40:46   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:40:46   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:40:46   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:40:46 Setting target compatibility to 11
28-May-2026 15:41:00 Note: Some input files use or override a deprecated API.
28-May-2026 15:41:00 Note: Recompile with -Xlint:deprecation for details.
28-May-2026 15:41:00 Note: Some input files use unchecked or unsafe operations.
28-May-2026 15:41:00 Note: Recompile with -Xlint:unchecked for details.
28-May-2026 15:41:05
28-May-2026 15:41:05 > Task :processCloverResources NO-SOURCE
28-May-2026 15:41:05 > Task :cloverClasses
28-May-2026 15:41:06 > Task :copyHelp
28-May-2026 15:41:07 > Task :buildIndices
28-May-2026 15:41:07 > Task :copyResources
28-May-2026 15:41:07 > Task :copyChannelResources
28-May-2026 15:41:07
28-May-2026 15:41:07 > Task :createBuildProperties
28-May-2026 15:41:07 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
28-May-2026 15:41:07   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:41:07
28-May-2026 15:41:07 > Task :buildResources
28-May-2026 15:41:07 > Task :copyDocs
28-May-2026 15:41:07
28-May-2026 15:41:07 > Task :convertMdFiles
28-May-2026 15:41:07 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
28-May-2026 15:41:07 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/releaseprocess.html
28-May-2026 15:41:07 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
28-May-2026 15:41:07 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
28-May-2026 15:41:07 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/building.html
28-May-2026 15:41:07 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/addingWebClient.html
28-May-2026 15:41:07 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/jalview-projects.html
28-May-2026 15:41:07 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
28-May-2026 15:41:07
28-May-2026 15:41:07 > Task :releasesTemplates
28-May-2026 15:41:07 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
28-May-2026 15:41:07   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:41:07   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:41:07 Stripping rc/test/etc for TEST
28-May-2026 15:41:07 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
28-May-2026 15:41:07
28-May-2026 15:41:07 > Task :prepare
28-May-2026 15:41:09
28-May-2026 15:41:09 > Task :compileJava
28-May-2026 15:41:09 Setting target compatibility to 11
28-May-2026 15:41:15 Note: Some input files use or override a deprecated API.
28-May-2026 15:41:15 Note: Recompile with -Xlint:deprecation for details.
28-May-2026 15:41:15 Note: Some input files use unchecked or unsafe operations.
28-May-2026 15:41:15 Note: Recompile with -Xlint:unchecked for details.
28-May-2026 15:41:17
28-May-2026 15:41:17 > Task :compileTestJava
28-May-2026 15:41:17 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
28-May-2026 15:41:17   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:41:17   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:41:17 Setting target compatibility to 11
28-May-2026 15:41:23 Note: Some input files use or override a deprecated API.
28-May-2026 15:41:23 Note: Recompile with -Xlint:deprecation for details.
28-May-2026 15:41:23 Note: Some input files use unchecked or unsafe operations.
28-May-2026 15:41:23 Note: Recompile with -Xlint:unchecked for details.
28-May-2026 15:41:24
28-May-2026 15:41:24 > Task :processTestResources
28-May-2026 15:41:24 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
28-May-2026 15:41:24   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:41:24   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:41:24   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:41:24   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:41:24   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:41:24   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:41:24   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:41:24   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
28-May-2026 15:41:24
28-May-2026 15:41:24 > Task :testClasses
28-May-2026 15:41:26
28-May-2026 15:41:26 > Task :testTask0
28-May-2026 15:41:26 Running tests WITH clover
28-May-2026 15:41:28 WARNING: An illegal reflective access operation has occurred
28-May-2026 15:41:28 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
28-May-2026 15:41:28 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
28-May-2026 15:41:28 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
28-May-2026 15:41:28 WARNING: All illegal access operations will be denied in a future release
28-May-2026 15:46:25
28-May-2026 15:46:25 > Task :testTask1
28-May-2026 15:46:25 Running tests WITH clover
28-May-2026 15:46:26 WARNING: An illegal reflective access operation has occurred
28-May-2026 15:46:26 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
28-May-2026 15:46:26 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
28-May-2026 15:46:26 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
28-May-2026 15:46:26 WARNING: All illegal access operations will be denied in a future release
28-May-2026 15:48:33
28-May-2026 15:48:33 > Task :testTask2
28-May-2026 15:48:33 Running tests WITH clover
28-May-2026 15:48:35 WARNING: An illegal reflective access operation has occurred
28-May-2026 15:48:35 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
28-May-2026 15:48:35 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
28-May-2026 15:48:35 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
28-May-2026 15:48:35 WARNING: All illegal access operations will be denied in a future release
28-May-2026 15:48:38
28-May-2026 15:48:38 > Task :testTask3
28-May-2026 15:48:38 Running tests WITH clover
28-May-2026 15:48:39 WARNING: An illegal reflective access operation has occurred
28-May-2026 15:48:39 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
28-May-2026 15:48:39 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
28-May-2026 15:48:39 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
28-May-2026 15:48:39 WARNING: All illegal access operations will be denied in a future release
28-May-2026 15:48:58
28-May-2026 15:48:58 > Task :test NO-SOURCE
28-May-2026 15:48:58 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
28-May-2026 15:48:58 │jalview:testTask0 results: SUCCESS (2104 tests, 2104 successes, 0 failures, 0 skipped) in 4 minutes, 58.366 seconds   │
28-May-2026 15:48:58 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/tests/testTask0/index.html│
28-May-2026 15:48:58 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
28-May-2026 15:48:58 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 8.327 seconds        │
28-May-2026 15:48:58 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/tests/testTask1/index.html│
28-May-2026 15:48:58 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
28-May-2026 15:48:58 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 5.177 seconds                     │
28-May-2026 15:48:58 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/tests/testTask2/index.html│
28-May-2026 15:48:58 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
28-May-2026 15:48:58 │jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 21.625 seconds                  │
28-May-2026 15:48:58 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/tests/testTask3/index.html│
28-May-2026 15:48:58 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
28-May-2026 15:48:58 │OVERALL: results: SUCCESS (2181 tests, 2180 successes, 0 failures, 1 skipped) in 6 minutes, 93.495 seconds            │
28-May-2026 15:48:58 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
28-May-2026 15:48:58
28-May-2026 15:48:58 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
28-May-2026 15:48:58
28-May-2026 15:48:58 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
28-May-2026 15:48:58
28-May-2026 15:48:58 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
28-May-2026 15:48:58
28-May-2026 15:48:58 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
28-May-2026 15:48:58 Please consult deprecation warnings for more details.
28-May-2026 15:48:58
28-May-2026 15:48:58 BUILD SUCCESSFUL in 8m 33s
28-May-2026 15:48:58 21 actionable tasks: 20 executed, 1 up-to-date
28-May-2026 15:48:58 Finished task 'Run tests with openclover under gradle' with result: Success
28-May-2026 15:48:58 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
28-May-2026 15:48:58 Bamboo Artifactory Plugin version: 2.6.2
28-May-2026 15:48:58
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #3 (JB-GDB747-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-GDB747-JOB1
... using extra environment variables:
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bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_repository_revision_number=6a7235f462b663d348cdbc6a03f0b3016af28fd3
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB747-JOB1-3
JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048
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bamboo_planRepository_1_name=Jalview Gitlab
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bamboo_repository_48169034_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
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bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=6a7235f462b663d348cdbc6a03f0b3016af28fd3
bamboo_buildTimeStamp=2026-05-28T15:40:23.872+01:00
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bamboo_planRepository_previousRevision=378b2a60f0e594a59de7f5ac31f20b1148702c0a
bamboo_repository_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
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bamboo_repository_branch_name=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=6a7235f462b663d348cdbc6a03f0b3016af28fd3
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bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant
bamboo_repository_48169034_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
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
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bamboo_planRepository_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609
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bamboo_capability_system_git_executable=/bin/git
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bamboo_planRepository_1_previousRevision=378b2a60f0e594a59de7f5ac31f20b1148702c0a
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bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_repository_48169034_previous_revision_number=378b2a60f0e594a59de7f5ac31f20b1148702c0a
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bamboo_plan_storageTag=plan-47972499
bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle
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bamboo_planRepository_1_username=
bamboo_planRepository_type=gitv2
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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_repository_48169034_revision_number=6a7235f462b663d348cdbc6a03f0b3016af28fd3
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-GDB747-JOB1
bamboo_planKey=JB-GDB747
bamboo_repository_48169034_git_username=
bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_planRepository_username=
HOME=/home/bamboo
bamboo_planRepository_1_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
28-May-2026 15:48:59 2414
28-May-2026 15:49:05
28-May-2026 15:49:05 > Configure project :
28-May-2026 15:49:05 Using properties from file './utils/channels/default/channel_gradle.properties'
28-May-2026 15:49:05 JALVIEW_VERSION is set to '2.12.0'
28-May-2026 15:49:05 HEADLESS BUILD
28-May-2026 15:49:05 J2S ENABLED
28-May-2026 15:49:05 Using a LOCAL profile.
28-May-2026 15:49:06 eclipseDir exists
28-May-2026 15:49:08
28-May-2026 15:49:08 > Task :cloverHtmlReport
28-May-2026 15:49:08 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
28-May-2026 15:49:10 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/clover'
28-May-2026 15:50:06 Done. Processed 137 packages in 55808ms (407ms per package).
28-May-2026 15:50:13
28-May-2026 15:50:13 > Task :cloverXmlReport
28-May-2026 15:50:13 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
28-May-2026 15:50:16 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/clover/clover.xml'
28-May-2026 15:50:16
28-May-2026 15:50:16 > Task :cloverReport
28-May-2026 15:50:16
28-May-2026 15:50:16 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
28-May-2026 15:50:16
28-May-2026 15:50:16 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
28-May-2026 15:50:16
28-May-2026 15:50:16 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
28-May-2026 15:50:16
28-May-2026 15:50:16 BUILD SUCCESSFUL in 1m 17s
28-May-2026 15:50:16 2 actionable tasks: 2 executed
28-May-2026 15:50:16 Finished task 'Clover Report' with result: Success
28-May-2026 15:50:16 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
28-May-2026 15:50:16 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1...
28-May-2026 15:50:16 Finished task 'TestNG Parser' with result: Success
28-May-2026 15:50:16 Running post build plugin 'NCover Results Collector'
28-May-2026 15:50:16 Running post build plugin 'Artifact Copier'
28-May-2026 15:50:16 Publishing an artifact: Clover Report (System)
28-May-2026 15:50:18 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.043 s
28-May-2026 15:50:18 Publishing an artifact: TestNG report
28-May-2026 15:50:18 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/tests/test does not exist.
28-May-2026 15:50:18 The artifact hasn't been successfully published after 3.186 ms
28-May-2026 15:50:18 Running post build plugin 'Artifactory Release Management Staging'
28-May-2026 15:50:18 Running post build plugin 'Artifactory Build Info Copier'
28-May-2026 15:50:18 Running post build plugin 'Artifactory Gradle Properties Info Copier'
28-May-2026 15:50:18 Running post build plugin 'npm Cache Cleanup'
28-May-2026 15:50:18 Running post build plugin 'Clover Results Collector'
28-May-2026 15:50:18 Running post build plugin 'Docker Container Cleanup'
28-May-2026 15:50:18 Finalising the build...
28-May-2026 15:50:18 Stopping timer.
28-May-2026 15:50:18 Build JB-GDB747-JOB1-3 completed.
28-May-2026 15:50:18 Running on server: post build plugin 'NCover Results Collector'
28-May-2026 15:50:18 Running on server: post build plugin 'Build Hanging Detection Configuration'
28-May-2026 15:50:18 Running on server: post build plugin 'Clover Delta Calculator'
28-May-2026 15:50:18 Running on server: post build plugin 'Maven Dependencies Postprocessor'
28-May-2026 15:50:18 All post build plugins have finished
28-May-2026 15:50:18 Generating build results summary...
28-May-2026 15:50:19 Saving build results to disk...
28-May-2026 15:50:19 Logging substituted variables...
28-May-2026 15:50:19 Indexing build results...
28-May-2026 15:50:19 Finished building JB-GDB747-JOB1-3.