Build #4

Build: #4 failed

Job: Clover and Tests failed

Stages & jobs

  1. Default Stage

Build log

The build generated 278 lines of output. Download or view full build log

27-Nov-2025 15:32:16 Build Jalview Builds - Gradle Develop Build - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Clover and Tests #4 (JB-GDB729-JOB1-4) started building on agent Default Agent
27-Nov-2025 15:32:16
27-Nov-2025 15:32:16 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1
27-Nov-2025 15:32:16 Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Clover and Tests #4 (JB-GDB729-JOB1-4)
27-Nov-2025 15:32:16 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
27-Nov-2025 15:32:16 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1
27-Nov-2025 15:32:16 Updating source code to revision: acbb7d39481e53918a63f69cd008b4f6bbd7a588
27-Nov-2025 15:32:16 Fetching 'refs/heads/bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus' from 'https://gitlab.jalview.org/jalview/jalview.git'.
27-Nov-2025 15:32:17 Checking out revision acbb7d39481e53918a63f69cd008b4f6bbd7a588.
27-Nov-2025 15:32:17 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
27-Nov-2025 15:32:17    fcc5607..acbb7d3  bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus -> origin/bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus
27-Nov-2025 15:32:17 Already on 'bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus'
27-Nov-2025 15:32:17 Your branch is behind 'origin/bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus' by 1 commit, and can be fast-forwarded.
27-Nov-2025 15:32:17   (use "git pull" to update your local branch)
27-Nov-2025 15:32:17 HEAD is now at acbb7d3 JAL-835 fix format list tests for a3m
27-Nov-2025 15:32:17 Updated source code to revision: acbb7d39481e53918a63f69cd008b4f6bbd7a588
27-Nov-2025 15:32:17 Finished task 'Checkout Default Repository' with result: Success
27-Nov-2025 15:32:17 Running pre-build action: VCS Version Collector
27-Nov-2025 15:32:17 Running pre-build action: Artifactory Release Staging
27-Nov-2025 15:32:17 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
27-Nov-2025 15:32:17 Bamboo Artifactory Plugin version: 2.6.2
27-Nov-2025 15:32:17
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Clover and Tests #4 (JB-GDB729-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-GDB729-JOB1
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27-Nov-2025 15:32:17 444
27-Nov-2025 15:32:19
27-Nov-2025 15:32:19 > Configure project :
27-Nov-2025 15:32:19 Using properties from file './utils/channels/default/channel_gradle.properties'
27-Nov-2025 15:32:19 JALVIEW_VERSION is set to '2.11.5.1'
27-Nov-2025 15:32:19 HEADLESS BUILD
27-Nov-2025 15:32:19 J2S ENABLED
27-Nov-2025 15:32:19 Using a LOCAL profile.
27-Nov-2025 15:32:19 eclipseDir exists
27-Nov-2025 15:32:20
27-Nov-2025 15:32:20 > Task :clean
27-Nov-2025 15:32:20 > Task :cleanClover
27-Nov-2025 15:32:20 > Task :cleanTest UP-TO-DATE
27-Nov-2025 15:32:22
27-Nov-2025 15:32:22 > Task :cloverInstrJava
27-Nov-2025 15:32:22 Clover: About to instrument 1107 files
27-Nov-2025 15:32:22 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
27-Nov-2025 15:32:22 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/clover/clover.db'.
27-Nov-2025 15:32:22 Processing files at 1.9 source level.
27-Nov-2025 15:32:26 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?
27-Nov-2025 15:32:26 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?
27-Nov-2025 15:32:26 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?
27-Nov-2025 15:32:26 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?
27-Nov-2025 15:32:26 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?
27-Nov-2025 15:32:26 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?
27-Nov-2025 15:32:26 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?
27-Nov-2025 15:32:32 Clover all over. Instrumented 1107 files (112 packages).
27-Nov-2025 15:32:34
27-Nov-2025 15:32:34 > Task :cloverInstrTests
27-Nov-2025 15:32:34 Clover: About to instrument test files
27-Nov-2025 15:32:34 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
27-Nov-2025 15:32:34 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/clover/clover.db'.
27-Nov-2025 15:32:34 Processing files at 1.9 source level.
27-Nov-2025 15:32:38 Clover all over. Instrumented 293 files (52 packages).
27-Nov-2025 15:32:38 1624 test methods detected.
27-Nov-2025 15:32:38
27-Nov-2025 15:32:38 > Task :cloverInstr
27-Nov-2025 15:32:40
27-Nov-2025 15:32:40 > Task :compileCloverJava
27-Nov-2025 15:32:40 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
27-Nov-2025 15:32:40   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:32:40   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:32:40   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:32:40 Setting target compatibility to 11
27-Nov-2025 15:32:56 Note: Some input files use or override a deprecated API.
27-Nov-2025 15:32:56 Note: Recompile with -Xlint:deprecation for details.
27-Nov-2025 15:32:56 Note: Some input files use unchecked or unsafe operations.
27-Nov-2025 15:32:56 Note: Recompile with -Xlint:unchecked for details.
27-Nov-2025 15:33:02
27-Nov-2025 15:33:02 > Task :processCloverResources NO-SOURCE
27-Nov-2025 15:33:02 > Task :cloverClasses
27-Nov-2025 15:33:02 > Task :copyHelp
27-Nov-2025 15:33:03 > Task :buildIndices
27-Nov-2025 15:33:03 > Task :copyResources
27-Nov-2025 15:33:03 > Task :copyChannelResources
27-Nov-2025 15:33:03
27-Nov-2025 15:33:03 > Task :createBuildProperties
27-Nov-2025 15:33:03 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
27-Nov-2025 15:33:03   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:33:03
27-Nov-2025 15:33:03 > Task :buildResources
27-Nov-2025 15:33:03 > Task :copyDocs
27-Nov-2025 15:33:04
27-Nov-2025 15:33:04 > Task :convertMdFiles
27-Nov-2025 15:33:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
27-Nov-2025 15:33:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/resources/doc_build/doc/releaseprocess.html
27-Nov-2025 15:33:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
27-Nov-2025 15:33:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/resources/doc_build/doc/building.html
27-Nov-2025 15:33:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/resources/doc_build/doc/jalview-projects.html
27-Nov-2025 15:33:04
27-Nov-2025 15:33:04 > Task :releasesTemplates
27-Nov-2025 15:33:04 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
27-Nov-2025 15:33:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:33:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:33:04 Stripping rc/test/etc for TEST
27-Nov-2025 15:33:04 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
27-Nov-2025 15:33:04
27-Nov-2025 15:33:04 > Task :prepare
27-Nov-2025 15:33:06
27-Nov-2025 15:33:06 > Task :compileJava
27-Nov-2025 15:33:06 Setting target compatibility to 11
27-Nov-2025 15:33:11 Note: Some input files use or override a deprecated API.
27-Nov-2025 15:33:11 Note: Recompile with -Xlint:deprecation for details.
27-Nov-2025 15:33:11 Note: Some input files use unchecked or unsafe operations.
27-Nov-2025 15:33:11 Note: Recompile with -Xlint:unchecked for details.
27-Nov-2025 15:33:14
27-Nov-2025 15:33:14 > Task :compileTestJava
27-Nov-2025 15:33:14 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
27-Nov-2025 15:33:14   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:33:14   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:33:14 Setting target compatibility to 11
27-Nov-2025 15:33:19 Note: Some input files use or override a deprecated API.
27-Nov-2025 15:33:19 Note: Recompile with -Xlint:deprecation for details.
27-Nov-2025 15:33:19 Note: Some input files use unchecked or unsafe operations.
27-Nov-2025 15:33:19 Note: Recompile with -Xlint:unchecked for details.
27-Nov-2025 15:33:20
27-Nov-2025 15:33:20 > Task :processTestResources
27-Nov-2025 15:33:20 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
27-Nov-2025 15:33:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:33:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:33:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:33:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:33:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:33:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:33:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:33:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-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.
27-Nov-2025 15:33:20
27-Nov-2025 15:33:20 > Task :testClasses
27-Nov-2025 15:33:22
27-Nov-2025 15:33:22 > Task :testTask0
27-Nov-2025 15:33:22 Running tests WITH clover
27-Nov-2025 15:33:26 WARNING: An illegal reflective access operation has occurred
27-Nov-2025 15:33:26 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
27-Nov-2025 15:33:26 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
27-Nov-2025 15:33:26 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
27-Nov-2025 15:33:26 WARNING: All illegal access operations will be denied in a future release
27-Nov-2025 15:38:14
27-Nov-2025 15:38:14 > Task :testTask1
27-Nov-2025 15:38:14 Running tests WITH clover
27-Nov-2025 15:38:17 WARNING: An illegal reflective access operation has occurred
27-Nov-2025 15:38:17 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
27-Nov-2025 15:38:17 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
27-Nov-2025 15:38:17 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
27-Nov-2025 15:38:17 WARNING: All illegal access operations will be denied in a future release
27-Nov-2025 15:38:20
27-Nov-2025 15:38:20 Gradle suite > Gradle test > jalview.gui.AnnotationLabelsTest2.testIdWidthChanges[1](./test/files/annotation_label_width/sample.a2m, true, 50, 70, 100, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json, true, pLDDT, null, 114, 117) FAILED
27-Nov-2025 15:38:20     java.lang.AssertionError: idWidth (221) is not narrower than 117 expected [true] but found [false]
27-Nov-2025 15:38:20         at org.testng.Assert.fail(Assert.java:94)
27-Nov-2025 15:38:20         at org.testng.Assert.failNotEquals(Assert.java:496)
27-Nov-2025 15:38:20         at org.testng.Assert.assertTrue(Assert.java:42)
27-Nov-2025 15:38:20         at jalview.gui.AnnotationLabelsTest2.__CLR4_4_140rce13thp(AnnotationLabelsTest2.java:158)
27-Nov-2025 15:38:20         at jalview.gui.AnnotationLabelsTest2.testIdWidthChanges(AnnotationLabelsTest2.java:100)
27-Nov-2025 15:40:50
27-Nov-2025 15:40:50 62 tests completed, 1 failed
27-Nov-2025 15:40:50 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/tests/testTask1/index.html
27-Nov-2025 15:40:52
27-Nov-2025 15:40:52 > Task :testTask2
27-Nov-2025 15:40:52 Running tests WITH clover
27-Nov-2025 15:40:57
27-Nov-2025 15:40:57 > Task :testTask3
27-Nov-2025 15:40:57 Running tests WITH clover
27-Nov-2025 15:40:59 WARNING: An illegal reflective access operation has occurred
27-Nov-2025 15:40:59 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
27-Nov-2025 15:40:59 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
27-Nov-2025 15:40:59 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
27-Nov-2025 15:40:59 WARNING: All illegal access operations will be denied in a future release
27-Nov-2025 15:41:57
27-Nov-2025 15:41:57 FAILURE: Build failed with an exception.
27-Nov-2025 15:41:57
27-Nov-2025 15:41:57 * Where:
27-Nov-2025 15:41:57 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build.gradle' line: 1967
27-Nov-2025 15:41:57
27-Nov-2025 15:41:57 * What went wrong:
27-Nov-2025 15:41:57 Failed tests!
27-Nov-2025 15:41:57
27-Nov-2025 15:41:57 * Try:
27-Nov-2025 15:41:57 > Run with --stacktrace option to get the stack trace.
27-Nov-2025 15:41:57 > Run with --info or --debug option to get more log output.
27-Nov-2025 15:41:57 > Run with --scan to get full insights.
27-Nov-2025 15:41:57
27-Nov-2025 15:41:57 * Get more help at https://help.gradle.org
27-Nov-2025 15:41:57
27-Nov-2025 15:41:57 BUILD FAILED in 9m 39s
27-Nov-2025 15:41:57
27-Nov-2025 15:41:57 > Task :test NO-SOURCE
27-Nov-2025 15:41:57 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
27-Nov-2025 15:41:57 │jalview:testTask0 results: SUCCESS (1824 tests, 1824 successes, 0 failures, 0 skipped) in 4 minutes, 51.393 seconds   │
27-Nov-2025 15:41:57 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/tests/testTask0/index.html│
27-Nov-2025 15:41:57 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
27-Nov-2025 15:41:57 │jalview:testTask1 results: FAILURE (62 tests, 61 successes, 1 failures, 0 skipped) in 2 minutes, 38.250 seconds       │
27-Nov-2025 15:41:57 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/tests/testTask1/index.html│
27-Nov-2025 15:41:57 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
27-Nov-2025 15:41:57 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.337 seconds                     │
27-Nov-2025 15:41:57 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/tests/testTask2/index.html│
27-Nov-2025 15:41:57 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
27-Nov-2025 15:41:57 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 1.790 seconds        │
27-Nov-2025 15:41:57 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/tests/testTask3/index.html│
27-Nov-2025 15:41:57 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
27-Nov-2025 15:41:57 │OVERALL: results: FAILURE (1912 tests, 1911 successes, 1 failures, 0 skipped) in 7 minutes, 95.770 seconds            │
27-Nov-2025 15:41:57 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
27-Nov-2025 15:41:57
27-Nov-2025 15:41:57 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
27-Nov-2025 15:41:57
27-Nov-2025 15:41:57 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
27-Nov-2025 15:41:57
27-Nov-2025 15:41:57 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
27-Nov-2025 15:41:57
27-Nov-2025 15:41:57 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
27-Nov-2025 15:41:57 Please consult deprecation warnings for more details.
27-Nov-2025 15:41:57 21 actionable tasks: 20 executed, 1 up-to-date
27-Nov-2025 15:41:57
27-Nov-2025 15:41:57 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
27-Nov-2025 15:41:57 Finished task 'Run tests with openclover under gradle' with result: Failed
27-Nov-2025 15:41:57 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
27-Nov-2025 15:41:57 Bamboo Artifactory Plugin version: 2.6.2
27-Nov-2025 15:41:57
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Clover and Tests #4 (JB-GDB729-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-GDB729-JOB1
... using extra environment variables:
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bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB729-JOB1-4
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bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
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27-Nov-2025 15:41:57 444
27-Nov-2025 15:42:04
27-Nov-2025 15:42:04 > Configure project :
27-Nov-2025 15:42:04 Using properties from file './utils/channels/default/channel_gradle.properties'
27-Nov-2025 15:42:04 JALVIEW_VERSION is set to '2.11.5.1'
27-Nov-2025 15:42:04 HEADLESS BUILD
27-Nov-2025 15:42:04 J2S ENABLED
27-Nov-2025 15:42:05 Using a LOCAL profile.
27-Nov-2025 15:42:06 eclipseDir exists
27-Nov-2025 15:42:08
27-Nov-2025 15:42:08 > Task :cloverHtmlReport
27-Nov-2025 15:42:08 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
27-Nov-2025 15:42:10 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/clover'
27-Nov-2025 15:43:09 Done. Processed 116 packages in 59553ms (513ms per package).
27-Nov-2025 15:43:17
27-Nov-2025 15:43:17 > Task :cloverXmlReport
27-Nov-2025 15:43:17 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
27-Nov-2025 15:43:20 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/clover/clover.xml'
27-Nov-2025 15:43:20
27-Nov-2025 15:43:20 > Task :cloverReport
27-Nov-2025 15:43:20
27-Nov-2025 15:43:20 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
27-Nov-2025 15:43:20
27-Nov-2025 15:43:20 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
27-Nov-2025 15:43:20
27-Nov-2025 15:43:20 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
27-Nov-2025 15:43:20
27-Nov-2025 15:43:20 BUILD SUCCESSFUL in 1m 22s
27-Nov-2025 15:43:20 2 actionable tasks: 2 executed
27-Nov-2025 15:43:20 Finished task 'Clover Report' with result: Success
27-Nov-2025 15:43:20 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
27-Nov-2025 15:43:20 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1...
27-Nov-2025 15:43:20 Failing task since 1 failing test cases were found.
27-Nov-2025 15:43:20 Finished task 'TestNG Parser' with result: Failed
27-Nov-2025 15:43:20 Running post build plugin 'NCover Results Collector'
27-Nov-2025 15:43:20 Running post build plugin 'Artifact Copier'
27-Nov-2025 15:43:20 Publishing an artifact: Clover Report (System)
27-Nov-2025 15:43:28 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 7.366 s
27-Nov-2025 15:43:28 Publishing an artifact: TestNG report
27-Nov-2025 15:43:28 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB729-JOB1/build/reports/tests/test does not exist.
27-Nov-2025 15:43:28 The artifact hasn't been successfully published after 3.818 ms
27-Nov-2025 15:43:28 Running post build plugin 'Artifactory Release Management Staging'
27-Nov-2025 15:43:28 Running post build plugin 'Artifactory Build Info Copier'
27-Nov-2025 15:43:28 Running post build plugin 'Artifactory Gradle Properties Info Copier'
27-Nov-2025 15:43:28 Running post build plugin 'npm Cache Cleanup'
27-Nov-2025 15:43:28 Running post build plugin 'Clover Results Collector'
27-Nov-2025 15:43:28 Running post build plugin 'Docker Container Cleanup'
27-Nov-2025 15:43:28 Finalising the build...
27-Nov-2025 15:43:28 Stopping timer.
27-Nov-2025 15:43:28 Build JB-GDB729-JOB1-4 completed.
27-Nov-2025 15:43:28 Running on server: post build plugin 'NCover Results Collector'
27-Nov-2025 15:43:28 Running on server: post build plugin 'Build Hanging Detection Configuration'
27-Nov-2025 15:43:28 Running on server: post build plugin 'Clover Delta Calculator'
27-Nov-2025 15:43:28 Running on server: post build plugin 'Maven Dependencies Postprocessor'
27-Nov-2025 15:43:28 All post build plugins have finished
27-Nov-2025 15:43:28 Generating build results summary...
27-Nov-2025 15:43:29 Saving build results to disk...
27-Nov-2025 15:43:29 Logging substituted variables...
27-Nov-2025 15:43:29 Indexing build results...
27-Nov-2025 15:43:29 Finished building JB-GDB729-JOB1-4.