Build #8

Build and run tests under Java 11

Build: #8 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

10-Dec-2025 07:51:22 Build Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #8 (JB-GDB731-JOB1-8) started building on agent Default Agent
10-Dec-2025 07:51:22
10-Dec-2025 07:51:23 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1
10-Dec-2025 07:51:23 Executing build Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #8 (JB-GDB731-JOB1-8)
10-Dec-2025 07:51:23 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
10-Dec-2025 07:51:23 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1
10-Dec-2025 07:51:23 Updating source code to revision: b00f7c47ccd3e44f5d4402f33e29b4b95c337419
10-Dec-2025 07:51:23 Fetching 'refs/heads/development/Release_2_11_5_Branch' from 'https://gitlab.jalview.org/jalview/jalview.git'.
10-Dec-2025 07:51:23 Checking out revision b00f7c47ccd3e44f5d4402f33e29b4b95c337419.
10-Dec-2025 07:51:23 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
10-Dec-2025 07:51:23    3ad0f0a..b00f7c4  development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch
10-Dec-2025 07:51:23 * [new branch]      bug/JAL-4559_old_cli_args_in_JVL_docs -> origin/bug/JAL-4559_old_cli_args_in_JVL_docs
10-Dec-2025 07:51:23    c586364..9e8107e  releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch
10-Dec-2025 07:51:23 Already on 'development/Release_2_11_5_Branch'
10-Dec-2025 07:51:23 Your branch is behind 'origin/development/Release_2_11_5_Branch' by 3 commits, and can be fast-forwarded.
10-Dec-2025 07:51:23   (use "git pull" to update your local branch)
10-Dec-2025 07:51:23 HEAD is now at b00f7c4 JAL-4559 release notes
10-Dec-2025 07:51:23 Updated source code to revision: b00f7c47ccd3e44f5d4402f33e29b4b95c337419
10-Dec-2025 07:51:23 Finished task 'Checkout Default Repository' with result: Success
10-Dec-2025 07:51:23 Running pre-build action: VCS Version Collector
10-Dec-2025 07:51:23 Running pre-build action: Artifactory Release Staging
10-Dec-2025 07:51:23 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
10-Dec-2025 07:51:23 Bamboo Artifactory Plugin version: 2.6.2
10-Dec-2025 07:51:23
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #8 (JB-GDB731-JOB1-8)'
... 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-GDB731-JOB1
... using extra environment variables:
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10-Dec-2025 07:51:23 2414
10-Dec-2025 07:51:24 Starting a Gradle Daemon (subsequent builds will be faster)
10-Dec-2025 07:51:30
10-Dec-2025 07:51:30 > Configure project :
10-Dec-2025 07:51:30 Using properties from file './utils/channels/default/channel_gradle.properties'
10-Dec-2025 07:51:30 JALVIEW_VERSION is set to '2.11.5.1'
10-Dec-2025 07:51:30 HEADLESS BUILD
10-Dec-2025 07:51:30 J2S ENABLED
10-Dec-2025 07:51:30 Using a LOCAL profile.
10-Dec-2025 07:51:31 eclipseDir exists
10-Dec-2025 07:51:32
10-Dec-2025 07:51:32 > Task :clean
10-Dec-2025 07:51:32 > Task :cleanClover
10-Dec-2025 07:51:32 > Task :cleanTest UP-TO-DATE
10-Dec-2025 07:51:34
10-Dec-2025 07:51:34 > Task :cloverInstrJava
10-Dec-2025 07:51:34 Clover: About to instrument 1109 files
10-Dec-2025 07:51:34 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
10-Dec-2025 07:51:34 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover.db'.
10-Dec-2025 07:51:34 Processing files at 1.9 source level.
10-Dec-2025 07:51:37 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?
10-Dec-2025 07:51:37 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?
10-Dec-2025 07:51:37 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?
10-Dec-2025 07:51:37 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?
10-Dec-2025 07:51:37 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?
10-Dec-2025 07:51:37 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?
10-Dec-2025 07:51:37 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?
10-Dec-2025 07:51:43 Clover all over. Instrumented 1109 files (113 packages).
10-Dec-2025 07:51:45
10-Dec-2025 07:51:45 > Task :cloverInstrTests
10-Dec-2025 07:51:45 Clover: About to instrument test files
10-Dec-2025 07:51:45 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
10-Dec-2025 07:51:45 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover.db'.
10-Dec-2025 07:51:45 Processing files at 1.9 source level.
10-Dec-2025 07:51:47 Clover all over. Instrumented 293 files (52 packages).
10-Dec-2025 07:51:47 1627 test methods detected.
10-Dec-2025 07:51:47
10-Dec-2025 07:51:47 > Task :cloverInstr
10-Dec-2025 07:51:49
10-Dec-2025 07:51:49 > Task :compileCloverJava
10-Dec-2025 07:51:49 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
10-Dec-2025 07:51:49   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:51:49   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:51:49   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:51:49 Setting target compatibility to 11
10-Dec-2025 07:52:09 Note: Some input files use or override a deprecated API.
10-Dec-2025 07:52:09 Note: Recompile with -Xlint:deprecation for details.
10-Dec-2025 07:52:09 Note: Some input files use unchecked or unsafe operations.
10-Dec-2025 07:52:09 Note: Recompile with -Xlint:unchecked for details.
10-Dec-2025 07:52:15
10-Dec-2025 07:52:15 > Task :processCloverResources NO-SOURCE
10-Dec-2025 07:52:15 > Task :cloverClasses
10-Dec-2025 07:52:15 > Task :copyHelp
10-Dec-2025 07:52:16 > Task :buildIndices
10-Dec-2025 07:52:16 > Task :copyResources
10-Dec-2025 07:52:16 > Task :copyChannelResources
10-Dec-2025 07:52:16
10-Dec-2025 07:52:16 > Task :createBuildProperties
10-Dec-2025 07:52:16 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
10-Dec-2025 07:52:16   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:52:16
10-Dec-2025 07:52:16 > Task :buildResources
10-Dec-2025 07:52:17 > Task :copyDocs
10-Dec-2025 07:52:17
10-Dec-2025 07:52:17 > Task :convertMdFiles
10-Dec-2025 07:52:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
10-Dec-2025 07:52:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/releaseprocess.html
10-Dec-2025 07:52:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
10-Dec-2025 07:52:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/building.html
10-Dec-2025 07:52:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/jalview-projects.html
10-Dec-2025 07:52:18
10-Dec-2025 07:52:18 > Task :releasesTemplates
10-Dec-2025 07:52:18 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
10-Dec-2025 07:52:18   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:52:18   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:52:18 Stripping rc/test/etc for TEST
10-Dec-2025 07:52:18 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
10-Dec-2025 07:52:18
10-Dec-2025 07:52:18 > Task :prepare
10-Dec-2025 07:52:20
10-Dec-2025 07:52:20 > Task :compileJava
10-Dec-2025 07:52:20 Setting target compatibility to 11
10-Dec-2025 07:52:24 Note: Some input files use or override a deprecated API.
10-Dec-2025 07:52:24 Note: Recompile with -Xlint:deprecation for details.
10-Dec-2025 07:52:24 Note: Some input files use unchecked or unsafe operations.
10-Dec-2025 07:52:24 Note: Recompile with -Xlint:unchecked for details.
10-Dec-2025 07:52:29
10-Dec-2025 07:52:29 > Task :compileTestJava
10-Dec-2025 07:52:29 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
10-Dec-2025 07:52:29   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:52:29   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:52:29 Setting target compatibility to 11
10-Dec-2025 07:52:34 Note: Some input files use or override a deprecated API.
10-Dec-2025 07:52:34 Note: Recompile with -Xlint:deprecation for details.
10-Dec-2025 07:52:34 Note: Some input files use unchecked or unsafe operations.
10-Dec-2025 07:52:34 Note: Recompile with -Xlint:unchecked for details.
10-Dec-2025 07:52:35
10-Dec-2025 07:52:35 > Task :processTestResources
10-Dec-2025 07:52:35 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
10-Dec-2025 07:52:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:52:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:52:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:52:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:52:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:52:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:52:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:52:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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.
10-Dec-2025 07:52:35
10-Dec-2025 07:52:35 > Task :testClasses
10-Dec-2025 07:52:37
10-Dec-2025 07:52:37 > Task :testTask0
10-Dec-2025 07:52:37 Running tests WITH clover
10-Dec-2025 07:52:40 WARNING: An illegal reflective access operation has occurred
10-Dec-2025 07:52:40 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
10-Dec-2025 07:52:40 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
10-Dec-2025 07:52:40 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
10-Dec-2025 07:52:40 WARNING: All illegal access operations will be denied in a future release
10-Dec-2025 07:53:33
10-Dec-2025 07:53:33 Gradle suite > Gradle test > jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy FAILED
10-Dec-2025 07:53:33     java.lang.ArrayIndexOutOfBoundsException: Index 5 out of bounds for length 1
10-Dec-2025 07:53:33         at jalview.gui.AlignViewportTest.__CLR4_4_1lfq8443uue(AlignViewportTest.java:478)
10-Dec-2025 07:53:33         at jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy(AlignViewportTest.java:446)
10-Dec-2025 07:56:42
10-Dec-2025 07:56:42 1835 tests completed, 1 failed
10-Dec-2025 07:56:42 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask0/index.html
10-Dec-2025 07:56:45
10-Dec-2025 07:56:45 > Task :testTask1
10-Dec-2025 07:56:45 Running tests WITH clover
10-Dec-2025 07:56:46 WARNING: An illegal reflective access operation has occurred
10-Dec-2025 07:56:46 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
10-Dec-2025 07:56:46 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
10-Dec-2025 07:56:46 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
10-Dec-2025 07:56:46 WARNING: All illegal access operations will be denied in a future release
10-Dec-2025 07:58:50
10-Dec-2025 07:58:50 > Task :testTask2
10-Dec-2025 07:58:50 Running tests WITH clover
10-Dec-2025 07:58:54
10-Dec-2025 07:58:54 > Task :testTask3
10-Dec-2025 07:58:54 Running tests WITH clover
10-Dec-2025 07:58:55 WARNING: An illegal reflective access operation has occurred
10-Dec-2025 07:58:55 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
10-Dec-2025 07:58:55 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
10-Dec-2025 07:58:55 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
10-Dec-2025 07:58:55 WARNING: All illegal access operations will be denied in a future release
10-Dec-2025 07:59:39
10-Dec-2025 07:59:39 > Task :test NO-SOURCE
10-Dec-2025 07:59:39 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
10-Dec-2025 07:59:39 │jalview:testTask0 results: FAILURE (1835 tests, 1834 successes, 1 failures, 0 skipped) in 4 minutes, 6.391 seconds    │
10-Dec-2025 07:59:39 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask0/index.html│
10-Dec-2025 07:59:39 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
10-Dec-2025 07:59:39 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 5.804 seconds        │
10-Dec-2025 07:59:39 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask1/index.html│
10-Dec-2025 07:59:39 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
10-Dec-2025 07:59:39 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.210 seconds                     │
10-Dec-2025 07:59:39 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask2/index.html│
10-Dec-2025 07:59:39 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
10-Dec-2025 07:59:39 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 46.956 seconds                  │
10-Dec-2025 07:59:39 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask3/index.html│
10-Dec-2025 07:59:39 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
10-Dec-2025 07:59:39 │OVERALL: results: FAILURE (1923 tests, 1922 successes, 1 failures, 0 skipped) in 6 minutes, 62.361 seconds            │
10-Dec-2025 07:59:39 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
10-Dec-2025 07:59:39
10-Dec-2025 07:59:39 FAILURE: Build failed with an exception.
10-Dec-2025 07:59:39
10-Dec-2025 07:59:39 * Where:
10-Dec-2025 07:59:39 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build.gradle' line: 1967
10-Dec-2025 07:59:39
10-Dec-2025 07:59:39 * What went wrong:
10-Dec-2025 07:59:39 Failed tests!
10-Dec-2025 07:59:39
10-Dec-2025 07:59:39 * Try:
10-Dec-2025 07:59:39 > Run with --stacktrace option to get the stack trace.
10-Dec-2025 07:59:39 > Run with --info or --debug option to get more log output.
10-Dec-2025 07:59:39 > Run with --scan to get full insights.
10-Dec-2025 07:59:39
10-Dec-2025 07:59:39 * Get more help at https://help.gradle.org
10-Dec-2025 07:59:39
10-Dec-2025 07:59:39 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
10-Dec-2025 07:59:39
10-Dec-2025 07:59:39 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
10-Dec-2025 07:59:39
10-Dec-2025 07:59:39 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
10-Dec-2025 07:59:39
10-Dec-2025 07:59:39 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
10-Dec-2025 07:59:39 Please consult deprecation warnings for more details.
10-Dec-2025 07:59:39 21 actionable tasks: 20 executed, 1 up-to-date
10-Dec-2025 07:59:39
10-Dec-2025 07:59:39 BUILD FAILED in 8m 15s
10-Dec-2025 07:59:40
10-Dec-2025 07:59:40 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
10-Dec-2025 07:59:40 Finished task 'Run tests with openclover under gradle' with result: Failed
10-Dec-2025 07:59:40 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
10-Dec-2025 07:59:40 Bamboo Artifactory Plugin version: 2.6.2
10-Dec-2025 07:59:40
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #8 (JB-GDB731-JOB1-8)'
... 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-GDB731-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=development/Release_2_11_5_Branch
bamboo_repository_46498610_previous_revision_number=3ad0f0a7896b330c0e763c467d1076bede27b59a
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=development/Release_2_11_5_Branch
bamboo_repository_revision_number=b00f7c47ccd3e44f5d4402f33e29b4b95c337419
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB731-JOB1-8
JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048
bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1
bamboo_planRepository_1_name=Jalview Gitlab
bamboo_buildKey=JB-GDB731-JOB1
bamboo_repository_46498610_git_username=
bamboo_shortPlanName=development-Release_2_11_5_Branch
bamboo_planRepository_name=Jalview Gitlab
LOGNAME=bamboo
bamboo_buildNumber=8
PWD=/
bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse
bamboo_shortJobName=Clover and Tests
bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB731-JOB1-8
bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
SHELL=/bin/bash
bamboo_repository_46498610_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_agentId=196609
bamboo_planName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch
bamboo_repository_46498610_revision_number=b00f7c47ccd3e44f5d4402f33e29b4b95c337419
bamboo_shortPlanKey=GDB731
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=b00f7c47ccd3e44f5d4402f33e29b4b95c337419
bamboo_buildTimeStamp=2025-12-10T07:51:22.960Z
bamboo_repository_previous_revision_number=3ad0f0a7896b330c0e763c467d1076bede27b59a
bamboo_planRepository_previousRevision=3ad0f0a7896b330c0e763c467d1076bede27b59a
bamboo_repository_git_branch=development/Release_2_11_5_Branch
bamboo_buildResultKey=JB-GDB731-JOB1-8
bamboo_repository_branch_name=development/Release_2_11_5_Branch
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=b00f7c47ccd3e44f5d4402f33e29b4b95c337419
SHLVL=1
bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant
bamboo_repository_name=Jalview Gitlab
bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test
JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/
LANG=en_GB.UTF-8
bamboo_buildFailed=true
bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk
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bamboo_planRepository_branch=development/Release_2_11_5_Branch
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bamboo_planRepository_1_previousRevision=3ad0f0a7896b330c0e763c467d1076bede27b59a
bamboo_repository_46498610_git_branch=development/Release_2_11_5_Branch
bamboo_planRepository_branchDisplayName=development/Release_2_11_5_Branch
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=development/Release_2_11_5_Branch
_=/usr/bin/java
bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11
bamboo_capability_system_builderivy_Ivy=/usr
bamboo_plan_storageTag=plan-46302791
bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle
bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache
bamboo_planRepository_1_username=
bamboo_planRepository_type=gitv2
USER=bamboo
bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache
bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_capability_system_builder_ant_Ant=/usr/share/ant
bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven
bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp
bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1
bamboo_planKey=JB-GDB731
bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_planRepository_username=
bamboo_repository_46498610_name=Jalview Gitlab
HOME=/home/bamboo
bamboo_planRepository_1_branchName=development/Release_2_11_5_Branch
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
10-Dec-2025 07:59:40 2414
10-Dec-2025 07:59:44
10-Dec-2025 07:59:44 > Configure project :
10-Dec-2025 07:59:44 Using properties from file './utils/channels/default/channel_gradle.properties'
10-Dec-2025 07:59:44 JALVIEW_VERSION is set to '2.11.5.1'
10-Dec-2025 07:59:44 HEADLESS BUILD
10-Dec-2025 07:59:44 J2S ENABLED
10-Dec-2025 07:59:45 Using a LOCAL profile.
10-Dec-2025 07:59:45 eclipseDir exists
10-Dec-2025 07:59:48
10-Dec-2025 07:59:48 > Task :cloverHtmlReport
10-Dec-2025 07:59:48 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
10-Dec-2025 07:59:49 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/clover'
10-Dec-2025 08:00:33 Done. Processed 117 packages in 44762ms (382ms per package).
10-Dec-2025 08:00:38
10-Dec-2025 08:00:38 > Task :cloverXmlReport
10-Dec-2025 08:00:38 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
10-Dec-2025 08:00:39 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/clover/clover.xml'
10-Dec-2025 08:00:39
10-Dec-2025 08:00:39 > Task :cloverReport
10-Dec-2025 08:00:39
10-Dec-2025 08:00:39 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
10-Dec-2025 08:00:39
10-Dec-2025 08:00:39 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
10-Dec-2025 08:00:39
10-Dec-2025 08:00:39 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
10-Dec-2025 08:00:39
10-Dec-2025 08:00:39 BUILD SUCCESSFUL in 59s
10-Dec-2025 08:00:39 2 actionable tasks: 2 executed
10-Dec-2025 08:00:39 Finished task 'Clover Report' with result: Success
10-Dec-2025 08:00:39 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
10-Dec-2025 08:00:39 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1...
10-Dec-2025 08:00:39 Failing task since 1 failing test cases were found.
10-Dec-2025 08:00:39 Finished task 'TestNG Parser' with result: Failed
10-Dec-2025 08:00:39 Running post build plugin 'NCover Results Collector'
10-Dec-2025 08:00:39 Running post build plugin 'Artifact Copier'
10-Dec-2025 08:00:39 Publishing an artifact: Clover Report (System)
10-Dec-2025 08:00:41 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.841 s
10-Dec-2025 08:00:41 Publishing an artifact: TestNG report
10-Dec-2025 08:00:41 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/test does not exist.
10-Dec-2025 08:00:41 The artifact hasn't been successfully published after 1.192 ms
10-Dec-2025 08:00:41 Running post build plugin 'Artifactory Release Management Staging'
10-Dec-2025 08:00:41 Running post build plugin 'Artifactory Build Info Copier'
10-Dec-2025 08:00:41 Running post build plugin 'Artifactory Gradle Properties Info Copier'
10-Dec-2025 08:00:41 Running post build plugin 'npm Cache Cleanup'
10-Dec-2025 08:00:41 Running post build plugin 'Clover Results Collector'
10-Dec-2025 08:00:41 Running post build plugin 'Docker Container Cleanup'
10-Dec-2025 08:00:41 Finalising the build...
10-Dec-2025 08:00:41 Stopping timer.
10-Dec-2025 08:00:41 Build JB-GDB731-JOB1-8 completed.
10-Dec-2025 08:00:41 Running on server: post build plugin 'NCover Results Collector'
10-Dec-2025 08:00:41 Running on server: post build plugin 'Build Hanging Detection Configuration'
10-Dec-2025 08:00:41 Running on server: post build plugin 'Clover Delta Calculator'
10-Dec-2025 08:00:41 Running on server: post build plugin 'Maven Dependencies Postprocessor'
10-Dec-2025 08:00:41 All post build plugins have finished
10-Dec-2025 08:00:41 Generating build results summary...
10-Dec-2025 08:00:41 Saving build results to disk...
10-Dec-2025 08:00:41 Logging substituted variables...
10-Dec-2025 08:00:41 Indexing build results...
10-Dec-2025 08:00:41 Finished building JB-GDB731-JOB1-8.