Build #9

Build: #9 failed

Job: Clover and Tests failed

Stages & jobs

  1. Default Stage

Build log

The build generated 277 lines of output. Download or view full build log

01-Dec-2025 15:35:14 Build Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests #9 (JB-GDB722-JOB1-9) started building on agent Default Agent
01-Dec-2025 15:35:14
01-Dec-2025 15:35:14 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1
01-Dec-2025 15:35:14 Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests #9 (JB-GDB722-JOB1-9)
01-Dec-2025 15:35:14 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
01-Dec-2025 15:35:14 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1
01-Dec-2025 15:35:14 Updating source code to revision: aa9b04d454c094e49d21b391333c4abf661ee162
01-Dec-2025 15:35:14 Fetching 'refs/heads/bug/JAL-4603_export_svg_files_missing_part_of_sequence' from 'https://gitlab.jalview.org/jalview/jalview.git'.
01-Dec-2025 15:35:14 Checking out revision aa9b04d454c094e49d21b391333c4abf661ee162.
01-Dec-2025 15:35:14 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
01-Dec-2025 15:35:14    cc05d28..aa9b04d  bug/JAL-4603_export_svg_files_missing_part_of_sequence -> origin/bug/JAL-4603_export_svg_files_missing_part_of_sequence
01-Dec-2025 15:35:14 Already on 'bug/JAL-4603_export_svg_files_missing_part_of_sequence'
01-Dec-2025 15:35:14 Your branch is behind 'origin/bug/JAL-4603_export_svg_files_missing_part_of_sequence' by 1 commit, and can be fast-forwarded.
01-Dec-2025 15:35:14   (use "git pull" to update your local branch)
01-Dec-2025 15:35:15 HEAD is now at aa9b04d JAL-4635 redo patching of zeus URL to fix failing test
01-Dec-2025 15:35:15 Updated source code to revision: aa9b04d454c094e49d21b391333c4abf661ee162
01-Dec-2025 15:35:15 Finished task 'Checkout Default Repository' with result: Success
01-Dec-2025 15:35:15 Running pre-build action: VCS Version Collector
01-Dec-2025 15:35:15 Running pre-build action: Artifactory Release Staging
01-Dec-2025 15:35:15 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
01-Dec-2025 15:35:15 Bamboo Artifactory Plugin version: 2.6.2
01-Dec-2025 15:35:15
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests #9 (JB-GDB722-JOB1-9)'
... 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-GDB722-JOB1
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01-Dec-2025 15:35:15 444
01-Dec-2025 15:35:17
01-Dec-2025 15:35:17 > Configure project :
01-Dec-2025 15:35:17 Using properties from file './utils/channels/default/channel_gradle.properties'
01-Dec-2025 15:35:17 JALVIEW_VERSION is set to '2.11.5.1'
01-Dec-2025 15:35:17 HEADLESS BUILD
01-Dec-2025 15:35:17 J2S ENABLED
01-Dec-2025 15:35:17 Using a LOCAL profile.
01-Dec-2025 15:35:17 eclipseDir exists
01-Dec-2025 15:35:18
01-Dec-2025 15:35:18 > Task :clean
01-Dec-2025 15:35:18 > Task :cleanClover
01-Dec-2025 15:35:18 > Task :cleanTest UP-TO-DATE
01-Dec-2025 15:35:20
01-Dec-2025 15:35:20 > Task :cloverInstrJava
01-Dec-2025 15:35:20 Clover: About to instrument 1109 files
01-Dec-2025 15:35:20 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
01-Dec-2025 15:35:20 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover.db'.
01-Dec-2025 15:35:20 Processing files at 1.9 source level.
01-Dec-2025 15:35:24 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?
01-Dec-2025 15:35:24 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?
01-Dec-2025 15:35:24 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?
01-Dec-2025 15:35:24 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?
01-Dec-2025 15:35:24 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?
01-Dec-2025 15:35:24 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?
01-Dec-2025 15:35:24 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?
01-Dec-2025 15:35:31 Clover all over. Instrumented 1109 files (113 packages).
01-Dec-2025 15:35:33
01-Dec-2025 15:35:33 > Task :cloverInstrTests
01-Dec-2025 15:35:33 Clover: About to instrument test files
01-Dec-2025 15:35:33 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
01-Dec-2025 15:35:33 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover.db'.
01-Dec-2025 15:35:33 Processing files at 1.9 source level.
01-Dec-2025 15:35:36 Clover all over. Instrumented 293 files (52 packages).
01-Dec-2025 15:35:36 1625 test methods detected.
01-Dec-2025 15:35:36
01-Dec-2025 15:35:36 > Task :cloverInstr
01-Dec-2025 15:35:38
01-Dec-2025 15:35:38 > Task :compileCloverJava
01-Dec-2025 15:35:38 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
01-Dec-2025 15:35:38   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:35:38   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:35:38   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:35:38 Setting target compatibility to 11
01-Dec-2025 15:35:55 Note: Some input files use or override a deprecated API.
01-Dec-2025 15:35:55 Note: Recompile with -Xlint:deprecation for details.
01-Dec-2025 15:35:55 Note: Some input files use unchecked or unsafe operations.
01-Dec-2025 15:35:55 Note: Recompile with -Xlint:unchecked for details.
01-Dec-2025 15:36:02
01-Dec-2025 15:36:02 > Task :processCloverResources NO-SOURCE
01-Dec-2025 15:36:02 > Task :cloverClasses
01-Dec-2025 15:36:02 > Task :copyHelp
01-Dec-2025 15:36:03 > Task :buildIndices
01-Dec-2025 15:36:03 > Task :copyResources
01-Dec-2025 15:36:03 > Task :copyChannelResources
01-Dec-2025 15:36:03
01-Dec-2025 15:36:03 > Task :createBuildProperties
01-Dec-2025 15:36:03 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
01-Dec-2025 15:36:03   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:36:03
01-Dec-2025 15:36:03 > Task :buildResources
01-Dec-2025 15:36:03 > Task :copyDocs
01-Dec-2025 15:36:03
01-Dec-2025 15:36:03 > Task :convertMdFiles
01-Dec-2025 15:36:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
01-Dec-2025 15:36:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/releaseprocess.html
01-Dec-2025 15:36:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
01-Dec-2025 15:36:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/building.html
01-Dec-2025 15:36:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/jalview-projects.html
01-Dec-2025 15:36:04
01-Dec-2025 15:36:04 > Task :releasesTemplates
01-Dec-2025 15:36:04 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
01-Dec-2025 15:36:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:36:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:36:04 Stripping rc/test/etc for TEST
01-Dec-2025 15:36:04 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
01-Dec-2025 15:36:04
01-Dec-2025 15:36:04 > Task :prepare
01-Dec-2025 15:36:06
01-Dec-2025 15:36:06 > Task :compileJava
01-Dec-2025 15:36:06 Setting target compatibility to 11
01-Dec-2025 15:36:12 Note: Some input files use or override a deprecated API.
01-Dec-2025 15:36:12 Note: Recompile with -Xlint:deprecation for details.
01-Dec-2025 15:36:12 Note: Some input files use unchecked or unsafe operations.
01-Dec-2025 15:36:12 Note: Recompile with -Xlint:unchecked for details.
01-Dec-2025 15:36:14
01-Dec-2025 15:36:14 > Task :compileTestJava
01-Dec-2025 15:36:14 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
01-Dec-2025 15:36:14   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:36:14   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:36:14 Setting target compatibility to 11
01-Dec-2025 15:36:19 Note: Some input files use or override a deprecated API.
01-Dec-2025 15:36:19 Note: Recompile with -Xlint:deprecation for details.
01-Dec-2025 15:36:19 Note: Some input files use unchecked or unsafe operations.
01-Dec-2025 15:36:19 Note: Recompile with -Xlint:unchecked for details.
01-Dec-2025 15:36:20
01-Dec-2025 15:36:20 > Task :processTestResources
01-Dec-2025 15:36:20 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
01-Dec-2025 15:36:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:36:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:36:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:36:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:36:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:36:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:36:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:36:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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.
01-Dec-2025 15:36:20
01-Dec-2025 15:36:20 > Task :testClasses
01-Dec-2025 15:36:22
01-Dec-2025 15:36:22 > Task :testTask0
01-Dec-2025 15:36:22 Running tests WITH clover
01-Dec-2025 15:36:26 WARNING: An illegal reflective access operation has occurred
01-Dec-2025 15:36:26 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
01-Dec-2025 15:36:26 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
01-Dec-2025 15:36:26 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
01-Dec-2025 15:36:26 WARNING: All illegal access operations will be denied in a future release
01-Dec-2025 15:37:30
01-Dec-2025 15:37:30 Gradle suite > Gradle test > jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy FAILED
01-Dec-2025 15:37:30     java.lang.AssertionError: Expected occupancy to be non-null in column 5 expected object to not be null
01-Dec-2025 15:37:30         at org.testng.Assert.fail(Assert.java:94)
01-Dec-2025 15:37:30         at org.testng.Assert.assertNotNull(Assert.java:406)
01-Dec-2025 15:37:30         at jalview.gui.AlignViewportTest.__CLR4_4_1lfq8443us9(AlignViewportTest.java:478)
01-Dec-2025 15:37:30         at jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy(AlignViewportTest.java:446)
01-Dec-2025 15:40:57 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask0/index.html
01-Dec-2025 15:40:57
01-Dec-2025 15:40:57 1829 tests completed, 1 failed
01-Dec-2025 15:41:00
01-Dec-2025 15:41:00 > Task :testTask1
01-Dec-2025 15:41:00 Running tests WITH clover
01-Dec-2025 15:41:02 WARNING: An illegal reflective access operation has occurred
01-Dec-2025 15:41:02 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
01-Dec-2025 15:41:02 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
01-Dec-2025 15:41:02 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
01-Dec-2025 15:41:02 WARNING: All illegal access operations will be denied in a future release
01-Dec-2025 15:43:39
01-Dec-2025 15:43:39 > Task :testTask2
01-Dec-2025 15:43:39 Running tests WITH clover
01-Dec-2025 15:43:43
01-Dec-2025 15:43:43 > Task :testTask3
01-Dec-2025 15:43:43 Running tests WITH clover
01-Dec-2025 15:43:46 WARNING: An illegal reflective access operation has occurred
01-Dec-2025 15:43:46 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
01-Dec-2025 15:43:46 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
01-Dec-2025 15:43:46 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
01-Dec-2025 15:43:46 WARNING: All illegal access operations will be denied in a future release
01-Dec-2025 15:44:43
01-Dec-2025 15:44:43 FAILURE: Build failed with an exception.
01-Dec-2025 15:44:43
01-Dec-2025 15:44:43 * Where:
01-Dec-2025 15:44:43 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build.gradle' line: 1967
01-Dec-2025 15:44:43
01-Dec-2025 15:44:43 * What went wrong:
01-Dec-2025 15:44:43 Failed tests!
01-Dec-2025 15:44:43
01-Dec-2025 15:44:43 * Try:
01-Dec-2025 15:44:43 > Run with --stacktrace option to get the stack trace.
01-Dec-2025 15:44:43 > Run with --info or --debug option to get more log output.
01-Dec-2025 15:44:43 > Run with --scan to get full insights.
01-Dec-2025 15:44:43
01-Dec-2025 15:44:43 * Get more help at https://help.gradle.org
01-Dec-2025 15:44:43
01-Dec-2025 15:44:43 BUILD FAILED in 9m 27s
01-Dec-2025 15:44:43
01-Dec-2025 15:44:43 > Task :test NO-SOURCE
01-Dec-2025 15:44:43 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
01-Dec-2025 15:44:43 │jalview:testTask0 results: FAILURE (1829 tests, 1828 successes, 1 failures, 0 skipped) in 4 minutes, 36.028 seconds   │
01-Dec-2025 15:44:43 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask0/index.html│
01-Dec-2025 15:44:43 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
01-Dec-2025 15:44:43 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 39.296 seconds       │
01-Dec-2025 15:44:43 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask1/index.html│
01-Dec-2025 15:44:43 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
01-Dec-2025 15:44:43 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.323 seconds                     │
01-Dec-2025 15:44:43 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask2/index.html│
01-Dec-2025 15:44:43 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
01-Dec-2025 15:44:43 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 0.611 seconds        │
01-Dec-2025 15:44:43 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask3/index.html│
01-Dec-2025 15:44:43 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
01-Dec-2025 15:44:43 │OVERALL: results: FAILURE (1917 tests, 1916 successes, 1 failures, 0 skipped) in 7 minutes, 80.258 seconds            │
01-Dec-2025 15:44:43 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
01-Dec-2025 15:44:43
01-Dec-2025 15:44:43 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
01-Dec-2025 15:44:43
01-Dec-2025 15:44:43 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
01-Dec-2025 15:44:43
01-Dec-2025 15:44:43 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
01-Dec-2025 15:44:43
01-Dec-2025 15:44:43 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
01-Dec-2025 15:44:43 Please consult deprecation warnings for more details.
01-Dec-2025 15:44:43 21 actionable tasks: 20 executed, 1 up-to-date
01-Dec-2025 15:44:43
01-Dec-2025 15:44:43 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
01-Dec-2025 15:44:43 Finished task 'Run tests with openclover under gradle' with result: Failed
01-Dec-2025 15:44:43 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
01-Dec-2025 15:44:43 Bamboo Artifactory Plugin version: 2.6.2
01-Dec-2025 15:44:43
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests #9 (JB-GDB722-JOB1-9)'
... 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-GDB722-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=bug/JAL-4603_export_svg_files_missing_part_of_sequence
bamboo_repository_revision_number=aa9b04d454c094e49d21b391333c4abf661ee162
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB722-JOB1-9
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-GDB722-JOB1
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bamboo_repository_46498555_previous_revision_number=cc05d28187e3100fd060e6b7e3b1795477c23e62
bamboo_shortPlanName=bug-JAL-4603_export_svg_files_missing_part_of_sequence
bamboo_planRepository_name=Jalview Gitlab
LOGNAME=bamboo
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bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse
bamboo_shortJobName=Clover and Tests
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bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
SHELL=/bin/bash
bamboo_repository_46498555_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_agentId=196609
bamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence
bamboo_shortPlanKey=GDB722
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bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=aa9b04d454c094e49d21b391333c4abf661ee162
bamboo_buildTimeStamp=2025-12-01T15:35:14.380Z
bamboo_repository_previous_revision_number=cc05d28187e3100fd060e6b7e3b1795477c23e62
bamboo_planRepository_previousRevision=cc05d28187e3100fd060e6b7e3b1795477c23e62
bamboo_repository_git_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence
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bamboo_repository_branch_name=bug/JAL-4603_export_svg_files_missing_part_of_sequence
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests
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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/
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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=
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USER=bamboo
bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache
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bamboo_capability_system_builder_ant_Ant=/usr/share/ant
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bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1
bamboo_planKey=JB-GDB722
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bamboo_planRepository_username=
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bamboo_repository_46498555_branch_name=bug/JAL-4603_export_svg_files_missing_part_of_sequence
HOME=/home/bamboo
bamboo_planRepository_1_branchName=bug/JAL-4603_export_svg_files_missing_part_of_sequence
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01-Dec-2025 15:44:43 444
01-Dec-2025 15:44:50
01-Dec-2025 15:44:50 > Configure project :
01-Dec-2025 15:44:50 Using properties from file './utils/channels/default/channel_gradle.properties'
01-Dec-2025 15:44:50 JALVIEW_VERSION is set to '2.11.5.1'
01-Dec-2025 15:44:50 HEADLESS BUILD
01-Dec-2025 15:44:50 J2S ENABLED
01-Dec-2025 15:44:50 Using a LOCAL profile.
01-Dec-2025 15:44:52 eclipseDir exists
01-Dec-2025 15:44:54
01-Dec-2025 15:44:54 > Task :cloverHtmlReport
01-Dec-2025 15:44:54 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
01-Dec-2025 15:44:57 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/clover'
01-Dec-2025 15:45:52 Done. Processed 117 packages in 55895ms (477ms per package).
01-Dec-2025 15:45:59
01-Dec-2025 15:45:59 > Task :cloverXmlReport
01-Dec-2025 15:45:59 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
01-Dec-2025 15:46:03 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/clover/clover.xml'
01-Dec-2025 15:46:04
01-Dec-2025 15:46:04 > Task :cloverReport
01-Dec-2025 15:46:04
01-Dec-2025 15:46:04 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
01-Dec-2025 15:46:04
01-Dec-2025 15:46:04 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
01-Dec-2025 15:46:04
01-Dec-2025 15:46:04 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
01-Dec-2025 15:46:04
01-Dec-2025 15:46:04 BUILD SUCCESSFUL in 1m 19s
01-Dec-2025 15:46:04 2 actionable tasks: 2 executed
01-Dec-2025 15:46:04 Finished task 'Clover Report' with result: Success
01-Dec-2025 15:46:04 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
01-Dec-2025 15:46:04 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1...
01-Dec-2025 15:46:04 Failing task since 1 failing test cases were found.
01-Dec-2025 15:46:04 Finished task 'TestNG Parser' with result: Failed
01-Dec-2025 15:46:04 Running post build plugin 'NCover Results Collector'
01-Dec-2025 15:46:04 Running post build plugin 'Artifact Copier'
01-Dec-2025 15:46:04 Publishing an artifact: Clover Report (System)
01-Dec-2025 15:46:09 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 5.142 s
01-Dec-2025 15:46:09 Publishing an artifact: TestNG report
01-Dec-2025 15:46:09 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/test does not exist.
01-Dec-2025 15:46:09 The artifact hasn't been successfully published after 3.949 ms
01-Dec-2025 15:46:09 Running post build plugin 'Artifactory Release Management Staging'
01-Dec-2025 15:46:09 Running post build plugin 'Artifactory Build Info Copier'
01-Dec-2025 15:46:09 Running post build plugin 'Artifactory Gradle Properties Info Copier'
01-Dec-2025 15:46:09 Running post build plugin 'npm Cache Cleanup'
01-Dec-2025 15:46:09 Running post build plugin 'Clover Results Collector'
01-Dec-2025 15:46:09 Running post build plugin 'Docker Container Cleanup'
01-Dec-2025 15:46:09 Finalising the build...
01-Dec-2025 15:46:09 Stopping timer.
01-Dec-2025 15:46:09 Build JB-GDB722-JOB1-9 completed.
01-Dec-2025 15:46:09 Running on server: post build plugin 'NCover Results Collector'
01-Dec-2025 15:46:09 Running on server: post build plugin 'Build Hanging Detection Configuration'
01-Dec-2025 15:46:09 Running on server: post build plugin 'Clover Delta Calculator'
01-Dec-2025 15:46:09 Running on server: post build plugin 'Maven Dependencies Postprocessor'
01-Dec-2025 15:46:09 All post build plugins have finished
01-Dec-2025 15:46:09 Generating build results summary...
01-Dec-2025 15:46:09 Saving build results to disk...
01-Dec-2025 15:46:10 Logging substituted variables...
01-Dec-2025 15:46:10 Indexing build results...
01-Dec-2025 15:46:10 Finished building JB-GDB722-JOB1-9.