Build #1

Build: #1 failed

Job: Clover and Tests failed

Stages & jobs

  1. Default Stage

Build log

The build generated 299 lines of output. Download or view full build log

12-Nov-2025 13:01:08 Build Jalview Builds - Gradle Develop Build - feature-JAL-4602_Hide_All_SS_consensus_for_single_provider - Clover and Tests #1 (JB-GDB725-JOB1-1) started building on agent Default Agent
12-Nov-2025 13:01:08
12-Nov-2025 13:01:08 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1
12-Nov-2025 13:01:08 Executing build Jalview Builds - Gradle Develop Build - feature-JAL-4602_Hide_All_SS_consensus_for_single_provider - Clover and Tests #1 (JB-GDB725-JOB1-1)
12-Nov-2025 13:01:08 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
12-Nov-2025 13:01:08 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1
12-Nov-2025 13:01:08 Updating source code to revision: e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d
12-Nov-2025 13:01:08 Fetching 'refs/heads/feature/JAL-4602_Hide_All_SS_consensus_for_single_provider' from 'https://gitlab.jalview.org/jalview/jalview.git'.
12-Nov-2025 13:01:10 Checking out revision e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d.
12-Nov-2025 13:01:10 Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/.git'.
12-Nov-2025 13:01:10 Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1'...
12-Nov-2025 13:01:10 done.
12-Nov-2025 13:01:16 Branch feature/JAL-4602_Hide_All_SS_consensus_for_single_provider set up to track remote branch feature/JAL-4602_Hide_All_SS_consensus_for_single_provider from origin.
12-Nov-2025 13:01:16 Switched to a new branch 'feature/JAL-4602_Hide_All_SS_consensus_for_single_provider'
12-Nov-2025 13:01:16 Updated source code to revision: e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d
12-Nov-2025 13:01:16 Finished task 'Checkout Default Repository' with result: Success
12-Nov-2025 13:01:16 Running pre-build action: VCS Version Collector
12-Nov-2025 13:01:16 Running pre-build action: Artifactory Release Staging
12-Nov-2025 13:01:16 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
12-Nov-2025 13:01:16 Bamboo Artifactory Plugin version: 2.6.2
12-Nov-2025 13:01:16
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4602_Hide_All_SS_consensus_for_single_provider - Clover and Tests #1 (JB-GDB725-JOB1-1)'
... 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-GDB725-JOB1
... using extra environment variables:
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bamboo_repository_revision_number=e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB725-JOB1-1
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bamboo_shortPlanName=feature-JAL-4602_Hide_All_SS_consensus_for_single_provider
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bamboo_shortJobName=Clover and Tests
bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB725-JOB1-1
bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
SHELL=/bin/bash
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bamboo_planName=Jalview Builds - Gradle Develop Build - feature-JAL-4602_Hide_All_SS_consensus_for_single_provider
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bamboo_buildTimeStamp=2025-11-12T13:01:07.747Z
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bamboo_repository_name=Jalview Gitlab
JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/
LANG=en_GB.UTF-8
bamboo_buildFailed=false
bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk
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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-GDB725-JOB1
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bamboo_planRepository_username=
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bamboo_planRepository_1_branchName=feature/JAL-4602_Hide_All_SS_consensus_for_single_provider
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12-Nov-2025 13:01:16 444
12-Nov-2025 13:01:17 Starting a Gradle Daemon (subsequent builds will be faster)
12-Nov-2025 13:01:26
12-Nov-2025 13:01:26 > Configure project :
12-Nov-2025 13:01:26 Using properties from file './utils/channels/default/channel_gradle.properties'
12-Nov-2025 13:01:26 JALVIEW_VERSION is set to '2.11.5.1'
12-Nov-2025 13:01:26 HEADLESS BUILD
12-Nov-2025 13:01:26 J2S ENABLED
12-Nov-2025 13:01:27 Using a LOCAL profile.
12-Nov-2025 13:01:28 eclipseDir exists
12-Nov-2025 13:01:28
12-Nov-2025 13:01:28 > Task :clean
12-Nov-2025 13:01:28 > Task :cleanClover
12-Nov-2025 13:01:28 > Task :cleanTest UP-TO-DATE
12-Nov-2025 13:01:31
12-Nov-2025 13:01:31 > Task :cloverInstrJava
12-Nov-2025 13:01:31 Clover: About to instrument 1106 files
12-Nov-2025 13:01:31 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
12-Nov-2025 13:01:31 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/clover/clover.db'.
12-Nov-2025 13:01:31 Processing files at 1.9 source level.
12-Nov-2025 13:01:37 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?
12-Nov-2025 13:01:37 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?
12-Nov-2025 13:01:37 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?
12-Nov-2025 13:01:37 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?
12-Nov-2025 13:01:37 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?
12-Nov-2025 13:01:37 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?
12-Nov-2025 13:01:37 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?
12-Nov-2025 13:01:43 Clover all over. Instrumented 1106 files (112 packages).
12-Nov-2025 13:01:45
12-Nov-2025 13:01:45 > Task :cloverInstrTests
12-Nov-2025 13:01:45 Clover: About to instrument test files
12-Nov-2025 13:01:45 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
12-Nov-2025 13:01:45 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/clover/clover.db'.
12-Nov-2025 13:01:45 Processing files at 1.9 source level.
12-Nov-2025 13:01:48 Clover all over. Instrumented 293 files (52 packages).
12-Nov-2025 13:01:48 1618 test methods detected.
12-Nov-2025 13:01:48
12-Nov-2025 13:01:48 > Task :cloverInstr
12-Nov-2025 13:01:54
12-Nov-2025 13:01:54 > Task :compileCloverJava
12-Nov-2025 13:01:54 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
12-Nov-2025 13:01:54   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:01:54   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:01:54   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:01:54 Setting target compatibility to 11
12-Nov-2025 13:02:20 Note: Some input files use or override a deprecated API.
12-Nov-2025 13:02:20 Note: Recompile with -Xlint:deprecation for details.
12-Nov-2025 13:02:20 Note: Some input files use unchecked or unsafe operations.
12-Nov-2025 13:02:20 Note: Recompile with -Xlint:unchecked for details.
12-Nov-2025 13:02:28
12-Nov-2025 13:02:28 > Task :processCloverResources NO-SOURCE
12-Nov-2025 13:02:28 > Task :cloverClasses
12-Nov-2025 13:02:29 > Task :copyHelp
12-Nov-2025 13:02:31 > Task :buildIndices
12-Nov-2025 13:02:31 > Task :copyResources
12-Nov-2025 13:02:31 > Task :copyChannelResources
12-Nov-2025 13:02:31
12-Nov-2025 13:02:31 > Task :createBuildProperties
12-Nov-2025 13:02:31 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
12-Nov-2025 13:02:31   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:02:31
12-Nov-2025 13:02:31 > Task :buildResources
12-Nov-2025 13:02:31 > Task :copyDocs
12-Nov-2025 13:02:31
12-Nov-2025 13:02:31 > Task :convertMdFiles
12-Nov-2025 13:02:31 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
12-Nov-2025 13:02:31 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/resources/doc_build/doc/releaseprocess.html
12-Nov-2025 13:02:31 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
12-Nov-2025 13:02:31 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/resources/doc_build/doc/building.html
12-Nov-2025 13:02:31 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/resources/doc_build/doc/jalview-projects.html
12-Nov-2025 13:02:31
12-Nov-2025 13:02:31 > Task :releasesTemplates
12-Nov-2025 13:02:31 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
12-Nov-2025 13:02:31   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:02:31   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:02:31 Stripping rc/test/etc for TEST
12-Nov-2025 13:02:31 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
12-Nov-2025 13:02:31
12-Nov-2025 13:02:31 > Task :prepare
12-Nov-2025 13:02:34
12-Nov-2025 13:02:34 > Task :compileJava
12-Nov-2025 13:02:34 Setting target compatibility to 11
12-Nov-2025 13:02:41 Note: Some input files use or override a deprecated API.
12-Nov-2025 13:02:41 Note: Recompile with -Xlint:deprecation for details.
12-Nov-2025 13:02:41 Note: Some input files use unchecked or unsafe operations.
12-Nov-2025 13:02:41 Note: Recompile with -Xlint:unchecked for details.
12-Nov-2025 13:02:46
12-Nov-2025 13:02:46 > Task :compileTestJava
12-Nov-2025 13:02:46 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
12-Nov-2025 13:02:46   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:02:46   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:02:46 Setting target compatibility to 11
12-Nov-2025 13:02:51 Note: Some input files use or override a deprecated API.
12-Nov-2025 13:02:51 Note: Recompile with -Xlint:deprecation for details.
12-Nov-2025 13:02:51 Note: Some input files use unchecked or unsafe operations.
12-Nov-2025 13:02:51 Note: Recompile with -Xlint:unchecked for details.
12-Nov-2025 13:02:52
12-Nov-2025 13:02:52 > Task :processTestResources
12-Nov-2025 13:02:52 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
12-Nov-2025 13:02:52   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:02:52   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:02:52   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:02:52   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:02:52   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:02:52   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:02:52   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-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.
12-Nov-2025 13:02:52
12-Nov-2025 13:02:52 > Task :testClasses
12-Nov-2025 13:02:54
12-Nov-2025 13:02:54 > Task :testTask0
12-Nov-2025 13:02:54 Running tests WITH clover
12-Nov-2025 13:02:56 WARNING: An illegal reflective access operation has occurred
12-Nov-2025 13:02:56 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
12-Nov-2025 13:02:56 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
12-Nov-2025 13:02:56 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
12-Nov-2025 13:02:56 WARNING: All illegal access operations will be denied in a future release
12-Nov-2025 13:03:26
12-Nov-2025 13:03:26 Gradle suite > Gradle test > jalview.bin.HiDPISettingTest2.testHiDPISettings[0](1) FAILED
12-Nov-2025 13:03:26     java.lang.AssertionError: Did not find Debug scale message line 'Desktop graphics transform scale='
12-Nov-2025 13:03:26         at org.testng.Assert.fail(Assert.java:94)
12-Nov-2025 13:03:26         at jalview.bin.HiDPISettingTest2.__CLR4_4_1j7qxj94asf(HiDPISettingTest2.java:222)
12-Nov-2025 13:03:26         at jalview.bin.HiDPISettingTest2.testHiDPISettings(HiDPISettingTest2.java:164)
12-Nov-2025 13:03:36
12-Nov-2025 13:03:36 Gradle suite > Gradle test > jalview.bin.HiDPISettingTest2.testHiDPISettings[1](2) FAILED
12-Nov-2025 13:03:36     java.lang.AssertionError: Did not find Debug scale message line 'Desktop graphics transform scale='
12-Nov-2025 13:03:36         at org.testng.Assert.fail(Assert.java:94)
12-Nov-2025 13:03:36         at jalview.bin.HiDPISettingTest2.__CLR4_4_1j7qxj94asf(HiDPISettingTest2.java:222)
12-Nov-2025 13:03:36         at jalview.bin.HiDPISettingTest2.testHiDPISettings(HiDPISettingTest2.java:164)
12-Nov-2025 13:03:47
12-Nov-2025 13:03:47 Gradle suite > Gradle test > jalview.bin.HiDPISettingTest2.testHiDPISettings[2](4) FAILED
12-Nov-2025 13:03:47     java.lang.AssertionError: Did not find Debug scale message line 'Desktop graphics transform scale='
12-Nov-2025 13:03:47         at org.testng.Assert.fail(Assert.java:94)
12-Nov-2025 13:03:47         at jalview.bin.HiDPISettingTest2.__CLR4_4_1j7qxj94asf(HiDPISettingTest2.java:222)
12-Nov-2025 13:03:47         at jalview.bin.HiDPISettingTest2.testHiDPISettings(HiDPISettingTest2.java:164)
12-Nov-2025 13:03:58
12-Nov-2025 13:03:58 Gradle suite > Gradle test > jalview.bin.HiDPISettingTest2.testHiDPISettings[3](10) FAILED
12-Nov-2025 13:03:58     java.lang.AssertionError: Did not find Debug scale message line 'Desktop graphics transform scale='
12-Nov-2025 13:03:58         at org.testng.Assert.fail(Assert.java:94)
12-Nov-2025 13:03:58         at jalview.bin.HiDPISettingTest2.__CLR4_4_1j7qxj94asf(HiDPISettingTest2.java:222)
12-Nov-2025 13:03:58         at jalview.bin.HiDPISettingTest2.testHiDPISettings(HiDPISettingTest2.java:164)
12-Nov-2025 13:04:16
12-Nov-2025 13:04:16 Gradle suite > Gradle test > jalview.util.Log4jTest.testLog4j FAILED
12-Nov-2025 13:04:16     java.lang.AssertionError: Did not find Log4j Test message line 'Logging to STDERR'
12-Nov-2025 13:04:16         at org.testng.Assert.fail(Assert.java:94)
12-Nov-2025 13:04:16         at jalview.util.Log4jTest.__CLR4_4_1kdolov3q0d(Log4jTest.java:194)
12-Nov-2025 13:04:16         at jalview.util.Log4jTest.testLog4j(Log4jTest.java:160)
12-Nov-2025 13:08:28
12-Nov-2025 13:08:28 1819 tests completed, 5 failed
12-Nov-2025 13:08:29 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/reports/tests/testTask0/index.html
12-Nov-2025 13:08:31
12-Nov-2025 13:08:31 > Task :testTask1
12-Nov-2025 13:08:31 Running tests WITH clover
12-Nov-2025 13:08:33 WARNING: An illegal reflective access operation has occurred
12-Nov-2025 13:08:33 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
12-Nov-2025 13:08:33 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
12-Nov-2025 13:08:33 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
12-Nov-2025 13:08:33 WARNING: All illegal access operations will be denied in a future release
12-Nov-2025 13:11:20
12-Nov-2025 13:11:20 > Task :testTask2
12-Nov-2025 13:11:20 Running tests WITH clover
12-Nov-2025 13:11:25
12-Nov-2025 13:11:25 > Task :testTask3
12-Nov-2025 13:11:25 Running tests WITH clover
12-Nov-2025 13:11:28 WARNING: An illegal reflective access operation has occurred
12-Nov-2025 13:11:28 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
12-Nov-2025 13:11:28 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
12-Nov-2025 13:11:28 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
12-Nov-2025 13:11:28 WARNING: All illegal access operations will be denied in a future release
12-Nov-2025 13:12:28
12-Nov-2025 13:12:28 > Task :test NO-SOURCE
12-Nov-2025 13:12:28
12-Nov-2025 13:12:28 FAILURE: Build failed with an exception.
12-Nov-2025 13:12:28
12-Nov-2025 13:12:28 * Where:
12-Nov-2025 13:12:28 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build.gradle' line: 1967
12-Nov-2025 13:12:28
12-Nov-2025 13:12:28 * What went wrong:
12-Nov-2025 13:12:28 Failed tests!
12-Nov-2025 13:12:28
12-Nov-2025 13:12:28 * Try:
12-Nov-2025 13:12:28 > Run with --stacktrace option to get the stack trace.
12-Nov-2025 13:12:28 > Run with --info or --debug option to get more log output.
12-Nov-2025 13:12:28 > Run with --scan to get full insights.
12-Nov-2025 13:12:28
12-Nov-2025 13:12:28 * Get more help at https://help.gradle.org
12-Nov-2025 13:12:28
12-Nov-2025 13:12:28 BUILD FAILED in 11m 11s
12-Nov-2025 13:12:28 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
12-Nov-2025 13:12:28 │jalview:testTask0 results: FAILURE (1819 tests, 1814 successes, 5 failures, 0 skipped) in 5 minutes, 36.111 seconds   │
12-Nov-2025 13:12:28 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/reports/tests/testTask0/index.html│
12-Nov-2025 13:12:28 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
12-Nov-2025 13:12:28 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 48.940 seconds       │
12-Nov-2025 13:12:28 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/reports/tests/testTask1/index.html│
12-Nov-2025 13:12:28 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
12-Nov-2025 13:12:28 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 5.046 seconds                     │
12-Nov-2025 13:12:28 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/reports/tests/testTask2/index.html│
12-Nov-2025 13:12:28 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
12-Nov-2025 13:12:28 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 4.973 seconds        │
12-Nov-2025 13:12:28 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/reports/tests/testTask3/index.html│
12-Nov-2025 13:12:28 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
12-Nov-2025 13:12:28 │OVERALL: results: FAILURE (1907 tests, 1902 successes, 5 failures, 0 skipped) in 8 minutes, 95.070 seconds            │
12-Nov-2025 13:12:28 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
12-Nov-2025 13:12:28
12-Nov-2025 13:12:28 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
12-Nov-2025 13:12:28
12-Nov-2025 13:12:28 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
12-Nov-2025 13:12:28
12-Nov-2025 13:12:28 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
12-Nov-2025 13:12:28
12-Nov-2025 13:12:28 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
12-Nov-2025 13:12:28 Please consult deprecation warnings for more details.
12-Nov-2025 13:12:28 21 actionable tasks: 20 executed, 1 up-to-date
12-Nov-2025 13:12:29
12-Nov-2025 13:12:29 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
12-Nov-2025 13:12:29 Finished task 'Run tests with openclover under gradle' with result: Failed
12-Nov-2025 13:12:29 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
12-Nov-2025 13:12:29 Bamboo Artifactory Plugin version: 2.6.2
12-Nov-2025 13:12:29
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4602_Hide_All_SS_consensus_for_single_provider - Clover and Tests #1 (JB-GDB725-JOB1-1)'
... 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-GDB725-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=feature/JAL-4602_Hide_All_SS_consensus_for_single_provider
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=feature/JAL-4602_Hide_All_SS_consensus_for_single_provider
bamboo_repository_revision_number=e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB725-JOB1-1
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-GDB725-JOB1
bamboo_planRepository_1_name=Jalview Gitlab
bamboo_buildKey=JB-GDB725-JOB1
bamboo_shortPlanName=feature-JAL-4602_Hide_All_SS_consensus_for_single_provider
bamboo_planRepository_name=Jalview Gitlab
LOGNAME=bamboo
bamboo_buildNumber=1
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-GDB725-JOB1-1
bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
SHELL=/bin/bash
bamboo_agentId=196609
bamboo_planName=Jalview Builds - Gradle Develop Build - feature-JAL-4602_Hide_All_SS_consensus_for_single_provider
bamboo_shortPlanKey=GDB725
bamboo_repository_46498573_git_username=
bamboo_shortJobKey=JOB1
bamboo_repository_46498573_name=Jalview Gitlab
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d
bamboo_buildTimeStamp=2025-11-12T13:01:07.747Z
bamboo_repository_git_branch=feature/JAL-4602_Hide_All_SS_consensus_for_single_provider
bamboo_buildResultKey=JB-GDB725-JOB1-1
bamboo_repository_branch_name=feature/JAL-4602_Hide_All_SS_consensus_for_single_provider
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - feature-JAL-4602_Hide_All_SS_consensus_for_single_provider - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d
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
bamboo_repository_46498573_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_planRepository_branch=feature/JAL-4602_Hide_All_SS_consensus_for_single_provider
bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609
bamboo_jobFailed=true
bamboo_capability_system_git_executable=/bin/git
bamboo_repository_git_username=
bamboo_planRepository_branchDisplayName=feature/JAL-4602_Hide_All_SS_consensus_for_single_provider
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=feature/JAL-4602_Hide_All_SS_consensus_for_single_provider
_=/usr/bin/java
bamboo_repository_46498573_git_branch=feature/JAL-4602_Hide_All_SS_consensus_for_single_provider
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-46302717
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_repository_46498573_revision_number=e0ed80e7c5755b4fbc2c1a6976f9666e246ac59d
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-GDB725-JOB1
bamboo_planKey=JB-GDB725
bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_repository_46498573_branch_name=feature/JAL-4602_Hide_All_SS_consensus_for_single_provider
bamboo_planRepository_username=
HOME=/home/bamboo
bamboo_planRepository_1_branchName=feature/JAL-4602_Hide_All_SS_consensus_for_single_provider
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
12-Nov-2025 13:12:29 444
12-Nov-2025 13:12:36
12-Nov-2025 13:12:36 > Configure project :
12-Nov-2025 13:12:36 Using properties from file './utils/channels/default/channel_gradle.properties'
12-Nov-2025 13:12:36 JALVIEW_VERSION is set to '2.11.5.1'
12-Nov-2025 13:12:36 HEADLESS BUILD
12-Nov-2025 13:12:36 J2S ENABLED
12-Nov-2025 13:12:37 Using a LOCAL profile.
12-Nov-2025 13:12:37 eclipseDir exists
12-Nov-2025 13:12:40
12-Nov-2025 13:12:40 > Task :cloverHtmlReport
12-Nov-2025 13:12:40 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
12-Nov-2025 13:12:43 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/reports/clover'
12-Nov-2025 13:13:39 Done. Processed 116 packages in 56720ms (488ms per package).
12-Nov-2025 13:13:47
12-Nov-2025 13:13:47 > Task :cloverXmlReport
12-Nov-2025 13:13:47 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
12-Nov-2025 13:13:49 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/reports/clover/clover.xml'
12-Nov-2025 13:13:49
12-Nov-2025 13:13:49 > Task :cloverReport
12-Nov-2025 13:13:49
12-Nov-2025 13:13:49 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
12-Nov-2025 13:13:49
12-Nov-2025 13:13:49 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
12-Nov-2025 13:13:49
12-Nov-2025 13:13:49 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
12-Nov-2025 13:13:49
12-Nov-2025 13:13:49 BUILD SUCCESSFUL in 1m 20s
12-Nov-2025 13:13:49 2 actionable tasks: 2 executed
12-Nov-2025 13:13:49 Finished task 'Clover Report' with result: Success
12-Nov-2025 13:13:49 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
12-Nov-2025 13:13:49 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1...
12-Nov-2025 13:13:50 Failing task since 5 failing test cases were found.
12-Nov-2025 13:13:50 Finished task 'TestNG Parser' with result: Failed
12-Nov-2025 13:13:50 Running post build plugin 'NCover Results Collector'
12-Nov-2025 13:13:50 Running post build plugin 'Artifact Copier'
12-Nov-2025 13:13:50 Publishing an artifact: Clover Report (System)
12-Nov-2025 13:13:56 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 6.022 s
12-Nov-2025 13:13:56 Publishing an artifact: TestNG report
12-Nov-2025 13:13:56 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB725-JOB1/build/reports/tests/test does not exist.
12-Nov-2025 13:13:56 The artifact hasn't been successfully published after 4.003 ms
12-Nov-2025 13:13:56 Running post build plugin 'Artifactory Release Management Staging'
12-Nov-2025 13:13:56 Running post build plugin 'Artifactory Build Info Copier'
12-Nov-2025 13:13:56 Running post build plugin 'Artifactory Gradle Properties Info Copier'
12-Nov-2025 13:13:56 Running post build plugin 'npm Cache Cleanup'
12-Nov-2025 13:13:56 Running post build plugin 'Clover Results Collector'
12-Nov-2025 13:13:56 Running post build plugin 'Docker Container Cleanup'
12-Nov-2025 13:13:56 Finalising the build...
12-Nov-2025 13:13:56 Stopping timer.
12-Nov-2025 13:13:56 Build JB-GDB725-JOB1-1 completed.
12-Nov-2025 13:13:56 Running on server: post build plugin 'NCover Results Collector'
12-Nov-2025 13:13:56 Running on server: post build plugin 'Build Hanging Detection Configuration'
12-Nov-2025 13:13:56 Running on server: post build plugin 'Clover Delta Calculator'
12-Nov-2025 13:13:56 Running on server: post build plugin 'Maven Dependencies Postprocessor'
12-Nov-2025 13:13:56 All post build plugins have finished
12-Nov-2025 13:13:56 Generating build results summary...
12-Nov-2025 13:13:56 Saving build results to disk...
12-Nov-2025 13:13:56 Logging substituted variables...
12-Nov-2025 13:13:57 Indexing build results...
12-Nov-2025 13:13:57 Finished building JB-GDB725-JOB1-1.