Build #3

Build: #3 was successful

Job: Clover and Tests was successful

Stages & jobs

  1. Default Stage

Build log

The build generated 312 lines of output. Download or view full build log

07-Jan-2026 02:48:48 Build Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests #3 (JB-GDB738-JOB1-3) started building on agent Default Agent
07-Jan-2026 02:48:48
07-Jan-2026 02:48:48 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1
07-Jan-2026 02:48:48 Executing build Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests #3 (JB-GDB738-JOB1-3)
07-Jan-2026 02:48:48 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
07-Jan-2026 02:48:48 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1
07-Jan-2026 02:48:48 Updating source code to revision: 89c895478e2de885c6475780e1191e8b19fe1dff
07-Jan-2026 02:48:48 Fetching 'refs/heads/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp' from 'https://gitlab.jalview.org/jalview/jalview.git'.
07-Jan-2026 02:48:49 Checking out revision 89c895478e2de885c6475780e1191e8b19fe1dff.
07-Jan-2026 02:48:49 Already on 'feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp'
07-Jan-2026 02:48:49 Updated source code to revision: 89c895478e2de885c6475780e1191e8b19fe1dff
07-Jan-2026 02:48:49 Finished task 'Checkout Default Repository' with result: Success
07-Jan-2026 02:48:49 Running pre-build action: VCS Version Collector
07-Jan-2026 02:48:49 Running pre-build action: Artifactory Release Staging
07-Jan-2026 02:48:49 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
07-Jan-2026 02:48:49 Bamboo Artifactory Plugin version: 2.6.2
07-Jan-2026 02:48:49
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests #3 (JB-GDB738-JOB1-3)'
... running command line:
/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test
... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1
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07-Jan-2026 02:48:49 2414
07-Jan-2026 02:48:50
07-Jan-2026 02:48:50 > Configure project :
07-Jan-2026 02:48:50 Using properties from file './utils/channels/default/channel_gradle.properties'
07-Jan-2026 02:48:50 JALVIEW_VERSION is set to '2.12.0'
07-Jan-2026 02:48:50 HEADLESS BUILD
07-Jan-2026 02:48:50 J2S ENABLED
07-Jan-2026 02:48:50 Using a LOCAL profile.
07-Jan-2026 02:48:50 eclipseDir exists
07-Jan-2026 02:48:50
07-Jan-2026 02:48:50 > Task :clean
07-Jan-2026 02:48:50 > Task :cleanClover
07-Jan-2026 02:48:50 > Task :cleanTest UP-TO-DATE
07-Jan-2026 02:48:52
07-Jan-2026 02:48:52 > Task :cloverInstrJava
07-Jan-2026 02:48:52 Clover: About to instrument 1255 files
07-Jan-2026 02:48:52 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
07-Jan-2026 02:48:52 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover.db'.
07-Jan-2026 02:48:52 Processing files at 1.9 source level.
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:48:55 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?
07-Jan-2026 02:49:01 Clover all over. Instrumented 1255 files (133 packages).
07-Jan-2026 02:49:03
07-Jan-2026 02:49:03 > Task :cloverInstrTests
07-Jan-2026 02:49:03 Clover: About to instrument test files
07-Jan-2026 02:49:03 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
07-Jan-2026 02:49:03 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover.db'.
07-Jan-2026 02:49:03 Processing files at 1.9 source level.
07-Jan-2026 02:49:05 Clover all over. Instrumented 316 files (58 packages).
07-Jan-2026 02:49:05 1774 test methods detected.
07-Jan-2026 02:49:05
07-Jan-2026 02:49:05 > Task :cloverInstr
07-Jan-2026 02:49:07
07-Jan-2026 02:49:07 > Task :compileCloverJava
07-Jan-2026 02:49:07 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
07-Jan-2026 02:49:07   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:07   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:07   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:07 Setting target compatibility to 11
07-Jan-2026 02:49:19 Note: Some input files use or override a deprecated API.
07-Jan-2026 02:49:19 Note: Recompile with -Xlint:deprecation for details.
07-Jan-2026 02:49:19 Note: Some input files use unchecked or unsafe operations.
07-Jan-2026 02:49:19 Note: Recompile with -Xlint:unchecked for details.
07-Jan-2026 02:49:24
07-Jan-2026 02:49:24 > Task :processCloverResources NO-SOURCE
07-Jan-2026 02:49:24 > Task :cloverClasses
07-Jan-2026 02:49:24 > Task :copyHelp
07-Jan-2026 02:49:25 > Task :buildIndices
07-Jan-2026 02:49:25 > Task :copyResources
07-Jan-2026 02:49:25 > Task :copyChannelResources
07-Jan-2026 02:49:25
07-Jan-2026 02:49:25 > Task :createBuildProperties
07-Jan-2026 02:49:25 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
07-Jan-2026 02:49:25   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:25
07-Jan-2026 02:49:25 > Task :buildResources
07-Jan-2026 02:49:25 > Task :copyDocs
07-Jan-2026 02:49:25
07-Jan-2026 02:49:25 > Task :convertMdFiles
07-Jan-2026 02:49:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
07-Jan-2026 02:49:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/releaseprocess.html
07-Jan-2026 02:49:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
07-Jan-2026 02:49:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
07-Jan-2026 02:49:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/building.html
07-Jan-2026 02:49:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/addingWebClient.html
07-Jan-2026 02:49:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/jalview-projects.html
07-Jan-2026 02:49:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
07-Jan-2026 02:49:26
07-Jan-2026 02:49:26 > Task :releasesTemplates
07-Jan-2026 02:49:26 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
07-Jan-2026 02:49:26   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:26   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:26 Stripping rc/test/etc for TEST
07-Jan-2026 02:49:26 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
07-Jan-2026 02:49:26
07-Jan-2026 02:49:26 > Task :prepare
07-Jan-2026 02:49:28
07-Jan-2026 02:49:28 > Task :compileJava
07-Jan-2026 02:49:28 Setting target compatibility to 11
07-Jan-2026 02:49:32 Note: Some input files use or override a deprecated API.
07-Jan-2026 02:49:32 Note: Recompile with -Xlint:deprecation for details.
07-Jan-2026 02:49:32 Note: Some input files use unchecked or unsafe operations.
07-Jan-2026 02:49:32 Note: Recompile with -Xlint:unchecked for details.
07-Jan-2026 02:49:35
07-Jan-2026 02:49:35 > Task :compileTestJava
07-Jan-2026 02:49:35 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
07-Jan-2026 02:49:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:35   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:35 Setting target compatibility to 11
07-Jan-2026 02:49:39 Note: Some input files use or override a deprecated API.
07-Jan-2026 02:49:39 Note: Recompile with -Xlint:deprecation for details.
07-Jan-2026 02:49:39 Note: Some input files use unchecked or unsafe operations.
07-Jan-2026 02:49:39 Note: Recompile with -Xlint:unchecked for details.
07-Jan-2026 02:49:40
07-Jan-2026 02:49:40 > Task :processTestResources
07-Jan-2026 02:49:40 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
07-Jan-2026 02:49:40   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:40   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:40   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:40   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:40   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:40   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:40   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:40   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-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.
07-Jan-2026 02:49:40
07-Jan-2026 02:49:40 > Task :testClasses
07-Jan-2026 02:49:42
07-Jan-2026 02:49:42 > Task :testTask0
07-Jan-2026 02:49:42 Running tests WITH clover
07-Jan-2026 02:49:43 WARNING: An illegal reflective access operation has occurred
07-Jan-2026 02:49:43 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
07-Jan-2026 02:49:43 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
07-Jan-2026 02:49:43 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
07-Jan-2026 02:49:43 WARNING: All illegal access operations will be denied in a future release
07-Jan-2026 02:52:09 [148.377s][warning][gc,alloc] AWT-EventQueue-0: Retried waiting for GCLocker too often allocating 135080516 words
07-Jan-2026 02:54:20
07-Jan-2026 02:54:20 > Task :testTask1
07-Jan-2026 02:54:20 Running tests WITH clover
07-Jan-2026 02:54:21 WARNING: An illegal reflective access operation has occurred
07-Jan-2026 02:54:21 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
07-Jan-2026 02:54:21 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
07-Jan-2026 02:54:21 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
07-Jan-2026 02:54:21 WARNING: All illegal access operations will be denied in a future release
07-Jan-2026 02:56:21
07-Jan-2026 02:56:21 > Task :testTask2
07-Jan-2026 02:56:21 Running tests WITH clover
07-Jan-2026 02:56:22 WARNING: An illegal reflective access operation has occurred
07-Jan-2026 02:56:22 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
07-Jan-2026 02:56:22 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
07-Jan-2026 02:56:22 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
07-Jan-2026 02:56:22 WARNING: All illegal access operations will be denied in a future release
07-Jan-2026 02:56:26
07-Jan-2026 02:56:26 > Task :testTask3
07-Jan-2026 02:56:26 Running tests WITH clover
07-Jan-2026 02:56:27 WARNING: An illegal reflective access operation has occurred
07-Jan-2026 02:56:27 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
07-Jan-2026 02:56:27 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
07-Jan-2026 02:56:27 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
07-Jan-2026 02:56:27 WARNING: All illegal access operations will be denied in a future release
07-Jan-2026 02:56:44
07-Jan-2026 02:56:44 > Task :test NO-SOURCE
07-Jan-2026 02:56:44 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
07-Jan-2026 02:56:44 │jalview:testTask0 results: SUCCESS (2107 tests, 2107 successes, 0 failures, 0 skipped) in 4 minutes, 37.769 seconds   │
07-Jan-2026 02:56:44 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/testTask0/index.html│
07-Jan-2026 02:56:44 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
07-Jan-2026 02:56:44 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 0.858 seconds        │
07-Jan-2026 02:56:44 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/testTask1/index.html│
07-Jan-2026 02:56:44 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
07-Jan-2026 02:56:44 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.675 seconds                     │
07-Jan-2026 02:56:44 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/testTask2/index.html│
07-Jan-2026 02:56:44 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
07-Jan-2026 02:56:44 │jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 19.714 seconds                  │
07-Jan-2026 02:56:44 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/testTask3/index.html│
07-Jan-2026 02:56:44 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
07-Jan-2026 02:56:44 │OVERALL: results: SUCCESS (2184 tests, 2183 successes, 0 failures, 1 skipped) in 6 minutes, 63.016 seconds            │
07-Jan-2026 02:56:44 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
07-Jan-2026 02:56:44
07-Jan-2026 02:56:44 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
07-Jan-2026 02:56:44
07-Jan-2026 02:56:44 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
07-Jan-2026 02:56:44
07-Jan-2026 02:56:44 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
07-Jan-2026 02:56:44
07-Jan-2026 02:56:44 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
07-Jan-2026 02:56:44 Please consult deprecation warnings for more details.
07-Jan-2026 02:56:44
07-Jan-2026 02:56:44 BUILD SUCCESSFUL in 7m 55s
07-Jan-2026 02:56:44 21 actionable tasks: 20 executed, 1 up-to-date
07-Jan-2026 02:56:44 Finished task 'Run tests with openclover under gradle' with result: Success
07-Jan-2026 02:56:44 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
07-Jan-2026 02:56:44 Bamboo Artifactory Plugin version: 2.6.2
07-Jan-2026 02:56:44
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Clover and Tests #3 (JB-GDB738-JOB1-3)'
... running command line:
/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport
... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1
... using extra environment variables:
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bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
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bamboo_repository_revision_number=89c895478e2de885c6475780e1191e8b19fe1dff
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB738-JOB1-3
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bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test
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bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
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-GDB738-JOB1
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bamboo_planRepository_username=
HOME=/home/bamboo
bamboo_planRepository_1_branchName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp
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07-Jan-2026 02:56:44 2414
07-Jan-2026 02:56:49
07-Jan-2026 02:56:49 > Configure project :
07-Jan-2026 02:56:49 Using properties from file './utils/channels/default/channel_gradle.properties'
07-Jan-2026 02:56:49 JALVIEW_VERSION is set to '2.12.0'
07-Jan-2026 02:56:49 HEADLESS BUILD
07-Jan-2026 02:56:49 J2S ENABLED
07-Jan-2026 02:56:49 Using a LOCAL profile.
07-Jan-2026 02:56:50 eclipseDir exists
07-Jan-2026 02:56:52
07-Jan-2026 02:56:52 > Task :cloverHtmlReport
07-Jan-2026 02:56:52 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
07-Jan-2026 02:56:53 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/clover'
07-Jan-2026 02:57:37 ERROR: Invalid Java source found or Clover failed to parse it: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/src/jalview/schemes/ResidueProperties.java
07-Jan-2026 02:57:43 Done. Processed 137 packages in 49260ms (359ms per package).
07-Jan-2026 02:57:48
07-Jan-2026 02:57:48 > Task :cloverXmlReport
07-Jan-2026 02:57:48 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
07-Jan-2026 02:57:49 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/clover/clover.xml'
07-Jan-2026 02:57:49
07-Jan-2026 02:57:49 > Task :cloverReport
07-Jan-2026 02:57:49
07-Jan-2026 02:57:49 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
07-Jan-2026 02:57:49
07-Jan-2026 02:57:49 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
07-Jan-2026 02:57:49
07-Jan-2026 02:57:49 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
07-Jan-2026 02:57:49
07-Jan-2026 02:57:49 BUILD SUCCESSFUL in 1m 4s
07-Jan-2026 02:57:49 2 actionable tasks: 2 executed
07-Jan-2026 02:57:49 Finished task 'Clover Report' with result: Success
07-Jan-2026 02:57:49 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
07-Jan-2026 02:57:49 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1...
07-Jan-2026 02:57:49 Finished task 'TestNG Parser' with result: Success
07-Jan-2026 02:57:49 Running post build plugin 'NCover Results Collector'
07-Jan-2026 02:57:49 Running post build plugin 'Artifact Copier'
07-Jan-2026 02:57:49 Publishing an artifact: Clover Report (System)
07-Jan-2026 02:57:51 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.940 s
07-Jan-2026 02:57:51 Publishing an artifact: TestNG report
07-Jan-2026 02:57:51 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB738-JOB1/build/reports/tests/test does not exist.
07-Jan-2026 02:57:51 The artifact hasn't been successfully published after 1.379 ms
07-Jan-2026 02:57:51 Running post build plugin 'Artifactory Release Management Staging'
07-Jan-2026 02:57:51 Running post build plugin 'Artifactory Build Info Copier'
07-Jan-2026 02:57:51 Running post build plugin 'Artifactory Gradle Properties Info Copier'
07-Jan-2026 02:57:51 Running post build plugin 'npm Cache Cleanup'
07-Jan-2026 02:57:51 Running post build plugin 'Clover Results Collector'
07-Jan-2026 02:57:51 Running post build plugin 'Docker Container Cleanup'
07-Jan-2026 02:57:51 Finalising the build...
07-Jan-2026 02:57:51 Stopping timer.
07-Jan-2026 02:57:51 Build JB-GDB738-JOB1-3 completed.
07-Jan-2026 02:57:51 Running on server: post build plugin 'NCover Results Collector'
07-Jan-2026 02:57:51 Running on server: post build plugin 'Build Hanging Detection Configuration'
07-Jan-2026 02:57:51 Running on server: post build plugin 'Clover Delta Calculator'
07-Jan-2026 02:57:51 Running on server: post build plugin 'Maven Dependencies Postprocessor'
07-Jan-2026 02:57:51 All post build plugins have finished
07-Jan-2026 02:57:51 Generating build results summary...
07-Jan-2026 02:57:51 Saving build results to disk...
07-Jan-2026 02:57:51 Logging substituted variables...
07-Jan-2026 02:57:51 Indexing build results...
07-Jan-2026 02:57:51 Finished building JB-GDB738-JOB1-3.