Build #4

Build and run tests under Java 11

Build: #4 was successful

Job: Clover and Tests was successful

Stages & jobs

  1. Default Stage

Build log

The build generated 249 lines of output. Download or view full build log

11-Feb-2026 11:22:23 Build Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests #4 (JB-GDB740-JOB1-4) started building on agent Default Agent
11-Feb-2026 11:22:23
11-Feb-2026 11:22:23 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1
11-Feb-2026 11:22:23 Executing build Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests #4 (JB-GDB740-JOB1-4)
11-Feb-2026 11:22:23 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
11-Feb-2026 11:22:23 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1
11-Feb-2026 11:22:23 Updating source code to revision: 1617d0ed323d507874712592b848e1ffdcec2883
11-Feb-2026 11:22:23 Fetching 'refs/heads/citation.cff' from 'https://gitlab.jalview.org/jalview/jalview.git'.
11-Feb-2026 11:22:23 Checking out revision 1617d0ed323d507874712592b848e1ffdcec2883.
11-Feb-2026 11:22:23 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
11-Feb-2026 11:22:23    6f3ab10..1617d0e  citation.cff -> origin/citation.cff
11-Feb-2026 11:22:24 Already on 'citation.cff'
11-Feb-2026 11:22:24 Your branch is behind 'origin/citation.cff' by 1 commit, and can be fast-forwarded.
11-Feb-2026 11:22:24   (use "git pull" to update your local branch)
11-Feb-2026 11:22:24 HEAD is now at 1617d0e JAL-4651 make it all valid
11-Feb-2026 11:22:24 Updated source code to revision: 1617d0ed323d507874712592b848e1ffdcec2883
11-Feb-2026 11:22:24 Finished task 'Checkout Default Repository' with result: Success
11-Feb-2026 11:22:24 Running pre-build action: VCS Version Collector
11-Feb-2026 11:22:24 Running pre-build action: Artifactory Release Staging
11-Feb-2026 11:22:24 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
11-Feb-2026 11:22:24 Bamboo Artifactory Plugin version: 2.6.2
11-Feb-2026 11:22:24
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests #4 (JB-GDB740-JOB1-4)'
... running command line:
/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test
... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1
... using extra environment variables:
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11-Feb-2026 11:22:24 2414
11-Feb-2026 11:22:26
11-Feb-2026 11:22:26 > Configure project :
11-Feb-2026 11:22:26 Using properties from file './utils/channels/default/channel_gradle.properties'
11-Feb-2026 11:22:26 JALVIEW_VERSION is set to '2.11.5.1'
11-Feb-2026 11:22:26 HEADLESS BUILD
11-Feb-2026 11:22:26 J2S ENABLED
11-Feb-2026 11:22:26 Using a LOCAL profile.
11-Feb-2026 11:22:26 eclipseDir exists
11-Feb-2026 11:22:27
11-Feb-2026 11:22:27 > Task :clean
11-Feb-2026 11:22:27 > Task :cleanClover
11-Feb-2026 11:22:27 > Task :cleanTest UP-TO-DATE
11-Feb-2026 11:22:29
11-Feb-2026 11:22:29 > Task :cloverInstrJava
11-Feb-2026 11:22:29 Clover: About to instrument 1109 files
11-Feb-2026 11:22:29 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Feb-2026 11:22:29 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/clover/clover.db'.
11-Feb-2026 11:22:29 Processing files at 1.9 source level.
11-Feb-2026 11:22:31 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?
11-Feb-2026 11:22:31 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?
11-Feb-2026 11:22:31 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?
11-Feb-2026 11:22:31 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?
11-Feb-2026 11:22:31 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?
11-Feb-2026 11:22:31 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?
11-Feb-2026 11:22:31 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?
11-Feb-2026 11:22:38 Clover all over. Instrumented 1109 files (113 packages).
11-Feb-2026 11:22:40
11-Feb-2026 11:22:40 > Task :cloverInstrTests
11-Feb-2026 11:22:40 Clover: About to instrument test files
11-Feb-2026 11:22:40 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Feb-2026 11:22:40 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/clover/clover.db'.
11-Feb-2026 11:22:40 Processing files at 1.9 source level.
11-Feb-2026 11:22:42 Clover all over. Instrumented 293 files (52 packages).
11-Feb-2026 11:22:42 1627 test methods detected.
11-Feb-2026 11:22:42
11-Feb-2026 11:22:42 > Task :cloverInstr
11-Feb-2026 11:22:44
11-Feb-2026 11:22:44 > Task :compileCloverJava
11-Feb-2026 11:22:44 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
11-Feb-2026 11:22:44   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:22:44   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:22:44   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:22:44 Setting target compatibility to 11
11-Feb-2026 11:22:56 Note: Some input files use or override a deprecated API.
11-Feb-2026 11:22:56 Note: Recompile with -Xlint:deprecation for details.
11-Feb-2026 11:22:56 Note: Some input files use unchecked or unsafe operations.
11-Feb-2026 11:22:56 Note: Recompile with -Xlint:unchecked for details.
11-Feb-2026 11:23:02
11-Feb-2026 11:23:02 > Task :processCloverResources NO-SOURCE
11-Feb-2026 11:23:02 > Task :cloverClasses
11-Feb-2026 11:23:02 > Task :copyHelp
11-Feb-2026 11:23:03 > Task :buildIndices
11-Feb-2026 11:23:03 > Task :copyResources
11-Feb-2026 11:23:03 > Task :copyChannelResources
11-Feb-2026 11:23:03
11-Feb-2026 11:23:03 > Task :createBuildProperties
11-Feb-2026 11:23:03 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
11-Feb-2026 11:23:03   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:23:03
11-Feb-2026 11:23:03 > Task :buildResources
11-Feb-2026 11:23:03 > Task :copyDocs
11-Feb-2026 11:23:03
11-Feb-2026 11:23:03 > Task :convertMdFiles
11-Feb-2026 11:23:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
11-Feb-2026 11:23:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/releaseprocess.html
11-Feb-2026 11:23:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
11-Feb-2026 11:23:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/building.html
11-Feb-2026 11:23:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/resources/doc_build/doc/jalview-projects.html
11-Feb-2026 11:23:04
11-Feb-2026 11:23:04 > Task :releasesTemplates
11-Feb-2026 11:23:04 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
11-Feb-2026 11:23:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:23:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:23:04 Stripping rc/test/etc for TEST
11-Feb-2026 11:23:04 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
11-Feb-2026 11:23:04
11-Feb-2026 11:23:04 > Task :prepare
11-Feb-2026 11:23:06
11-Feb-2026 11:23:06 > Task :compileJava
11-Feb-2026 11:23:06 Setting target compatibility to 11
11-Feb-2026 11:23:10 Note: Some input files use or override a deprecated API.
11-Feb-2026 11:23:10 Note: Recompile with -Xlint:deprecation for details.
11-Feb-2026 11:23:10 Note: Some input files use unchecked or unsafe operations.
11-Feb-2026 11:23:10 Note: Recompile with -Xlint:unchecked for details.
11-Feb-2026 11:23:13
11-Feb-2026 11:23:13 > Task :compileTestJava
11-Feb-2026 11:23:13 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
11-Feb-2026 11:23:13   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:23:13   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:23:13 Setting target compatibility to 11
11-Feb-2026 11:23:16 Note: Some input files use or override a deprecated API.
11-Feb-2026 11:23:16 Note: Recompile with -Xlint:deprecation for details.
11-Feb-2026 11:23:16 Note: Some input files use unchecked or unsafe operations.
11-Feb-2026 11:23:16 Note: Recompile with -Xlint:unchecked for details.
11-Feb-2026 11:23:17
11-Feb-2026 11:23:17 > Task :processTestResources
11-Feb-2026 11:23:17 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
11-Feb-2026 11:23:17   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:23:17   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:23:17   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:23:17   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:23:17   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:23:17   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:23:17   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:23:17   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-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.
11-Feb-2026 11:23:17
11-Feb-2026 11:23:17 > Task :testClasses
11-Feb-2026 11:23:19
11-Feb-2026 11:23:19 > Task :testTask0
11-Feb-2026 11:23:19 Running tests WITH clover
11-Feb-2026 11:23:21 WARNING: An illegal reflective access operation has occurred
11-Feb-2026 11:23:21 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
11-Feb-2026 11:23:21 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
11-Feb-2026 11:23:21 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
11-Feb-2026 11:23:21 WARNING: All illegal access operations will be denied in a future release
11-Feb-2026 11:27:48
11-Feb-2026 11:27:48 > Task :testTask1
11-Feb-2026 11:27:48 Running tests WITH clover
11-Feb-2026 11:27:50 WARNING: An illegal reflective access operation has occurred
11-Feb-2026 11:27:50 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
11-Feb-2026 11:27:50 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
11-Feb-2026 11:27:50 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
11-Feb-2026 11:27:50 WARNING: All illegal access operations will be denied in a future release
11-Feb-2026 11:30:08
11-Feb-2026 11:30:08 > Task :testTask2
11-Feb-2026 11:30:08 Running tests WITH clover
11-Feb-2026 11:30:11
11-Feb-2026 11:30:11 > Task :testTask3
11-Feb-2026 11:30:11 Running tests WITH clover
11-Feb-2026 11:30:13 WARNING: An illegal reflective access operation has occurred
11-Feb-2026 11:30:13 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
11-Feb-2026 11:30:13 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
11-Feb-2026 11:30:13 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
11-Feb-2026 11:30:13 WARNING: All illegal access operations will be denied in a future release
11-Feb-2026 11:31:04
11-Feb-2026 11:31:04 > Task :test NO-SOURCE
11-Feb-2026 11:31:04 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
11-Feb-2026 11:31:04 │jalview:testTask0 results: SUCCESS (1835 tests, 1835 successes, 0 failures, 0 skipped) in 4 minutes, 28.761 seconds   │
11-Feb-2026 11:31:04 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/testTask0/index.html│
11-Feb-2026 11:31:04 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Feb-2026 11:31:04 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 19.560 seconds       │
11-Feb-2026 11:31:04 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/testTask1/index.html│
11-Feb-2026 11:31:04 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Feb-2026 11:31:04 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.198 seconds                     │
11-Feb-2026 11:31:04 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/testTask2/index.html│
11-Feb-2026 11:31:04 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Feb-2026 11:31:04 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 54.220 seconds                  │
11-Feb-2026 11:31:04 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/testTask3/index.html│
11-Feb-2026 11:31:04 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Feb-2026 11:31:04 │OVERALL: results: SUCCESS (1923 tests, 1923 successes, 0 failures, 0 skipped) in 6 minutes, 105.739 seconds           │
11-Feb-2026 11:31:04 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
11-Feb-2026 11:31:04
11-Feb-2026 11:31:04 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
11-Feb-2026 11:31:04
11-Feb-2026 11:31:04 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
11-Feb-2026 11:31:04
11-Feb-2026 11:31:04 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
11-Feb-2026 11:31:04
11-Feb-2026 11:31:04 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
11-Feb-2026 11:31:04 Please consult deprecation warnings for more details.
11-Feb-2026 11:31:04
11-Feb-2026 11:31:04 BUILD SUCCESSFUL in 8m 39s
11-Feb-2026 11:31:04 21 actionable tasks: 20 executed, 1 up-to-date
11-Feb-2026 11:31:04 Finished task 'Run tests with openclover under gradle' with result: Success
11-Feb-2026 11:31:04 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
11-Feb-2026 11:31:04 Bamboo Artifactory Plugin version: 2.6.2
11-Feb-2026 11:31:04
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests #4 (JB-GDB740-JOB1-4)'
... running command line:
/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport
... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=citation.cff
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=citation.cff
bamboo_repository_revision_number=1617d0ed323d507874712592b848e1ffdcec2883
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB740-JOB1-4
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-GDB740-JOB1
bamboo_planRepository_1_name=Jalview Gitlab
bamboo_buildKey=JB-GDB740-JOB1
bamboo_repository_48168989_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_shortPlanName=citation.cff
bamboo_planRepository_name=Jalview Gitlab
LOGNAME=bamboo
bamboo_buildNumber=4
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-GDB740-JOB1-4
bamboo_repository_48168989_git_branch=citation.cff
bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
SHELL=/bin/bash
bamboo_agentId=196609
bamboo_planName=Jalview Builds - Gradle Develop Build - citation.cff
bamboo_shortPlanKey=GDB740
bamboo_repository_48168989_previous_revision_number=6f3ab10eeeb41f56f66de76b7b65d8ef9364c322
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=1617d0ed323d507874712592b848e1ffdcec2883
bamboo_buildTimeStamp=2026-02-11T11:22:23.489Z
bamboo_repository_previous_revision_number=6f3ab10eeeb41f56f66de76b7b65d8ef9364c322
bamboo_planRepository_previousRevision=6f3ab10eeeb41f56f66de76b7b65d8ef9364c322
bamboo_repository_git_branch=citation.cff
bamboo_buildResultKey=JB-GDB740-JOB1-4
bamboo_repository_branch_name=citation.cff
bamboo_repository_48168989_name=Jalview Gitlab
bamboo_repository_48168989_branch_name=citation.cff
bamboo_repository_48168989_git_username=
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - citation.cff - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=1617d0ed323d507874712592b848e1ffdcec2883
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=false
bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk
bamboo_repository_48168989_revision_number=1617d0ed323d507874712592b848e1ffdcec2883
bamboo_planRepository_branch=citation.cff
bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609
bamboo_jobFailed=false
bamboo_capability_system_git_executable=/bin/git
bamboo_repository_git_username=
bamboo_planRepository_1_previousRevision=6f3ab10eeeb41f56f66de76b7b65d8ef9364c322
bamboo_planRepository_branchDisplayName=citation.cff
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=citation.cff
_=/usr/bin/java
bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11
bamboo_capability_system_builderivy_Ivy=/usr
bamboo_plan_storageTag=plan-47972409
bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle
bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache
bamboo_planRepository_1_username=
bamboo_planRepository_type=gitv2
USER=bamboo
bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache
bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_capability_system_builder_ant_Ant=/usr/share/ant
bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven
bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp
bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1
bamboo_planKey=JB-GDB740
bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_planRepository_username=
HOME=/home/bamboo
bamboo_planRepository_1_branchName=citation.cff
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
11-Feb-2026 11:31:04 2414
11-Feb-2026 11:31:10
11-Feb-2026 11:31:10 > Configure project :
11-Feb-2026 11:31:10 Using properties from file './utils/channels/default/channel_gradle.properties'
11-Feb-2026 11:31:10 JALVIEW_VERSION is set to '2.11.5.1'
11-Feb-2026 11:31:10 HEADLESS BUILD
11-Feb-2026 11:31:10 J2S ENABLED
11-Feb-2026 11:31:10 Using a LOCAL profile.
11-Feb-2026 11:31:11 eclipseDir exists
11-Feb-2026 11:31:13
11-Feb-2026 11:31:13 > Task :cloverHtmlReport
11-Feb-2026 11:31:13 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Feb-2026 11:31:15 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/clover'
11-Feb-2026 11:32:01 Done. Processed 117 packages in 46445ms (396ms per package).
11-Feb-2026 11:32:06
11-Feb-2026 11:32:06 > Task :cloverXmlReport
11-Feb-2026 11:32:06 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Feb-2026 11:32:08 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/clover/clover.xml'
11-Feb-2026 11:32:08
11-Feb-2026 11:32:08 > Task :cloverReport
11-Feb-2026 11:32:08
11-Feb-2026 11:32:08 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
11-Feb-2026 11:32:08
11-Feb-2026 11:32:08 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
11-Feb-2026 11:32:08
11-Feb-2026 11:32:08 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
11-Feb-2026 11:32:08
11-Feb-2026 11:32:08 BUILD SUCCESSFUL in 1m 3s
11-Feb-2026 11:32:08 2 actionable tasks: 2 executed
11-Feb-2026 11:32:08 Finished task 'Clover Report' with result: Success
11-Feb-2026 11:32:08 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
11-Feb-2026 11:32:08 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1...
11-Feb-2026 11:32:08 Finished task 'TestNG Parser' with result: Success
11-Feb-2026 11:32:08 Running post build plugin 'NCover Results Collector'
11-Feb-2026 11:32:08 Running post build plugin 'Artifact Copier'
11-Feb-2026 11:32:08 Publishing an artifact: Clover Report (System)
11-Feb-2026 11:32:10 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.589 s
11-Feb-2026 11:32:10 Publishing an artifact: TestNG report
11-Feb-2026 11:32:10 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB740-JOB1/build/reports/tests/test does not exist.
11-Feb-2026 11:32:10 The artifact hasn't been successfully published after 2.197 ms
11-Feb-2026 11:32:10 Running post build plugin 'Artifactory Release Management Staging'
11-Feb-2026 11:32:10 Running post build plugin 'Artifactory Build Info Copier'
11-Feb-2026 11:32:10 Running post build plugin 'Artifactory Gradle Properties Info Copier'
11-Feb-2026 11:32:10 Running post build plugin 'npm Cache Cleanup'
11-Feb-2026 11:32:10 Running post build plugin 'Clover Results Collector'
11-Feb-2026 11:32:10 Running post build plugin 'Docker Container Cleanup'
11-Feb-2026 11:32:10 Finalising the build...
11-Feb-2026 11:32:10 Stopping timer.
11-Feb-2026 11:32:10 Build JB-GDB740-JOB1-4 completed.
11-Feb-2026 11:32:10 Running on server: post build plugin 'NCover Results Collector'
11-Feb-2026 11:32:10 Running on server: post build plugin 'Build Hanging Detection Configuration'
11-Feb-2026 11:32:10 Running on server: post build plugin 'Clover Delta Calculator'
11-Feb-2026 11:32:10 Running on server: post build plugin 'Maven Dependencies Postprocessor'
11-Feb-2026 11:32:10 All post build plugins have finished
11-Feb-2026 11:32:10 Generating build results summary...
11-Feb-2026 11:32:10 Saving build results to disk...
11-Feb-2026 11:32:10 Logging substituted variables...
11-Feb-2026 11:32:10 Indexing build results...
11-Feb-2026 11:32:10 Finished building JB-GDB740-JOB1-4.