Build #1

Build: #1 failed

Job: Clover and Tests failed

Stages & jobs

  1. Default Stage

Build log

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

27-Nov-2025 16:51:07 Build Jalview Builds - Gradle Develop Build - patch-JAL-4601_stk_ss_annots_showhide - Clover and Tests #1 (JB-GDB730-JOB1-1) started building on agent Default Agent
27-Nov-2025 16:51:07
27-Nov-2025 16:51:08 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1
27-Nov-2025 16:51:08 Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4601_stk_ss_annots_showhide - Clover and Tests #1 (JB-GDB730-JOB1-1)
27-Nov-2025 16:51:08 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
27-Nov-2025 16:51:08 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1
27-Nov-2025 16:51:08 Updating source code to revision: 3640cfb3a1a72b0a7514f5406b223cad955aa1fc
27-Nov-2025 16:51:08 Fetching 'refs/heads/patch/JAL-4601_stk_ss_annots_showhide' from 'https://gitlab.jalview.org/jalview/jalview.git'.
27-Nov-2025 16:51:09 Checking out revision 3640cfb3a1a72b0a7514f5406b223cad955aa1fc.
27-Nov-2025 16:51:09 Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/.git'.
27-Nov-2025 16:51:09 Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1'...
27-Nov-2025 16:51:09 done.
27-Nov-2025 16:51:16 Branch patch/JAL-4601_stk_ss_annots_showhide set up to track remote branch patch/JAL-4601_stk_ss_annots_showhide from origin.
27-Nov-2025 16:51:16 Switched to a new branch 'patch/JAL-4601_stk_ss_annots_showhide'
27-Nov-2025 16:51:16 Updated source code to revision: 3640cfb3a1a72b0a7514f5406b223cad955aa1fc
27-Nov-2025 16:51:16 Finished task 'Checkout Default Repository' with result: Success
27-Nov-2025 16:51:16 Running pre-build action: VCS Version Collector
27-Nov-2025 16:51:16 Running pre-build action: Artifactory Release Staging
27-Nov-2025 16:51:16 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
27-Nov-2025 16:51:16 Bamboo Artifactory Plugin version: 2.6.2
27-Nov-2025 16:51:16
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4601_stk_ss_annots_showhide - Clover and Tests #1 (JB-GDB730-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-GDB730-JOB1
... using extra environment variables:
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27-Nov-2025 16:51:16 444
27-Nov-2025 16:51:20
27-Nov-2025 16:51:20 > Configure project :
27-Nov-2025 16:51:20 Using properties from file './utils/channels/default/channel_gradle.properties'
27-Nov-2025 16:51:20 JALVIEW_VERSION is set to '2.11.5.1'
27-Nov-2025 16:51:20 HEADLESS BUILD
27-Nov-2025 16:51:20 J2S ENABLED
27-Nov-2025 16:51:20 Using a LOCAL profile.
27-Nov-2025 16:51:20 eclipseDir exists
27-Nov-2025 16:51:20
27-Nov-2025 16:51:20 > Task :clean
27-Nov-2025 16:51:20 > Task :cleanClover
27-Nov-2025 16:51:20 > Task :cleanTest UP-TO-DATE
27-Nov-2025 16:51:22
27-Nov-2025 16:51:22 > Task :cloverInstrJava
27-Nov-2025 16:51:22 Clover: About to instrument 1107 files
27-Nov-2025 16:51:22 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
27-Nov-2025 16:51:22 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/clover/clover.db'.
27-Nov-2025 16:51:22 Processing files at 1.9 source level.
27-Nov-2025 16:51:27 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?
27-Nov-2025 16:51:27 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?
27-Nov-2025 16:51:27 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?
27-Nov-2025 16:51:27 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?
27-Nov-2025 16:51:27 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?
27-Nov-2025 16:51:27 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?
27-Nov-2025 16:51:27 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?
27-Nov-2025 16:51:34 Clover all over. Instrumented 1107 files (112 packages).
27-Nov-2025 16:51:36
27-Nov-2025 16:51:36 > Task :cloverInstrTests
27-Nov-2025 16:51:36 Clover: About to instrument test files
27-Nov-2025 16:51:36 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
27-Nov-2025 16:51:36 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/clover/clover.db'.
27-Nov-2025 16:51:36 Processing files at 1.9 source level.
27-Nov-2025 16:51:39 Clover all over. Instrumented 293 files (52 packages).
27-Nov-2025 16:51:39 1624 test methods detected.
27-Nov-2025 16:51:39
27-Nov-2025 16:51:39 > Task :cloverInstr
27-Nov-2025 16:51:43
27-Nov-2025 16:51:43 > Task :compileCloverJava
27-Nov-2025 16:51:43 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
27-Nov-2025 16:51:43   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:51:43   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:51:43   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:51:43 Setting target compatibility to 11
27-Nov-2025 16:52:02 Note: Some input files use or override a deprecated API.
27-Nov-2025 16:52:02 Note: Recompile with -Xlint:deprecation for details.
27-Nov-2025 16:52:02 Note: Some input files use unchecked or unsafe operations.
27-Nov-2025 16:52:02 Note: Recompile with -Xlint:unchecked for details.
27-Nov-2025 16:52:09
27-Nov-2025 16:52:09 > Task :processCloverResources NO-SOURCE
27-Nov-2025 16:52:09 > Task :cloverClasses
27-Nov-2025 16:52:09 > Task :copyHelp
27-Nov-2025 16:52:11 > Task :buildIndices
27-Nov-2025 16:52:11 > Task :copyResources
27-Nov-2025 16:52:11 > Task :copyChannelResources
27-Nov-2025 16:52:11
27-Nov-2025 16:52:11 > Task :createBuildProperties
27-Nov-2025 16:52:11 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
27-Nov-2025 16:52:11   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:52:11
27-Nov-2025 16:52:11 > Task :buildResources
27-Nov-2025 16:52:11 > Task :copyDocs
27-Nov-2025 16:52:11
27-Nov-2025 16:52:11 > Task :convertMdFiles
27-Nov-2025 16:52:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
27-Nov-2025 16:52:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/resources/doc_build/doc/releaseprocess.html
27-Nov-2025 16:52:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
27-Nov-2025 16:52:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/resources/doc_build/doc/building.html
27-Nov-2025 16:52:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/resources/doc_build/doc/jalview-projects.html
27-Nov-2025 16:52:11
27-Nov-2025 16:52:11 > Task :releasesTemplates
27-Nov-2025 16:52:11 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
27-Nov-2025 16:52:11   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:52:11   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:52:11 Stripping rc/test/etc for TEST
27-Nov-2025 16:52:11 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
27-Nov-2025 16:52:11
27-Nov-2025 16:52:11 > Task :prepare
27-Nov-2025 16:52:13
27-Nov-2025 16:52:13 > Task :compileJava
27-Nov-2025 16:52:13 Setting target compatibility to 11
27-Nov-2025 16:52:19 Note: Some input files use or override a deprecated API.
27-Nov-2025 16:52:19 Note: Recompile with -Xlint:deprecation for details.
27-Nov-2025 16:52:19 Note: Some input files use unchecked or unsafe operations.
27-Nov-2025 16:52:19 Note: Recompile with -Xlint:unchecked for details.
27-Nov-2025 16:52:22
27-Nov-2025 16:52:22 > Task :compileTestJava
27-Nov-2025 16:52:22 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
27-Nov-2025 16:52:22   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:52:22   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:52:22 Setting target compatibility to 11
27-Nov-2025 16:52:27 Note: Some input files use or override a deprecated API.
27-Nov-2025 16:52:27 Note: Recompile with -Xlint:deprecation for details.
27-Nov-2025 16:52:27 Note: Some input files use unchecked or unsafe operations.
27-Nov-2025 16:52:27 Note: Recompile with -Xlint:unchecked for details.
27-Nov-2025 16:52:28
27-Nov-2025 16:52:28 > Task :processTestResources
27-Nov-2025 16:52:28 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
27-Nov-2025 16:52:28   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:52:28   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:52:28   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:52:28   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:52:28   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:52:28   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:52:28   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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.
27-Nov-2025 16:52:28
27-Nov-2025 16:52:28 > Task :testClasses
27-Nov-2025 16:52:30
27-Nov-2025 16:52:30 > Task :testTask0
27-Nov-2025 16:52:30 Running tests WITH clover
27-Nov-2025 16:52:33 WARNING: An illegal reflective access operation has occurred
27-Nov-2025 16:52:33 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
27-Nov-2025 16:52:33 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
27-Nov-2025 16:52:33 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
27-Nov-2025 16:52:33 WARNING: All illegal access operations will be denied in a future release
27-Nov-2025 16:57:22
27-Nov-2025 16:57:22 > Task :testTask1
27-Nov-2025 16:57:22 Running tests WITH clover
27-Nov-2025 16:57:24 WARNING: An illegal reflective access operation has occurred
27-Nov-2025 16:57:24 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
27-Nov-2025 16:57:24 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
27-Nov-2025 16:57:24 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
27-Nov-2025 16:57:24 WARNING: All illegal access operations will be denied in a future release
27-Nov-2025 16:57:28
27-Nov-2025 16:57:28 Gradle suite > Gradle test > jalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges[0](./test/files/annotation_label_width/sample.a2m, false, 50, 70, 100, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json, true, pLDDT, null, 114, 117) FAILED
27-Nov-2025 16:57:28     java.lang.AssertionError: idWidth is not set to the manually set width 100 expected [100] but found [68]
27-Nov-2025 16:57:28         at org.testng.Assert.fail(Assert.java:94)
27-Nov-2025 16:57:28         at org.testng.Assert.failNotEquals(Assert.java:496)
27-Nov-2025 16:57:28         at org.testng.Assert.assertEquals(Assert.java:125)
27-Nov-2025 16:57:28         at org.testng.Assert.assertEquals(Assert.java:372)
27-Nov-2025 16:57:28         at jalview.gui.AnnotationLabelsTest2.__CLR4_4_1roan143tio(AnnotationLabelsTest2.java:202)
27-Nov-2025 16:57:28         at jalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges(AnnotationLabelsTest2.java:171)
27-Nov-2025 17:00:04
27-Nov-2025 17:00:04 62 tests completed, 1 failed
27-Nov-2025 17:00:04 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/tests/testTask1/index.html
27-Nov-2025 17:00:06
27-Nov-2025 17:00:06 > Task :testTask2
27-Nov-2025 17:00:06 Running tests WITH clover
27-Nov-2025 17:00:11
27-Nov-2025 17:00:11 > Task :testTask3
27-Nov-2025 17:00:11 Running tests WITH clover
27-Nov-2025 17:00:14 WARNING: An illegal reflective access operation has occurred
27-Nov-2025 17:00:14 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
27-Nov-2025 17:00:14 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
27-Nov-2025 17:00:14 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
27-Nov-2025 17:00:14 WARNING: All illegal access operations will be denied in a future release
27-Nov-2025 17:01:12
27-Nov-2025 17:01:12 > Task :test NO-SOURCE
27-Nov-2025 17:01:12
27-Nov-2025 17:01:12 FAILURE: Build failed with an exception.
27-Nov-2025 17:01:12
27-Nov-2025 17:01:12 * Where:
27-Nov-2025 17:01:12 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build.gradle' line: 1967
27-Nov-2025 17:01:12
27-Nov-2025 17:01:12 * What went wrong:
27-Nov-2025 17:01:12 Failed tests!
27-Nov-2025 17:01:12
27-Nov-2025 17:01:12 * Try:
27-Nov-2025 17:01:12 > Run with --stacktrace option to get the stack trace.
27-Nov-2025 17:01:12 > Run with --info or --debug option to get more log output.
27-Nov-2025 17:01:12 > Run with --scan to get full insights.
27-Nov-2025 17:01:12
27-Nov-2025 17:01:12 * Get more help at https://help.gradle.org
27-Nov-2025 17:01:12
27-Nov-2025 17:01:12 BUILD FAILED in 9m 55s
27-Nov-2025 17:01:12 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
27-Nov-2025 17:01:12 │jalview:testTask0 results: SUCCESS (1824 tests, 1824 successes, 0 failures, 0 skipped) in 4 minutes, 50.988 seconds   │
27-Nov-2025 17:01:12 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/tests/testTask0/index.html│
27-Nov-2025 17:01:12 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
27-Nov-2025 17:01:12 │jalview:testTask1 results: FAILURE (62 tests, 61 successes, 1 failures, 0 skipped) in 2 minutes, 43.876 seconds       │
27-Nov-2025 17:01:12 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/tests/testTask1/index.html│
27-Nov-2025 17:01:12 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
27-Nov-2025 17:01:12 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.882 seconds                     │
27-Nov-2025 17:01:12 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/tests/testTask2/index.html│
27-Nov-2025 17:01:12 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
27-Nov-2025 17:01:12 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 3.400 seconds        │
27-Nov-2025 17:01:12 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/tests/testTask3/index.html│
27-Nov-2025 17:01:12 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
27-Nov-2025 17:01:12 │OVERALL: results: FAILURE (1912 tests, 1911 successes, 1 failures, 0 skipped) in 7 minutes, 103.146 seconds           │
27-Nov-2025 17:01:12 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
27-Nov-2025 17:01:12
27-Nov-2025 17:01:12 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
27-Nov-2025 17:01:12
27-Nov-2025 17:01:12 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
27-Nov-2025 17:01:12
27-Nov-2025 17:01:12 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
27-Nov-2025 17:01:12
27-Nov-2025 17:01:12 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
27-Nov-2025 17:01:12 Please consult deprecation warnings for more details.
27-Nov-2025 17:01:12 21 actionable tasks: 20 executed, 1 up-to-date
27-Nov-2025 17:01:12
27-Nov-2025 17:01:12 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
27-Nov-2025 17:01:12 Finished task 'Run tests with openclover under gradle' with result: Failed
27-Nov-2025 17:01:12 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
27-Nov-2025 17:01:12 Bamboo Artifactory Plugin version: 2.6.2
27-Nov-2025 17:01:12
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4601_stk_ss_annots_showhide - Clover and Tests #1 (JB-GDB730-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-GDB730-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=patch/JAL-4601_stk_ss_annots_showhide
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=patch/JAL-4601_stk_ss_annots_showhide
bamboo_repository_revision_number=3640cfb3a1a72b0a7514f5406b223cad955aa1fc
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB730-JOB1-1
bamboo_repository_46498605_git_branch=patch/JAL-4601_stk_ss_annots_showhide
JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048
bamboo_repository_46498605_branch_name=patch/JAL-4601_stk_ss_annots_showhide
bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1
bamboo_planRepository_1_name=Jalview Gitlab
bamboo_buildKey=JB-GDB730-JOB1
bamboo_shortPlanName=patch-JAL-4601_stk_ss_annots_showhide
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-GDB730-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 - patch-JAL-4601_stk_ss_annots_showhide
bamboo_shortPlanKey=GDB730
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=3640cfb3a1a72b0a7514f5406b223cad955aa1fc
bamboo_repository_previous_revision_number=3640cfb3a1a72b0a7514f5406b223cad955aa1fc
bamboo_buildTimeStamp=2025-11-27T16:51:07.875Z
bamboo_planRepository_previousRevision=3640cfb3a1a72b0a7514f5406b223cad955aa1fc
bamboo_repository_git_branch=patch/JAL-4601_stk_ss_annots_showhide
bamboo_buildResultKey=JB-GDB730-JOB1-1
bamboo_repository_branch_name=patch/JAL-4601_stk_ss_annots_showhide
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4601_stk_ss_annots_showhide - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_repository_46498605_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_planRepository_1_revision=3640cfb3a1a72b0a7514f5406b223cad955aa1fc
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_planRepository_branch=patch/JAL-4601_stk_ss_annots_showhide
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_1_previousRevision=3640cfb3a1a72b0a7514f5406b223cad955aa1fc
bamboo_planRepository_branchDisplayName=patch/JAL-4601_stk_ss_annots_showhide
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=patch/JAL-4601_stk_ss_annots_showhide
_=/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-46302781
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_repository_46498605_git_username=
bamboo_repository_46498605_previous_revision_number=3640cfb3a1a72b0a7514f5406b223cad955aa1fc
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-GDB730-JOB1
bamboo_planKey=JB-GDB730
bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_planRepository_username=
bamboo_repository_46498605_revision_number=3640cfb3a1a72b0a7514f5406b223cad955aa1fc
bamboo_repository_46498605_name=Jalview Gitlab
HOME=/home/bamboo
bamboo_planRepository_1_branchName=patch/JAL-4601_stk_ss_annots_showhide
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
27-Nov-2025 17:01:12 444
27-Nov-2025 17:01:20
27-Nov-2025 17:01:20 > Configure project :
27-Nov-2025 17:01:20 Using properties from file './utils/channels/default/channel_gradle.properties'
27-Nov-2025 17:01:20 JALVIEW_VERSION is set to '2.11.5.1'
27-Nov-2025 17:01:21 HEADLESS BUILD
27-Nov-2025 17:01:21 J2S ENABLED
27-Nov-2025 17:01:21 Using a LOCAL profile.
27-Nov-2025 17:01:22 eclipseDir exists
27-Nov-2025 17:01:24
27-Nov-2025 17:01:24 > Task :cloverHtmlReport
27-Nov-2025 17:01:24 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
27-Nov-2025 17:01:26 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/clover'
27-Nov-2025 17:02:22 Done. Processed 116 packages in 55787ms (480ms per package).
27-Nov-2025 17:02:31
27-Nov-2025 17:02:31 > Task :cloverXmlReport
27-Nov-2025 17:02:31 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
27-Nov-2025 17:02:33 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/clover/clover.xml'
27-Nov-2025 17:02:34
27-Nov-2025 17:02:34 > Task :cloverReport
27-Nov-2025 17:02:34
27-Nov-2025 17:02:34 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
27-Nov-2025 17:02:34
27-Nov-2025 17:02:34 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
27-Nov-2025 17:02:34
27-Nov-2025 17:02:34 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
27-Nov-2025 17:02:34
27-Nov-2025 17:02:34 BUILD SUCCESSFUL in 1m 21s
27-Nov-2025 17:02:34 2 actionable tasks: 2 executed
27-Nov-2025 17:02:34 Finished task 'Clover Report' with result: Success
27-Nov-2025 17:02:34 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
27-Nov-2025 17:02:34 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1...
27-Nov-2025 17:02:35 Failing task since 1 failing test cases were found.
27-Nov-2025 17:02:35 Finished task 'TestNG Parser' with result: Failed
27-Nov-2025 17:02:35 Running post build plugin 'NCover Results Collector'
27-Nov-2025 17:02:35 Running post build plugin 'Artifact Copier'
27-Nov-2025 17:02:35 Publishing an artifact: Clover Report (System)
27-Nov-2025 17:02:41 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 6.719 s
27-Nov-2025 17:02:41 Publishing an artifact: TestNG report
27-Nov-2025 17:02:41 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/tests/test does not exist.
27-Nov-2025 17:02:41 The artifact hasn't been successfully published after 4.169 ms
27-Nov-2025 17:02:41 Running post build plugin 'Artifactory Release Management Staging'
27-Nov-2025 17:02:41 Running post build plugin 'Artifactory Build Info Copier'
27-Nov-2025 17:02:41 Running post build plugin 'Artifactory Gradle Properties Info Copier'
27-Nov-2025 17:02:41 Running post build plugin 'npm Cache Cleanup'
27-Nov-2025 17:02:41 Running post build plugin 'Clover Results Collector'
27-Nov-2025 17:02:41 Running post build plugin 'Docker Container Cleanup'
27-Nov-2025 17:02:41 Finalising the build...
27-Nov-2025 17:02:41 Stopping timer.
27-Nov-2025 17:02:41 Build JB-GDB730-JOB1-1 completed.
27-Nov-2025 17:02:41 Running on server: post build plugin 'NCover Results Collector'
27-Nov-2025 17:02:41 Running on server: post build plugin 'Build Hanging Detection Configuration'
27-Nov-2025 17:02:41 Running on server: post build plugin 'Clover Delta Calculator'
27-Nov-2025 17:02:41 Running on server: post build plugin 'Maven Dependencies Postprocessor'
27-Nov-2025 17:02:41 All post build plugins have finished
27-Nov-2025 17:02:41 Generating build results summary...
27-Nov-2025 17:02:41 Saving build results to disk...
27-Nov-2025 17:02:42 Logging substituted variables...
27-Nov-2025 17:02:42 Indexing build results...
27-Nov-2025 17:02:42 Finished building JB-GDB730-JOB1-1.