Build #2

Build: #2 failed

Job: Clover and Tests failed

Stages & jobs

  1. Default Stage

Build log

The build generated 288 lines of output. Download or view full build log

11-Nov-2025 17:12:15 Build Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests #2 (JB-GDB724-JOB1-2) started building on agent Default Agent
11-Nov-2025 17:12:15
11-Nov-2025 17:12:15 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1
11-Nov-2025 17:12:15 Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests #2 (JB-GDB724-JOB1-2)
11-Nov-2025 17:12:15 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
11-Nov-2025 17:12:15 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1
11-Nov-2025 17:12:15 Updating source code to revision: 377f1f52a15db66fd5768669a50bfda03250a6c7
11-Nov-2025 17:12:15 Fetching 'refs/heads/patch/JAL-4626_alphafoldVersionTracker' from 'https://gitlab.jalview.org/jalview/jalview.git'.
11-Nov-2025 17:12:15 Checking out revision 377f1f52a15db66fd5768669a50bfda03250a6c7.
11-Nov-2025 17:12:15 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
11-Nov-2025 17:12:15    9c98e9d..377f1f5  patch/JAL-4626_alphafoldVersionTracker -> origin/patch/JAL-4626_alphafoldVersionTracker
11-Nov-2025 17:12:17 Your branch is behind 'origin/patch/JAL-4626_alphafoldVersionTracker' by 5 commits, and can be fast-forwarded.
11-Nov-2025 17:12:17   (use "git pull" to update your local branch)
11-Nov-2025 17:12:17 Already on 'patch/JAL-4626_alphafoldVersionTracker'
11-Nov-2025 17:12:17 HEAD is now at 377f1f5 Merge branch 'development/Release_2_11_5_Branch' into patch/JAL-4626_alphafoldVersionTracker
11-Nov-2025 17:12:17 Updated source code to revision: 377f1f52a15db66fd5768669a50bfda03250a6c7
11-Nov-2025 17:12:17 Finished task 'Checkout Default Repository' with result: Success
11-Nov-2025 17:12:17 Running pre-build action: VCS Version Collector
11-Nov-2025 17:12:17 Running pre-build action: Artifactory Release Staging
11-Nov-2025 17:12:17 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
11-Nov-2025 17:12:17 Bamboo Artifactory Plugin version: 2.6.2
11-Nov-2025 17:12:17
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests #2 (JB-GDB724-JOB1-2)'
... 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-GDB724-JOB1
... using extra environment variables:
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11-Nov-2025 17:12:17 444
11-Nov-2025 17:12:19
11-Nov-2025 17:12:19 > Configure project :
11-Nov-2025 17:12:19 Using properties from file './utils/channels/default/channel_gradle.properties'
11-Nov-2025 17:12:19 JALVIEW_VERSION is set to '2.11.5.1'
11-Nov-2025 17:12:19 HEADLESS BUILD
11-Nov-2025 17:12:19 J2S ENABLED
11-Nov-2025 17:12:19 Using a LOCAL profile.
11-Nov-2025 17:12:19 eclipseDir exists
11-Nov-2025 17:12:20
11-Nov-2025 17:12:20 > Task :clean
11-Nov-2025 17:12:20 > Task :cleanClover
11-Nov-2025 17:12:20 > Task :cleanTest UP-TO-DATE
11-Nov-2025 17:12:22
11-Nov-2025 17:12:22 > Task :cloverInstrJava
11-Nov-2025 17:12:22 Clover: About to instrument 1106 files
11-Nov-2025 17:12:22 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Nov-2025 17:12:22 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover.db'.
11-Nov-2025 17:12:22 Processing files at 1.9 source level.
11-Nov-2025 17:12:25 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-Nov-2025 17:12:25 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-Nov-2025 17:12:25 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-Nov-2025 17:12:25 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-Nov-2025 17:12:25 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-Nov-2025 17:12:25 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-Nov-2025 17:12:25 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-Nov-2025 17:12:31 Clover all over. Instrumented 1106 files (112 packages).
11-Nov-2025 17:12:34
11-Nov-2025 17:12:34 > Task :cloverInstrTests
11-Nov-2025 17:12:34 Clover: About to instrument test files
11-Nov-2025 17:12:34 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Nov-2025 17:12:34 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover.db'.
11-Nov-2025 17:12:34 Processing files at 1.9 source level.
11-Nov-2025 17:12:37 Clover all over. Instrumented 293 files (52 packages).
11-Nov-2025 17:12:37 1619 test methods detected.
11-Nov-2025 17:12:38
11-Nov-2025 17:12:38 > Task :cloverInstr
11-Nov-2025 17:12:39
11-Nov-2025 17:12:39 > Task :compileCloverJava
11-Nov-2025 17:12:39 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
11-Nov-2025 17:12:39   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:12:39   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:12:39   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:12:39 Setting target compatibility to 11
11-Nov-2025 17:12:55 Note: Some input files use or override a deprecated API.
11-Nov-2025 17:12:55 Note: Recompile with -Xlint:deprecation for details.
11-Nov-2025 17:12:55 Note: Some input files use unchecked or unsafe operations.
11-Nov-2025 17:12:55 Note: Recompile with -Xlint:unchecked for details.
11-Nov-2025 17:13:01
11-Nov-2025 17:13:01 > Task :processCloverResources NO-SOURCE
11-Nov-2025 17:13:01 > Task :cloverClasses
11-Nov-2025 17:13:02 > Task :copyHelp
11-Nov-2025 17:13:04 > Task :buildIndices
11-Nov-2025 17:13:04 > Task :copyResources
11-Nov-2025 17:13:04 > Task :copyChannelResources
11-Nov-2025 17:13:04
11-Nov-2025 17:13:04 > Task :createBuildProperties
11-Nov-2025 17:13:04 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
11-Nov-2025 17:13:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:13:04
11-Nov-2025 17:13:04 > Task :buildResources
11-Nov-2025 17:13:04 > Task :copyDocs
11-Nov-2025 17:13:04
11-Nov-2025 17:13:04 > Task :convertMdFiles
11-Nov-2025 17:13:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
11-Nov-2025 17:13:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/releaseprocess.html
11-Nov-2025 17:13:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
11-Nov-2025 17:13:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/building.html
11-Nov-2025 17:13:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/jalview-projects.html
11-Nov-2025 17:13:04
11-Nov-2025 17:13:04 > Task :releasesTemplates
11-Nov-2025 17:13:04 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
11-Nov-2025 17:13:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:13:04   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:13:04 Stripping rc/test/etc for TEST
11-Nov-2025 17:13:04 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
11-Nov-2025 17:13:04
11-Nov-2025 17:13:04 > Task :prepare
11-Nov-2025 17:13:06
11-Nov-2025 17:13:06 > Task :compileJava
11-Nov-2025 17:13:06 Setting target compatibility to 11
11-Nov-2025 17:13:12 Note: Some input files use or override a deprecated API.
11-Nov-2025 17:13:12 Note: Recompile with -Xlint:deprecation for details.
11-Nov-2025 17:13:12 Note: Some input files use unchecked or unsafe operations.
11-Nov-2025 17:13:12 Note: Recompile with -Xlint:unchecked for details.
11-Nov-2025 17:13:14
11-Nov-2025 17:13:14 > Task :compileTestJava
11-Nov-2025 17:13:14 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
11-Nov-2025 17:13:14   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:13:14   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:13:14 Setting target compatibility to 11
11-Nov-2025 17:13:19 Note: Some input files use or override a deprecated API.
11-Nov-2025 17:13:19 Note: Recompile with -Xlint:deprecation for details.
11-Nov-2025 17:13:19 Note: Some input files use unchecked or unsafe operations.
11-Nov-2025 17:13:19 Note: Recompile with -Xlint:unchecked for details.
11-Nov-2025 17:13:20
11-Nov-2025 17:13:20 > Task :processTestResources
11-Nov-2025 17:13:20 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
11-Nov-2025 17:13:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:13:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:13:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:13:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:13:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:13:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:13:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:13:20   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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-Nov-2025 17:13:20
11-Nov-2025 17:13:20 > Task :testClasses
11-Nov-2025 17:13:22
11-Nov-2025 17:13:22 > Task :testTask0
11-Nov-2025 17:13:22 Running tests WITH clover
11-Nov-2025 17:13:25 WARNING: An illegal reflective access operation has occurred
11-Nov-2025 17:13:25 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
11-Nov-2025 17:13:25 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
11-Nov-2025 17:13:25 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
11-Nov-2025 17:13:25 WARNING: All illegal access operations will be denied in a future release
11-Nov-2025 17:18:18
11-Nov-2025 17:18:18 > Task :testTask1
11-Nov-2025 17:18:18 Running tests WITH clover
11-Nov-2025 17:18:20 WARNING: An illegal reflective access operation has occurred
11-Nov-2025 17:18:20 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
11-Nov-2025 17:18:20 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
11-Nov-2025 17:18:20 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
11-Nov-2025 17:18:20 WARNING: All illegal access operations will be denied in a future release
11-Nov-2025 17:19:47
11-Nov-2025 17:19:47 Gradle suite > Gradle test > jalview.bin.CommandLineOperationsNG.testHeadlessModeOutputToStdout[6](./test/jalview/bin/argparser/testfiles/test1.fa ./test/jalview/bin/argparser/testfiles/test2.fa ./test/jalview/bin/argparser/testfiles/test3.fa --all --output -, test/jalview/bin/test1-3.fa, 13000) FAILED
11-Nov-2025 17:19:47     java.lang.AssertionError: STDOUT from jalview command did not match the comparison file expected [>TEST1/1-4
11-Nov-2025 17:19:47     AAAA
11-Nov-2025 17:19:47     >TEST2/1-4
11-Nov-2025 17:19:47     LLLL
11-Nov-2025 17:19:47     >TEST3/1-5
11-Nov-2025 17:19:47     AAARG
11-Nov-2025 17:19:47     ] but found [>TEST1/1-4
11-Nov-2025 17:19:47     AAAA
11-Nov-2025 17:19:47     >TEST2/1-4
11-Nov-2025 17:19:47     LLLL
11-Nov-2025 17:19:47     ]
11-Nov-2025 17:19:47         at org.testng.Assert.fail(Assert.java:94)
11-Nov-2025 17:19:47         at org.testng.Assert.failNotEquals(Assert.java:496)
11-Nov-2025 17:19:47         at org.testng.Assert.assertEquals(Assert.java:125)
11-Nov-2025 17:19:47         at org.testng.Assert.assertEquals(Assert.java:178)
11-Nov-2025 17:19:47         at jalview.bin.CommandLineOperationsNG.testHeadlessModeOutputToStdout(CommandLineOperationsNG.java:410)
11-Nov-2025 17:21:05
11-Nov-2025 17:21:05 62 tests completed, 1 failed
11-Nov-2025 17:21:05 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask1/index.html
11-Nov-2025 17:21:07
11-Nov-2025 17:21:07 > Task :testTask2
11-Nov-2025 17:21:07 Running tests WITH clover
11-Nov-2025 17:21:11
11-Nov-2025 17:21:11 > Task :testTask3
11-Nov-2025 17:21:11 Running tests WITH clover
11-Nov-2025 17:21:14 WARNING: An illegal reflective access operation has occurred
11-Nov-2025 17:21:14 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
11-Nov-2025 17:21:14 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
11-Nov-2025 17:21:14 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
11-Nov-2025 17:21:14 WARNING: All illegal access operations will be denied in a future release
11-Nov-2025 17:22:08
11-Nov-2025 17:22:08 > Task :test NO-SOURCE
11-Nov-2025 17:22:08 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
11-Nov-2025 17:22:08 │jalview:testTask0 results: SUCCESS (1819 tests, 1819 successes, 0 failures, 0 skipped) in 4 minutes, 54.973 seconds   │
11-Nov-2025 17:22:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask0/index.html│
11-Nov-2025 17:22:08 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Nov-2025 17:22:08 │jalview:testTask1 results: FAILURE (62 tests, 61 successes, 1 failures, 0 skipped) in 2 minutes, 49.218 seconds       │
11-Nov-2025 17:22:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask1/index.html│
11-Nov-2025 17:22:08 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Nov-2025 17:22:08 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.411 seconds                     │
11-Nov-2025 17:22:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask2/index.html│
11-Nov-2025 17:22:08 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Nov-2025 17:22:08 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 59.005 seconds                  │
11-Nov-2025 17:22:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask3/index.html│
11-Nov-2025 17:22:08 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Nov-2025 17:22:08 │OVERALL: results: FAILURE (1907 tests, 1906 successes, 1 failures, 0 skipped) in 6 minutes, 167.607 seconds           │
11-Nov-2025 17:22:08 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
11-Nov-2025 17:22:08
11-Nov-2025 17:22:08 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
11-Nov-2025 17:22:08
11-Nov-2025 17:22:08 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
11-Nov-2025 17:22:08
11-Nov-2025 17:22:08 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
11-Nov-2025 17:22:08
11-Nov-2025 17:22:08 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
11-Nov-2025 17:22:08 Please consult deprecation warnings for more details.
11-Nov-2025 17:22:08 21 actionable tasks: 20 executed, 1 up-to-date
11-Nov-2025 17:22:08
11-Nov-2025 17:22:08 FAILURE: Build failed with an exception.
11-Nov-2025 17:22:08
11-Nov-2025 17:22:08 * Where:
11-Nov-2025 17:22:08 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build.gradle' line: 1967
11-Nov-2025 17:22:08
11-Nov-2025 17:22:08 * What went wrong:
11-Nov-2025 17:22:08 Failed tests!
11-Nov-2025 17:22:08
11-Nov-2025 17:22:08 * Try:
11-Nov-2025 17:22:08 > Run with --stacktrace option to get the stack trace.
11-Nov-2025 17:22:08 > Run with --info or --debug option to get more log output.
11-Nov-2025 17:22:08 > Run with --scan to get full insights.
11-Nov-2025 17:22:08
11-Nov-2025 17:22:08 * Get more help at https://help.gradle.org
11-Nov-2025 17:22:08
11-Nov-2025 17:22:08 BUILD FAILED in 9m 51s
11-Nov-2025 17:22:09
11-Nov-2025 17:22:09 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
11-Nov-2025 17:22:09 Finished task 'Run tests with openclover under gradle' with result: Failed
11-Nov-2025 17:22:09 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
11-Nov-2025 17:22:09 Bamboo Artifactory Plugin version: 2.6.2
11-Nov-2025 17:22:09
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests #2 (JB-GDB724-JOB1-2)'
... 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-GDB724-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=patch/JAL-4626_alphafoldVersionTracker
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=patch/JAL-4626_alphafoldVersionTracker
bamboo_repository_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB724-JOB1-2
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-GDB724-JOB1
bamboo_planRepository_1_name=Jalview Gitlab
bamboo_buildKey=JB-GDB724-JOB1
bamboo_shortPlanName=patch-JAL-4626_alphafoldVersionTracker
bamboo_repository_46498567_git_branch=patch/JAL-4626_alphafoldVersionTracker
bamboo_planRepository_name=Jalview Gitlab
LOGNAME=bamboo
bamboo_buildNumber=2
PWD=/
bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse
bamboo_repository_46498567_git_username=
bamboo_shortJobName=Clover and Tests
bamboo_repository_46498567_previous_revision_number=9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616
bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB724-JOB1-2
bamboo_repository_46498567_name=Jalview Gitlab
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-4626_alphafoldVersionTracker
bamboo_shortPlanKey=GDB724
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=377f1f52a15db66fd5768669a50bfda03250a6c7
bamboo_buildTimeStamp=2025-11-11T17:12:15.523Z
bamboo_repository_previous_revision_number=9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616
bamboo_planRepository_previousRevision=9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616
bamboo_repository_git_branch=patch/JAL-4626_alphafoldVersionTracker
bamboo_buildResultKey=JB-GDB724-JOB1-2
bamboo_repository_branch_name=patch/JAL-4626_alphafoldVersionTracker
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=377f1f52a15db66fd5768669a50bfda03250a6c7
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-4626_alphafoldVersionTracker
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=9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616
bamboo_planRepository_branchDisplayName=patch/JAL-4626_alphafoldVersionTracker
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=patch/JAL-4626_alphafoldVersionTracker
_=/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-46302705
bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle
bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache
bamboo_repository_46498567_branch_name=patch/JAL-4626_alphafoldVersionTracker
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_46498567_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-GDB724-JOB1
bamboo_repository_46498567_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7
bamboo_planKey=JB-GDB724
bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_planRepository_username=
HOME=/home/bamboo
bamboo_planRepository_1_branchName=patch/JAL-4626_alphafoldVersionTracker
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
11-Nov-2025 17:22:09 444
11-Nov-2025 17:22:16
11-Nov-2025 17:22:16 > Configure project :
11-Nov-2025 17:22:16 Using properties from file './utils/channels/default/channel_gradle.properties'
11-Nov-2025 17:22:16 JALVIEW_VERSION is set to '2.11.5.1'
11-Nov-2025 17:22:16 HEADLESS BUILD
11-Nov-2025 17:22:16 J2S ENABLED
11-Nov-2025 17:22:17 Using a LOCAL profile.
11-Nov-2025 17:22:18 eclipseDir exists
11-Nov-2025 17:22:21
11-Nov-2025 17:22:21 > Task :cloverHtmlReport
11-Nov-2025 17:22:21 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Nov-2025 17:22:23 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/clover'
11-Nov-2025 17:23:18 Done. Processed 116 packages in 56002ms (482ms per package).
11-Nov-2025 17:23:24
11-Nov-2025 17:23:24 > Task :cloverXmlReport
11-Nov-2025 17:23:24 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Nov-2025 17:23:26 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/clover/clover.xml'
11-Nov-2025 17:23:26
11-Nov-2025 17:23:26 > Task :cloverReport
11-Nov-2025 17:23:26
11-Nov-2025 17:23:26 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
11-Nov-2025 17:23:26
11-Nov-2025 17:23:26 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
11-Nov-2025 17:23:26
11-Nov-2025 17:23:26 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
11-Nov-2025 17:23:26
11-Nov-2025 17:23:26 BUILD SUCCESSFUL in 1m 17s
11-Nov-2025 17:23:26 2 actionable tasks: 2 executed
11-Nov-2025 17:23:27 Finished task 'Clover Report' with result: Success
11-Nov-2025 17:23:27 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
11-Nov-2025 17:23:27 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1...
11-Nov-2025 17:23:27 Failing task since 1 failing test cases were found.
11-Nov-2025 17:23:27 Finished task 'TestNG Parser' with result: Failed
11-Nov-2025 17:23:27 Running post build plugin 'NCover Results Collector'
11-Nov-2025 17:23:27 Running post build plugin 'Artifact Copier'
11-Nov-2025 17:23:27 Publishing an artifact: Clover Report (System)
11-Nov-2025 17:23:32 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 5.700 s
11-Nov-2025 17:23:32 Publishing an artifact: TestNG report
11-Nov-2025 17:23:32 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/test does not exist.
11-Nov-2025 17:23:32 The artifact hasn't been successfully published after 4.223 ms
11-Nov-2025 17:23:32 Running post build plugin 'Artifactory Release Management Staging'
11-Nov-2025 17:23:32 Running post build plugin 'Artifactory Build Info Copier'
11-Nov-2025 17:23:32 Running post build plugin 'Artifactory Gradle Properties Info Copier'
11-Nov-2025 17:23:32 Running post build plugin 'npm Cache Cleanup'
11-Nov-2025 17:23:32 Running post build plugin 'Clover Results Collector'
11-Nov-2025 17:23:32 Running post build plugin 'Docker Container Cleanup'
11-Nov-2025 17:23:32 Finalising the build...
11-Nov-2025 17:23:32 Stopping timer.
11-Nov-2025 17:23:32 Build JB-GDB724-JOB1-2 completed.
11-Nov-2025 17:23:32 Running on server: post build plugin 'NCover Results Collector'
11-Nov-2025 17:23:32 Running on server: post build plugin 'Build Hanging Detection Configuration'
11-Nov-2025 17:23:32 Running on server: post build plugin 'Clover Delta Calculator'
11-Nov-2025 17:23:32 Running on server: post build plugin 'Maven Dependencies Postprocessor'
11-Nov-2025 17:23:32 All post build plugins have finished
11-Nov-2025 17:23:32 Generating build results summary...
11-Nov-2025 17:23:33 Saving build results to disk...
11-Nov-2025 17:23:33 Logging substituted variables...
11-Nov-2025 17:23:34 Indexing build results...
11-Nov-2025 17:23:34 Finished building JB-GDB724-JOB1-2.