Build #2

Build: #2 failed

Job: Clover and Tests failed

Stages & jobs

  1. Default Stage

Build log

The build generated 280 lines of output. Download or view full build log

11-Nov-2024 15:05:16 Build Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests #2 (JB-GDB642-JOB1-2) started building on agent Default Agent
11-Nov-2024 15:05:16
11-Nov-2024 15:05:16 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1
11-Nov-2024 15:05:16 Executing build Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests #2 (JB-GDB642-JOB1-2)
11-Nov-2024 15:05:16 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
11-Nov-2024 15:05:16 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1
11-Nov-2024 15:05:16 Updating source code to revision: f6be36d7152321642e41db9d8bdbd2580431541e
11-Nov-2024 15:05:16 Fetching 'refs/heads/features/JAL-4489_cluster_pca_and_pasimap' from 'http://source.jalview.org/git/jalview.git'.
11-Nov-2024 15:05:16 Checking out revision f6be36d7152321642e41db9d8bdbd2580431541e.
11-Nov-2024 15:05:16 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164
11-Nov-2024 15:05:16    3e7d1be..f6be36d  features/JAL-4489_cluster_pca_and_pasimap -> origin/features/JAL-4489_cluster_pca_and_pasimap
11-Nov-2024 15:05:18 Already on 'features/JAL-4489_cluster_pca_and_pasimap'
11-Nov-2024 15:05:18 Your branch is behind 'origin/features/JAL-4489_cluster_pca_and_pasimap' by 1 commit, and can be fast-forwarded.
11-Nov-2024 15:05:18   (use "git pull" to update your local branch)
11-Nov-2024 15:05:18 HEAD is now at f6be36d JAL-4489 organise imports
11-Nov-2024 15:05:18 Updated source code to revision: f6be36d7152321642e41db9d8bdbd2580431541e
11-Nov-2024 15:05:18 Finished task 'Checkout Default Repository' with result: Success
11-Nov-2024 15:05:18 Running pre-build action: VCS Version Collector
11-Nov-2024 15:05:18 Running pre-build action: Artifactory Release Staging
11-Nov-2024 15:05:18 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
11-Nov-2024 15:05:18 Bamboo Artifactory Plugin version: 2.6.2
11-Nov-2024 15:05:18
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests #2 (JB-GDB642-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-GDB642-JOB1
... using extra environment variables:
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11-Nov-2024 15:05:18 444
11-Nov-2024 15:05:19
11-Nov-2024 15:05:19 > Configure project :
11-Nov-2024 15:05:19 Using properties from file './utils/channels/default/channel_gradle.properties'
11-Nov-2024 15:05:19 JALVIEW_VERSION is set to '2.11.4.1'
11-Nov-2024 15:05:19 HEADLESS BUILD
11-Nov-2024 15:05:19 J2S ENABLED
11-Nov-2024 15:05:19 Using a LOCAL profile.
11-Nov-2024 15:05:19 eclipseDir exists
11-Nov-2024 15:05:19
11-Nov-2024 15:05:19 > Task :clean
11-Nov-2024 15:05:19 > Task :cleanClover
11-Nov-2024 15:05:19 > Task :cleanTest UP-TO-DATE
11-Nov-2024 15:05:21
11-Nov-2024 15:05:21 > Task :cloverInstrJava
11-Nov-2024 15:05:21 Clover: About to instrument 1106 files
11-Nov-2024 15:05:21 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Nov-2024 15:05:21 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover.db'.
11-Nov-2024 15:05:21 Processing files at 1.9 source level.
11-Nov-2024 15:05:24 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-2024 15:05:24 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-2024 15:05:24 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-2024 15:05:24 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-2024 15:05:24 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-2024 15:05:24 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-2024 15:05:24 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-2024 15:05:31 Clover all over. Instrumented 1106 files (112 packages).
11-Nov-2024 15:05:33
11-Nov-2024 15:05:33 > Task :cloverInstrTests
11-Nov-2024 15:05:33 Clover: About to instrument test files
11-Nov-2024 15:05:33 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Nov-2024 15:05:33 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover.db'.
11-Nov-2024 15:05:33 Processing files at 1.9 source level.
11-Nov-2024 15:05:36 Clover all over. Instrumented 291 files (52 packages).
11-Nov-2024 15:05:36 1594 test methods detected.
11-Nov-2024 15:05:36
11-Nov-2024 15:05:36 > Task :cloverInstr
11-Nov-2024 15:05:38
11-Nov-2024 15:05:38 > Task :compileCloverJava
11-Nov-2024 15:05:38 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
11-Nov-2024 15:05:38   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:05:38   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:05:38   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:05:38 Setting target compatibility to 11
11-Nov-2024 15:05:52 Note: Some input files use or override a deprecated API.
11-Nov-2024 15:05:52 Note: Recompile with -Xlint:deprecation for details.
11-Nov-2024 15:05:52 Note: Some input files use unchecked or unsafe operations.
11-Nov-2024 15:05:52 Note: Recompile with -Xlint:unchecked for details.
11-Nov-2024 15:05:56
11-Nov-2024 15:05:56 > Task :processCloverResources NO-SOURCE
11-Nov-2024 15:05:56 > Task :cloverClasses
11-Nov-2024 15:05:57 > Task :copyHelp
11-Nov-2024 15:05:58 > Task :buildIndices
11-Nov-2024 15:05:58 > Task :copyResources
11-Nov-2024 15:05:58 > Task :copyChannelResources
11-Nov-2024 15:05:58
11-Nov-2024 15:05:58 > Task :createBuildProperties
11-Nov-2024 15:05:58 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
11-Nov-2024 15:05:58   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:05:58
11-Nov-2024 15:05:58 > Task :buildResources
11-Nov-2024 15:05:58 > Task :copyDocs
11-Nov-2024 15:05:58
11-Nov-2024 15:05:58 > Task :convertMdFiles
11-Nov-2024 15:05:58 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
11-Nov-2024 15:05:58 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/releaseprocess.html
11-Nov-2024 15:05:58 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
11-Nov-2024 15:05:58 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/building.html
11-Nov-2024 15:05:58 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/jalview-projects.html
11-Nov-2024 15:05:58
11-Nov-2024 15:05:58 > Task :releasesTemplates
11-Nov-2024 15:05:58 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
11-Nov-2024 15:05:58   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:05:58   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:05:58 Stripping rc/test/etc for TEST
11-Nov-2024 15:05:58 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
11-Nov-2024 15:05:58
11-Nov-2024 15:05:58 > Task :prepare
11-Nov-2024 15:06:00
11-Nov-2024 15:06:00 > Task :compileJava
11-Nov-2024 15:06:00 Setting target compatibility to 11
11-Nov-2024 15:06:06 Note: Some input files use or override a deprecated API.
11-Nov-2024 15:06:06 Note: Recompile with -Xlint:deprecation for details.
11-Nov-2024 15:06:06 Note: Some input files use unchecked or unsafe operations.
11-Nov-2024 15:06:06 Note: Recompile with -Xlint:unchecked for details.
11-Nov-2024 15:06:10
11-Nov-2024 15:06:10 > Task :compileTestJava
11-Nov-2024 15:06:10 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
11-Nov-2024 15:06:10   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:06:10   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:06:10 Setting target compatibility to 11
11-Nov-2024 15:06:15 Note: Some input files use or override a deprecated API.
11-Nov-2024 15:06:15 Note: Recompile with -Xlint:deprecation for details.
11-Nov-2024 15:06:15 Note: Some input files use unchecked or unsafe operations.
11-Nov-2024 15:06:15 Note: Recompile with -Xlint:unchecked for details.
11-Nov-2024 15:06:16
11-Nov-2024 15:06:16 > Task :processTestResources
11-Nov-2024 15:06:16 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
11-Nov-2024 15:06:16   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:06:16   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:06:16   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:06:16   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:06:16   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:06:16   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:06:16   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:06:16   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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-2024 15:06:16
11-Nov-2024 15:06:16 > Task :testClasses
11-Nov-2024 15:06:18
11-Nov-2024 15:06:18 > Task :testTask0
11-Nov-2024 15:06:18 Running tests WITH clover
11-Nov-2024 15:06:21 WARNING: An illegal reflective access operation has occurred
11-Nov-2024 15:06:21 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
11-Nov-2024 15:06:21 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
11-Nov-2024 15:06:21 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
11-Nov-2024 15:06:21 WARNING: All illegal access operations will be denied in a future release
11-Nov-2024 15:09:59
11-Nov-2024 15:09:59 > Task :testTask1
11-Nov-2024 15:09:59 Running tests WITH clover
11-Nov-2024 15:10:00 WARNING: An illegal reflective access operation has occurred
11-Nov-2024 15:10:00 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
11-Nov-2024 15:10:00 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
11-Nov-2024 15:10:00 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
11-Nov-2024 15:10:00 WARNING: All illegal access operations will be denied in a future release
11-Nov-2024 15:11:35
11-Nov-2024 15:11:35 > Task :testTask2
11-Nov-2024 15:11:35 Running tests WITH clover
11-Nov-2024 15:11:39
11-Nov-2024 15:11:39 > Task :testTask3
11-Nov-2024 15:11:39 Running tests WITH clover
11-Nov-2024 15:11:40 WARNING: An illegal reflective access operation has occurred
11-Nov-2024 15:11:40 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
11-Nov-2024 15:11:40 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
11-Nov-2024 15:11:40 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
11-Nov-2024 15:11:40 WARNING: All illegal access operations will be denied in a future release
11-Nov-2024 15:12:26
11-Nov-2024 15:12:26 Gradle suite > Gradle test > jalview.bin.CommandsTest.structureImageOutputTest[3](--headless --noquit --open ./examples/1gaq.txt --append ./examples/3W5V.pdb --structure examples/1gaq.txt --seqid "1GAQ|A" --structureimage test/jalview/bin/argparser/testfiles/structureimage3-1gaq.png --structure examples/3W5V.pdb --seqid "3W5V|A" --structureimage test/jalview/bin/argparser/testfiles/structureimage3-3w5v.png --overwrite, [Ljava.lang.String;@402d6012) FAILED
11-Nov-2024 15:12:26     java.lang.AssertionError: Expected test/jalview/bin/argparser/testfiles/structureimage3-1gaq.png to be larger than test/jalview/bin/argparser/testfiles/structureimage3-3w5v.png expected [true] but found [false]
11-Nov-2024 15:12:26         at org.testng.Assert.fail(Assert.java:94)
11-Nov-2024 15:12:26         at org.testng.Assert.failNotEquals(Assert.java:496)
11-Nov-2024 15:12:26         at org.testng.Assert.assertTrue(Assert.java:42)
11-Nov-2024 15:12:26         at jalview.bin.CommandsTest.verifyOrderedFileSet(CommandsTest.java:297)
11-Nov-2024 15:12:26         at jalview.bin.CommandsTest.verifyIncreasingSize(CommandsTest.java:274)
11-Nov-2024 15:12:26         at jalview.bin.CommandsTest.__CLR4_4_1shrjyq47q9(CommandsTest.java:194)
11-Nov-2024 15:12:26         at jalview.bin.CommandsTest.structureImageOutputTest(CommandsTest.java:186)
11-Nov-2024 15:12:26
11-Nov-2024 15:12:26 25 tests completed, 1 failed
11-Nov-2024 15:12:26 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask3/index.html
11-Nov-2024 15:12:26
11-Nov-2024 15:12:26 FAILURE: Build failed with an exception.
11-Nov-2024 15:12:26
11-Nov-2024 15:12:26 * Where:
11-Nov-2024 15:12:26 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build.gradle' line: 1966
11-Nov-2024 15:12:26
11-Nov-2024 15:12:26 * What went wrong:
11-Nov-2024 15:12:26 Failed tests!
11-Nov-2024 15:12:26
11-Nov-2024 15:12:26 * Try:
11-Nov-2024 15:12:26 > Run with --stacktrace option to get the stack trace.
11-Nov-2024 15:12:26 > Run with --info or --debug option to get more log output.
11-Nov-2024 15:12:26 > Run with --scan to get full insights.
11-Nov-2024 15:12:26
11-Nov-2024 15:12:26 * Get more help at https://help.gradle.org
11-Nov-2024 15:12:26
11-Nov-2024 15:12:26
11-Nov-2024 15:12:26 BUILD FAILED in 7m 8s
11-Nov-2024 15:12:26 > Task :test NO-SOURCE
11-Nov-2024 15:12:26 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
11-Nov-2024 15:12:26 │jalview:testTask0 results: SUCCESS (1728 tests, 1728 successes, 0 failures, 0 skipped) in 3 minutes, 40.394 seconds   │
11-Nov-2024 15:12:26 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask0/index.html│
11-Nov-2024 15:12:26 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Nov-2024 15:12:26 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 36.185 seconds       │
11-Nov-2024 15:12:26 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask1/index.html│
11-Nov-2024 15:12:26 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Nov-2024 15:12:26 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.640 seconds                     │
11-Nov-2024 15:12:26 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask2/index.html│
11-Nov-2024 15:12:26 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Nov-2024 15:12:26 │jalview:testTask3 results: FAILURE (25 tests, 24 successes, 1 failures, 0 skipped) in 48.923 seconds                  │
11-Nov-2024 15:12:26 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask3/index.html│
11-Nov-2024 15:12:26 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
11-Nov-2024 15:12:26 │OVERALL: results: FAILURE (1803 tests, 1802 successes, 1 failures, 0 skipped) in 4 minutes, 129.142 seconds           │
11-Nov-2024 15:12:26 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
11-Nov-2024 15:12:26
11-Nov-2024 15:12:26 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
11-Nov-2024 15:12:26
11-Nov-2024 15:12:26 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-2024 15:12:26
11-Nov-2024 15:12:26 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
11-Nov-2024 15:12:26
11-Nov-2024 15:12:26 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
11-Nov-2024 15:12:26 Please consult deprecation warnings for more details.
11-Nov-2024 15:12:26 21 actionable tasks: 20 executed, 1 up-to-date
11-Nov-2024 15:12:26
11-Nov-2024 15:12:26 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-2024 15:12:26 Finished task 'Run tests with openclover under gradle' with result: Failed
11-Nov-2024 15:12:26 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
11-Nov-2024 15:12:26 Bamboo Artifactory Plugin version: 2.6.2
11-Nov-2024 15:12:26
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests #2 (JB-GDB642-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-GDB642-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=features/JAL-4489_cluster_pca_and_pasimap
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap
bamboo_repository_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB642-JOB1-2
bamboo_repository_46498184_git_branch=features/JAL-4489_cluster_pca_and_pasimap
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-GDB642-JOB1
bamboo_planRepository_1_name=Jalview Git
bamboo_buildKey=JB-GDB642-JOB1
bamboo_shortPlanName=features-JAL-4489_cluster_pca_and_pasimap
bamboo_planRepository_name=Jalview Git
LOGNAME=bamboo
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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-GDB642-JOB1-2
bamboo_repository_46498184_name=Jalview Git
bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git
SHELL=/bin/bash
bamboo_repository_46498184_git_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_agentId=196609
bamboo_planName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap
bamboo_shortPlanKey=GDB642
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=f6be36d7152321642e41db9d8bdbd2580431541e
bamboo_repository_46498184_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e
bamboo_buildTimeStamp=2024-11-11T15:05:16.749Z
bamboo_repository_previous_revision_number=3e7d1be29f1857c4d5cf237b1cf6420218752458
bamboo_planRepository_previousRevision=3e7d1be29f1857c4d5cf237b1cf6420218752458
bamboo_repository_git_branch=features/JAL-4489_cluster_pca_and_pasimap
bamboo_buildResultKey=JB-GDB642-JOB1-2
bamboo_repository_branch_name=features/JAL-4489_cluster_pca_and_pasimap
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=f6be36d7152321642e41db9d8bdbd2580431541e
SHLVL=1
bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant
bamboo_repository_name=Jalview Git
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/
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bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk
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bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609
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bamboo_repository_46498184_git_username=
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bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=features/JAL-4489_cluster_pca_and_pasimap
_=/usr/bin/java
bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11
bamboo_repository_46498184_previous_revision_number=3e7d1be29f1857c4d5cf237b1cf6420218752458
bamboo_capability_system_builderivy_Ivy=/usr
bamboo_plan_storageTag=plan-46301967
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=http://source.jalview.org/git/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-GDB642-JOB1
bamboo_planKey=JB-GDB642
bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_planRepository_username=
bamboo_repository_46498184_branch_name=features/JAL-4489_cluster_pca_and_pasimap
HOME=/home/bamboo
bamboo_planRepository_1_branchName=features/JAL-4489_cluster_pca_and_pasimap
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
11-Nov-2024 15:12:26 444
11-Nov-2024 15:12:32
11-Nov-2024 15:12:32 > Configure project :
11-Nov-2024 15:12:32 Using properties from file './utils/channels/default/channel_gradle.properties'
11-Nov-2024 15:12:32 JALVIEW_VERSION is set to '2.11.4.1'
11-Nov-2024 15:12:32 HEADLESS BUILD
11-Nov-2024 15:12:32 J2S ENABLED
11-Nov-2024 15:12:32 Using a LOCAL profile.
11-Nov-2024 15:12:33 eclipseDir exists
11-Nov-2024 15:12:35
11-Nov-2024 15:12:35 > Task :cloverHtmlReport
11-Nov-2024 15:12:35 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Nov-2024 15:12:36 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/clover'
11-Nov-2024 15:13:14 Done. Processed 116 packages in 37819ms (326ms per package).
11-Nov-2024 15:13:19
11-Nov-2024 15:13:19 > Task :cloverXmlReport
11-Nov-2024 15:13:19 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
11-Nov-2024 15:13:20 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/clover/clover.xml'
11-Nov-2024 15:13:21
11-Nov-2024 15:13:21 > Task :cloverReport
11-Nov-2024 15:13:21
11-Nov-2024 15:13:21 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
11-Nov-2024 15:13:21
11-Nov-2024 15:13:21 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-2024 15:13:21
11-Nov-2024 15:13:21 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
11-Nov-2024 15:13:21
11-Nov-2024 15:13:21 BUILD SUCCESSFUL in 54s
11-Nov-2024 15:13:21 2 actionable tasks: 2 executed
11-Nov-2024 15:13:21 Finished task 'Clover Report' with result: Success
11-Nov-2024 15:13:21 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
11-Nov-2024 15:13:21 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1...
11-Nov-2024 15:13:21 Failing task since 1 failing test cases were found.
11-Nov-2024 15:13:21 Finished task 'TestNG Parser' with result: Failed
11-Nov-2024 15:13:21 Running post build plugin 'NCover Results Collector'
11-Nov-2024 15:13:21 Running post build plugin 'Artifact Copier'
11-Nov-2024 15:13:21 Publishing an artifact: Clover Report (System)
11-Nov-2024 15:13:22 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.460 s
11-Nov-2024 15:13:22 Publishing an artifact: TestNG report
11-Nov-2024 15:13:22 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/test does not exist.
11-Nov-2024 15:13:22 The artifact hasn't been successfully published after 2.206 ms
11-Nov-2024 15:13:22 Running post build plugin 'Artifactory Release Management Staging'
11-Nov-2024 15:13:22 Running post build plugin 'Artifactory Build Info Copier'
11-Nov-2024 15:13:22 Running post build plugin 'Artifactory Gradle Properties Info Copier'
11-Nov-2024 15:13:22 Running post build plugin 'npm Cache Cleanup'
11-Nov-2024 15:13:22 Running post build plugin 'Clover Results Collector'
11-Nov-2024 15:13:22 Running post build plugin 'Docker Container Cleanup'
11-Nov-2024 15:13:22 Finalising the build...
11-Nov-2024 15:13:22 Stopping timer.
11-Nov-2024 15:13:22 Build JB-GDB642-JOB1-2 completed.
11-Nov-2024 15:13:22 Running on server: post build plugin 'NCover Results Collector'
11-Nov-2024 15:13:22 Running on server: post build plugin 'Build Hanging Detection Configuration'
11-Nov-2024 15:13:22 Running on server: post build plugin 'Clover Delta Calculator'
11-Nov-2024 15:13:22 Running on server: post build plugin 'Maven Dependencies Postprocessor'
11-Nov-2024 15:13:22 All post build plugins have finished
11-Nov-2024 15:13:22 Generating build results summary...
11-Nov-2024 15:13:23 Saving build results to disk...
11-Nov-2024 15:13:23 Logging substituted variables...
11-Nov-2024 15:13:23 Indexing build results...
11-Nov-2024 15:13:23 Finished building JB-GDB642-JOB1-2.