Build #3

Build: #3 was successful

Job: Clover and Tests was successful

Stages & jobs

  1. Default Stage

Build log

The build generated 259 lines of output. Download or view full build log

05-Nov-2025 13:15:12 Build Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Clover and Tests #3 (JB-GDB714-JOB1-3) started building on agent Default Agent
05-Nov-2025 13:15:12
05-Nov-2025 13:15:12 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1
05-Nov-2025 13:15:12 Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Clover and Tests #3 (JB-GDB714-JOB1-3)
05-Nov-2025 13:15:12 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
05-Nov-2025 13:15:12 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1
05-Nov-2025 13:15:12 Updating source code to revision: 0d10b35174aa38a4a48c5965e683dabe47dcd553
05-Nov-2025 13:15:12 Fetching 'refs/heads/bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' from 'https://gitlab.jalview.org/jalview/jalview.git'.
05-Nov-2025 13:15:12 Checking out revision 0d10b35174aa38a4a48c5965e683dabe47dcd553.
05-Nov-2025 13:15:13 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
05-Nov-2025 13:15:13    01b48f0..0d10b35  bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection -> origin/bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
05-Nov-2025 13:15:13 * [new branch]      bug/JAL-4594_ss_consensus_overlap_other_annot -> origin/bug/JAL-4594_ss_consensus_overlap_other_annot
05-Nov-2025 13:15:13    0ef8e14..12f0a1a  bug/JAL-4603_Export_files_missing_part_of_sequence -> origin/bug/JAL-4603_Export_files_missing_part_of_sequence
05-Nov-2025 13:15:13 * [new branch]      bug/JAL-4603_export_svg_files_missing_part_of_sequence -> origin/bug/JAL-4603_export_svg_files_missing_part_of_sequence
05-Nov-2025 13:15:13 * [new branch]      bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 -> origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12
05-Nov-2025 13:15:13    5883ea0..aca2c5f  development/Release_2_12_Branch -> origin/development/Release_2_12_Branch
05-Nov-2025 13:15:13 * [new branch]      feature/JAL-4521_Allow_PCA_tree_for_one_seq_mul_ss -> origin/feature/JAL-4521_Allow_PCA_tree_for_one_seq_mul_ss
05-Nov-2025 13:15:13 * [new branch]      feature/JAL-835_hhsuite_a3m_support -> origin/feature/JAL-835_hhsuite_a3m_support
05-Nov-2025 13:15:13 * [new branch]      improvement/JAL-4607_install4j_dark_mode_background_colour -> origin/improvement/JAL-4607_install4j_dark_mode_background_colour
05-Nov-2025 13:15:13 * [new branch]      improvement/JAL-4620_faster_sim_matrices -> origin/improvement/JAL-4620_faster_sim_matrices
05-Nov-2025 13:15:13 Already on 'bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection'
05-Nov-2025 13:15:13 Your branch is behind 'origin/bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' by 1 commit, and can be fast-forwarded.
05-Nov-2025 13:15:13   (use "git pull" to update your local branch)
05-Nov-2025 13:15:13 HEAD is now at 0d10b35 JAL-4604 Fixed Console logger being initiated too early and log level in props file not being set.  This was causing jalview.util.Log4jTest.testLog4j to fail.  Neatened the args in that test to use '--' to prevent mixed argstyle warning.
05-Nov-2025 13:15:13 Updated source code to revision: 0d10b35174aa38a4a48c5965e683dabe47dcd553
05-Nov-2025 13:15:13 Finished task 'Checkout Default Repository' with result: Success
05-Nov-2025 13:15:13 Running pre-build action: VCS Version Collector
05-Nov-2025 13:15:13 Running pre-build action: Artifactory Release Staging
05-Nov-2025 13:15:13 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
05-Nov-2025 13:15:13 Bamboo Artifactory Plugin version: 2.6.2
05-Nov-2025 13:15:13
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Clover and Tests #3 (JB-GDB714-JOB1-3)'
... running command line:
/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test
... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1
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05-Nov-2025 13:15:13 444
05-Nov-2025 13:15:14 Starting a Gradle Daemon (subsequent builds will be faster)
05-Nov-2025 13:15:22
05-Nov-2025 13:15:22 > Configure project :
05-Nov-2025 13:15:22 Using properties from file './utils/channels/default/channel_gradle.properties'
05-Nov-2025 13:15:22 JALVIEW_VERSION is set to '2.11.5.1'
05-Nov-2025 13:15:22 HEADLESS BUILD
05-Nov-2025 13:15:22 J2S ENABLED
05-Nov-2025 13:15:23 Using a LOCAL profile.
05-Nov-2025 13:15:24 eclipseDir exists
05-Nov-2025 13:15:25
05-Nov-2025 13:15:25 > Task :clean
05-Nov-2025 13:15:25 > Task :cleanClover
05-Nov-2025 13:15:25 > Task :cleanTest UP-TO-DATE
05-Nov-2025 13:15:27
05-Nov-2025 13:15:27 > Task :cloverInstrJava
05-Nov-2025 13:15:27 Clover: About to instrument 1106 files
05-Nov-2025 13:15:27 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
05-Nov-2025 13:15:27 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/clover/clover.db'.
05-Nov-2025 13:15:27 Processing files at 1.9 source level.
05-Nov-2025 13:15:32 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?
05-Nov-2025 13:15:32 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?
05-Nov-2025 13:15:32 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?
05-Nov-2025 13:15:32 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?
05-Nov-2025 13:15:32 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?
05-Nov-2025 13:15:32 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?
05-Nov-2025 13:15:32 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?
05-Nov-2025 13:15:39 Clover all over. Instrumented 1106 files (112 packages).
05-Nov-2025 13:15:42
05-Nov-2025 13:15:42 > Task :cloverInstrTests
05-Nov-2025 13:15:42 Clover: About to instrument test files
05-Nov-2025 13:15:42 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
05-Nov-2025 13:15:42 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/clover/clover.db'.
05-Nov-2025 13:15:42 Processing files at 1.9 source level.
05-Nov-2025 13:15:45 Clover all over. Instrumented 293 files (52 packages).
05-Nov-2025 13:15:45 1618 test methods detected.
05-Nov-2025 13:15:45
05-Nov-2025 13:15:45 > Task :cloverInstr
05-Nov-2025 13:15:47
05-Nov-2025 13:15:47 > Task :compileCloverJava
05-Nov-2025 13:15:47 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
05-Nov-2025 13:15:47   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:15:47   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:15:47   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:15:47 Setting target compatibility to 11
05-Nov-2025 13:16:13 Note: Some input files use or override a deprecated API.
05-Nov-2025 13:16:13 Note: Recompile with -Xlint:deprecation for details.
05-Nov-2025 13:16:13 Note: Some input files use unchecked or unsafe operations.
05-Nov-2025 13:16:13 Note: Recompile with -Xlint:unchecked for details.
05-Nov-2025 13:16:21
05-Nov-2025 13:16:21 > Task :processCloverResources NO-SOURCE
05-Nov-2025 13:16:21 > Task :cloverClasses
05-Nov-2025 13:16:21 > Task :copyHelp
05-Nov-2025 13:16:23 > Task :buildIndices
05-Nov-2025 13:16:23 > Task :copyResources
05-Nov-2025 13:16:23 > Task :copyChannelResources
05-Nov-2025 13:16:23
05-Nov-2025 13:16:23 > Task :createBuildProperties
05-Nov-2025 13:16:23 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
05-Nov-2025 13:16:23   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:16:23
05-Nov-2025 13:16:23 > Task :buildResources
05-Nov-2025 13:16:23 > Task :copyDocs
05-Nov-2025 13:16:23
05-Nov-2025 13:16:23 > Task :convertMdFiles
05-Nov-2025 13:16:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
05-Nov-2025 13:16:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/resources/doc_build/doc/releaseprocess.html
05-Nov-2025 13:16:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
05-Nov-2025 13:16:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/resources/doc_build/doc/building.html
05-Nov-2025 13:16:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/resources/doc_build/doc/jalview-projects.html
05-Nov-2025 13:16:24
05-Nov-2025 13:16:24 > Task :releasesTemplates
05-Nov-2025 13:16:24 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
05-Nov-2025 13:16:24   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:16:24   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:16:24 Stripping rc/test/etc for TEST
05-Nov-2025 13:16:24 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
05-Nov-2025 13:16:24
05-Nov-2025 13:16:24 > Task :prepare
05-Nov-2025 13:16:26
05-Nov-2025 13:16:26 > Task :compileJava
05-Nov-2025 13:16:26 Setting target compatibility to 11
05-Nov-2025 13:16:33 Note: Some input files use or override a deprecated API.
05-Nov-2025 13:16:33 Note: Recompile with -Xlint:deprecation for details.
05-Nov-2025 13:16:33 Note: Some input files use unchecked or unsafe operations.
05-Nov-2025 13:16:33 Note: Recompile with -Xlint:unchecked for details.
05-Nov-2025 13:16:37
05-Nov-2025 13:16:37 > Task :compileTestJava
05-Nov-2025 13:16:37 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
05-Nov-2025 13:16:37   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:16:37   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:16:37 Setting target compatibility to 11
05-Nov-2025 13:16:43 Note: Some input files use or override a deprecated API.
05-Nov-2025 13:16:43 Note: Recompile with -Xlint:deprecation for details.
05-Nov-2025 13:16:43 Note: Some input files use unchecked or unsafe operations.
05-Nov-2025 13:16:43 Note: Recompile with -Xlint:unchecked for details.
05-Nov-2025 13:16:44
05-Nov-2025 13:16:44 > Task :processTestResources
05-Nov-2025 13:16:44 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
05-Nov-2025 13:16:44   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:16:44   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:16:44   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:16:44   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:16:44   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:16:44   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:16:44   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:16:44   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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.
05-Nov-2025 13:16:44
05-Nov-2025 13:16:44 > Task :testClasses
05-Nov-2025 13:16:46
05-Nov-2025 13:16:46 > Task :testTask0
05-Nov-2025 13:16:46 Running tests WITH clover
05-Nov-2025 13:16:49 WARNING: An illegal reflective access operation has occurred
05-Nov-2025 13:16:49 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
05-Nov-2025 13:16:49 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
05-Nov-2025 13:16:49 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
05-Nov-2025 13:16:49 WARNING: All illegal access operations will be denied in a future release
05-Nov-2025 13:21:35
05-Nov-2025 13:21:35 > Task :testTask1
05-Nov-2025 13:21:35 Running tests WITH clover
05-Nov-2025 13:21:37 WARNING: An illegal reflective access operation has occurred
05-Nov-2025 13:21:37 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
05-Nov-2025 13:21:37 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
05-Nov-2025 13:21:37 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
05-Nov-2025 13:21:37 WARNING: All illegal access operations will be denied in a future release
05-Nov-2025 13:24:19
05-Nov-2025 13:24:19 > Task :testTask2
05-Nov-2025 13:24:19 Running tests WITH clover
05-Nov-2025 13:24:23
05-Nov-2025 13:24:23 > Task :testTask3
05-Nov-2025 13:24:23 Running tests WITH clover
05-Nov-2025 13:24:26 WARNING: An illegal reflective access operation has occurred
05-Nov-2025 13:24:26 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
05-Nov-2025 13:24:26 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
05-Nov-2025 13:24:26 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
05-Nov-2025 13:24:26 WARNING: All illegal access operations will be denied in a future release
05-Nov-2025 13:25:24
05-Nov-2025 13:25:24 > Task :test NO-SOURCE
05-Nov-2025 13:25:24 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
05-Nov-2025 13:25:24 │jalview:testTask0 results: SUCCESS (1819 tests, 1819 successes, 0 failures, 0 skipped) in 4 minutes, 47.538 seconds   │
05-Nov-2025 13:25:24 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/tests/testTask0/index.html│
05-Nov-2025 13:25:24 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
05-Nov-2025 13:25:24 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 43.887 seconds       │
05-Nov-2025 13:25:24 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/tests/testTask1/index.html│
05-Nov-2025 13:25:24 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
05-Nov-2025 13:25:24 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.351 seconds                     │
05-Nov-2025 13:25:24 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/tests/testTask2/index.html│
05-Nov-2025 13:25:24 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
05-Nov-2025 13:25:24 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 2.536 seconds        │
05-Nov-2025 13:25:24 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/tests/testTask3/index.html│
05-Nov-2025 13:25:24 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
05-Nov-2025 13:25:24 │OVERALL: results: SUCCESS (1907 tests, 1907 successes, 0 failures, 0 skipped) in 7 minutes, 98.312 seconds            │
05-Nov-2025 13:25:24 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
05-Nov-2025 13:25:24
05-Nov-2025 13:25:24 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
05-Nov-2025 13:25:24
05-Nov-2025 13:25:24 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
05-Nov-2025 13:25:24
05-Nov-2025 13:25:24 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
05-Nov-2025 13:25:24
05-Nov-2025 13:25:24 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
05-Nov-2025 13:25:24 Please consult deprecation warnings for more details.
05-Nov-2025 13:25:24
05-Nov-2025 13:25:24 BUILD SUCCESSFUL in 10m 10s
05-Nov-2025 13:25:24 21 actionable tasks: 20 executed, 1 up-to-date
05-Nov-2025 13:25:25 Finished task 'Run tests with openclover under gradle' with result: Success
05-Nov-2025 13:25:25 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
05-Nov-2025 13:25:25 Bamboo Artifactory Plugin version: 2.6.2
05-Nov-2025 13:25:25
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Clover and Tests #3 (JB-GDB714-JOB1-3)'
... running command line:
/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport
... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
bamboo_repository_revision_number=0d10b35174aa38a4a48c5965e683dabe47dcd553
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB714-JOB1-3
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-GDB714-JOB1
bamboo_planRepository_1_name=Jalview Gitlab
bamboo_buildKey=JB-GDB714-JOB1
bamboo_shortPlanName=bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
bamboo_repository_46498506_name=Jalview Gitlab
bamboo_planRepository_name=Jalview Gitlab
LOGNAME=bamboo
bamboo_buildNumber=3
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-GDB714-JOB1-3
bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
SHELL=/bin/bash
bamboo_agentId=196609
bamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
bamboo_shortPlanKey=GDB714
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=0d10b35174aa38a4a48c5965e683dabe47dcd553
bamboo_buildTimeStamp=2025-11-05T13:15:12.595Z
bamboo_repository_previous_revision_number=01b48f04818d683d5d0f90d7833ae0c6d4191a8c
bamboo_planRepository_previousRevision=01b48f04818d683d5d0f90d7833ae0c6d4191a8c
bamboo_repository_46498506_revision_number=0d10b35174aa38a4a48c5965e683dabe47dcd553
bamboo_repository_git_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
bamboo_buildResultKey=JB-GDB714-JOB1-3
bamboo_repository_branch_name=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
bamboo_repository_46498506_previous_revision_number=01b48f04818d683d5d0f90d7833ae0c6d4191a8c
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=0d10b35174aa38a4a48c5965e683dabe47dcd553
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/
bamboo_repository_46498506_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
LANG=en_GB.UTF-8
bamboo_buildFailed=false
bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk
bamboo_planRepository_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609
bamboo_jobFailed=false
bamboo_capability_system_git_executable=/bin/git
bamboo_repository_git_username=
bamboo_planRepository_1_previousRevision=01b48f04818d683d5d0f90d7833ae0c6d4191a8c
bamboo_planRepository_branchDisplayName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
_=/usr/bin/java
bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11
bamboo_repository_46498506_branch_name=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
bamboo_repository_46498506_git_username=
bamboo_capability_system_builderivy_Ivy=/usr
bamboo_plan_storageTag=plan-46302583
bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle
bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache
bamboo_planRepository_1_username=
bamboo_planRepository_type=gitv2
USER=bamboo
bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache
bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_capability_system_builder_ant_Ant=/usr/share/ant
bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven
bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp
bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1
bamboo_planKey=JB-GDB714
bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_planRepository_username=
bamboo_repository_46498506_git_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
HOME=/home/bamboo
bamboo_planRepository_1_branchName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
05-Nov-2025 13:25:25 444
05-Nov-2025 13:25:32
05-Nov-2025 13:25:32 > Configure project :
05-Nov-2025 13:25:32 Using properties from file './utils/channels/default/channel_gradle.properties'
05-Nov-2025 13:25:32 JALVIEW_VERSION is set to '2.11.5.1'
05-Nov-2025 13:25:32 HEADLESS BUILD
05-Nov-2025 13:25:32 J2S ENABLED
05-Nov-2025 13:25:33 Using a LOCAL profile.
05-Nov-2025 13:25:34 eclipseDir exists
05-Nov-2025 13:25:36
05-Nov-2025 13:25:36 > Task :cloverHtmlReport
05-Nov-2025 13:25:36 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
05-Nov-2025 13:25:38 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/clover'
05-Nov-2025 13:26:32 Done. Processed 116 packages in 54118ms (466ms per package).
05-Nov-2025 13:26:39
05-Nov-2025 13:26:39 > Task :cloverXmlReport
05-Nov-2025 13:26:39 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
05-Nov-2025 13:26:40 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/clover/clover.xml'
05-Nov-2025 13:26:40
05-Nov-2025 13:26:40 > Task :cloverReport
05-Nov-2025 13:26:40
05-Nov-2025 13:26:40 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
05-Nov-2025 13:26:40
05-Nov-2025 13:26:40 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
05-Nov-2025 13:26:40
05-Nov-2025 13:26:40 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
05-Nov-2025 13:26:40
05-Nov-2025 13:26:40 BUILD SUCCESSFUL in 1m 15s
05-Nov-2025 13:26:40 2 actionable tasks: 2 executed
05-Nov-2025 13:26:41 Finished task 'Clover Report' with result: Success
05-Nov-2025 13:26:41 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
05-Nov-2025 13:26:41 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1...
05-Nov-2025 13:26:41 Finished task 'TestNG Parser' with result: Success
05-Nov-2025 13:26:41 Running post build plugin 'NCover Results Collector'
05-Nov-2025 13:26:41 Running post build plugin 'Artifact Copier'
05-Nov-2025 13:26:41 Publishing an artifact: Clover Report (System)
05-Nov-2025 13:26:46 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 5.261 s
05-Nov-2025 13:26:46 Publishing an artifact: TestNG report
05-Nov-2025 13:26:46 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/tests/test does not exist.
05-Nov-2025 13:26:46 The artifact hasn't been successfully published after 4.602 ms
05-Nov-2025 13:26:46 Running post build plugin 'Artifactory Release Management Staging'
05-Nov-2025 13:26:46 Running post build plugin 'Artifactory Build Info Copier'
05-Nov-2025 13:26:46 Running post build plugin 'Artifactory Gradle Properties Info Copier'
05-Nov-2025 13:26:46 Running post build plugin 'npm Cache Cleanup'
05-Nov-2025 13:26:46 Running post build plugin 'Clover Results Collector'
05-Nov-2025 13:26:46 Running post build plugin 'Docker Container Cleanup'
05-Nov-2025 13:26:46 Finalising the build...
05-Nov-2025 13:26:46 Stopping timer.
05-Nov-2025 13:26:46 Build JB-GDB714-JOB1-3 completed.
05-Nov-2025 13:26:46 Running on server: post build plugin 'NCover Results Collector'
05-Nov-2025 13:26:46 Running on server: post build plugin 'Build Hanging Detection Configuration'
05-Nov-2025 13:26:46 Running on server: post build plugin 'Clover Delta Calculator'
05-Nov-2025 13:26:46 Running on server: post build plugin 'Maven Dependencies Postprocessor'
05-Nov-2025 13:26:46 All post build plugins have finished
05-Nov-2025 13:26:46 Generating build results summary...
05-Nov-2025 13:26:47 Saving build results to disk...
05-Nov-2025 13:26:47 Logging substituted variables...
05-Nov-2025 13:26:47 Indexing build results...
05-Nov-2025 13:26:47 Finished building JB-GDB714-JOB1-3.