Build #704

Build and run tests under Java 11

Build: #704 was successful

Job: Clover and Tests was successful

Stages & jobs

  1. Default Stage

Build log

The build generated 284 lines of output. Download or view full build log

18-Jun-2025 15:08:59 Build Jalview Builds - Gradle Develop Build - Clover and Tests #704 (JB-GDB-JOB1-704) started building on agent Default Agent
18-Jun-2025 15:08:59
18-Jun-2025 15:08:59 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1
18-Jun-2025 15:08:59 Executing build Jalview Builds - Gradle Develop Build - Clover and Tests #704 (JB-GDB-JOB1-704)
18-Jun-2025 15:08:59 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
18-Jun-2025 15:08:59 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1
18-Jun-2025 15:08:59 Updating source code to revision: a07a210e39b574048817742f680ad4bbcebb590c
18-Jun-2025 15:08:59 Fetching 'refs/heads/main' from 'https://gitlab.jalview.org/jalview/jalview.git'.
18-Jun-2025 15:08:59 Checking out revision a07a210e39b574048817742f680ad4bbcebb590c.
18-Jun-2025 15:09:01 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
18-Jun-2025 15:09:01    74108b5..2bd12a6  develop    -> origin/develop
18-Jun-2025 15:09:01 * [new branch]      bug/JAL-4504_updated_flatlaf_libs -> origin/bug/JAL-4504_updated_flatlaf_libs
18-Jun-2025 15:09:01 * [new branch]      bug/JAL-4507_Some_exported_annotations_being_reloaded_as_sequences -> origin/bug/JAL-4507_Some_exported_annotations_being_reloaded_as_sequences
18-Jun-2025 15:09:01 * [new branch]      development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch
18-Jun-2025 15:09:01 * [new branch]      feature/JAL-4386_JAL-4435_coloured_lines_for_providers -> origin/feature/JAL-4386_JAL-4435_coloured_lines_for_providers
18-Jun-2025 15:09:01 * [new branch]      feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels
18-Jun-2025 15:09:01 * [new branch]      feature/JAL-4527_import_export_annotation_file -> origin/feature/JAL-4527_import_export_annotation_file
18-Jun-2025 15:09:01 * [new branch]      feature/JAL_4548_show_PDBID_metadata_for_annot_tree -> origin/feature/JAL_4548_show_PDBID_metadata_for_annot_tree
18-Jun-2025 15:09:01 * [new branch]      features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 -> origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2
18-Jun-2025 15:09:01 * [new branch]      features/JAL-4527_ss_trees_from_annotationfile -> origin/features/JAL-4527_ss_trees_from_annotationfile
18-Jun-2025 15:09:01 * [new branch]      improvement/JAL-4530_add_applescript_to_allow_installation_to_home_applications_folder -> origin/improvement/JAL-4530_add_applescript_to_allow_installation_to_home_applications_folder
18-Jun-2025 15:09:01 * [new branch]      improvement/JAL-4541_slight_increase_in_robustness_of_analytics_from_jalview_desktop -> origin/improvement/JAL-4541_slight_increase_in_robustness_of_analytics_from_jalview_desktop
18-Jun-2025 15:09:01 * [new branch]      jims_2_12/JAL-4519_error_reporting_and_slivka -> origin/jims_2_12/JAL-4519_error_reporting_and_slivka
18-Jun-2025 15:09:01 * [new branch]      main       -> origin/main
18-Jun-2025 15:09:01 * [new branch]      mr_patch/JAL-4548_JAL-4411_JAL-3880_add_pdb_id_and_chaincode_to_annotations -> origin/mr_patch/JAL-4548_JAL-4411_JAL-3880_add_pdb_id_and_chaincode_to_annotations
18-Jun-2025 15:09:01 * [new branch]      patch/JAL-4501_patch_swingjs_jquery -> origin/patch/JAL-4501_patch_swingjs_jquery
18-Jun-2025 15:09:01 * [new branch]      patch/JAL-4501_patch_swingjs_jquery_2112_release -> origin/patch/JAL-4501_patch_swingjs_jquery_2112_release
18-Jun-2025 15:09:01 * [new branch]      patch/JAL-4501_patch_swingjs_jquery_2113_Series -> origin/patch/JAL-4501_patch_swingjs_jquery_2113_Series
18-Jun-2025 15:09:01 * [new branch]      patch/JAL-4501_patch_swingjs_jquery_2_11_2_3_Release_24thJan -> origin/patch/JAL-4501_patch_swingjs_jquery_2_11_2_3_Release_24thJan
18-Jun-2025 15:09:01 * [new branch]      patch/JAL-4501_patch_swingjs_jquery_2_11_3_2_Release -> origin/patch/JAL-4501_patch_swingjs_jquery_2_11_3_2_Release
18-Jun-2025 15:09:01 * [new branch]      patch/JAL-4555_sort_by_descr -> origin/patch/JAL-4555_sort_by_descr
18-Jun-2025 15:09:01 * [new branch]      patch/JAL-4557_fix_duplicated_cds_consensus -> origin/patch/JAL-4557_fix_duplicated_cds_consensus
18-Jun-2025 15:09:01 * [new branch]      patch/JAL-4557_fix_duplicated_cds_for_2_11_5_Branch -> origin/patch/JAL-4557_fix_duplicated_cds_for_2_11_5_Branch
18-Jun-2025 15:09:01 * [new branch]      patch/JAL-4564_JAL-4563_urls_and_structure_args -> origin/patch/JAL-4564_JAL-4563_urls_and_structure_args
18-Jun-2025 15:09:01 * [new branch]      releases/Release_2_11_2_3b1_Branch -> origin/releases/Release_2_11_2_3b1_Branch
18-Jun-2025 15:09:01 * [new branch]      releases/Release_2_11_3_3b1_Branch -> origin/releases/Release_2_11_3_3b1_Branch
18-Jun-2025 15:09:01 * [new branch]      releases/Release_2_11_4_Branch -> origin/releases/Release_2_11_4_Branch
18-Jun-2025 15:09:01 * [new branch]      spike/JAL-4517_customNodenamesInNewick -> origin/spike/JAL-4517_customNodenamesInNewick
18-Jun-2025 15:09:01 * [new branch]      spike/features/JAL-4529_alternativeFormats -> origin/spike/features/JAL-4529_alternativeFormats
18-Jun-2025 15:09:01 * [new tag]         Archived_Release_2_7 -> Archived_Release_2_7
18-Jun-2025 15:09:01 * [new tag]         Jalview_2_4_0b2 -> Jalview_2_4_0b2
18-Jun-2025 15:09:01 * [new tag]         Release_2_10_1 -> Release_2_10_1
18-Jun-2025 15:09:01 * [new tag]         Release_2_11_2_7 -> Release_2_11_2_7
18-Jun-2025 15:09:01 * [new tag]         Release_2_11_4_0 -> Release_2_11_4_0
18-Jun-2025 15:09:01 * [new tag]         Release_2_11_4_1 -> Release_2_11_4_1
18-Jun-2025 15:09:01 * [new tag]         Release_2_4_0 -> Release_2_4_0
18-Jun-2025 15:09:01 * [new tag]         Release_2_5_1 -> Release_2_5_1
18-Jun-2025 15:09:01 * [new tag]         Release_2_6_1 -> Release_2_6_1
18-Jun-2025 15:09:01 Branch main set up to track remote branch main from origin.
18-Jun-2025 15:09:01 Switched to a new branch 'main'
18-Jun-2025 15:09:02 Updated source code to revision: a07a210e39b574048817742f680ad4bbcebb590c
18-Jun-2025 15:09:02 Finished task 'Checkout Default Repository' with result: Success
18-Jun-2025 15:09:02 Running pre-build action: VCS Version Collector
18-Jun-2025 15:09:02 Running pre-build action: Artifactory Release Staging
18-Jun-2025 15:09:02 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
18-Jun-2025 15:09:02 Bamboo Artifactory Plugin version: 2.6.2
18-Jun-2025 15:09:02
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - Clover and Tests #704 (JB-GDB-JOB1-704)'
... 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-GDB-JOB1
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18-Jun-2025 15:09:02 444
18-Jun-2025 15:09:04
18-Jun-2025 15:09:04 > Configure project :
18-Jun-2025 15:09:04 Using properties from file './utils/channels/default/channel_gradle.properties'
18-Jun-2025 15:09:04 JALVIEW_VERSION is set to '2.11.4.1'
18-Jun-2025 15:09:04 HEADLESS BUILD
18-Jun-2025 15:09:04 J2S ENABLED
18-Jun-2025 15:09:04 Using a LOCAL profile.
18-Jun-2025 15:09:04 eclipseDir exists
18-Jun-2025 15:09:04
18-Jun-2025 15:09:04 > Task :clean
18-Jun-2025 15:09:04 > Task :cleanClover
18-Jun-2025 15:09:04 > Task :cleanTest UP-TO-DATE
18-Jun-2025 15:09:06
18-Jun-2025 15:09:06 > Task :cloverInstrJava
18-Jun-2025 15:09:06 Clover: About to instrument 1103 files
18-Jun-2025 15:09:06 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
18-Jun-2025 15:09:06 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover.db'.
18-Jun-2025 15:09:06 Processing files at 1.9 source level.
18-Jun-2025 15:09:09 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?
18-Jun-2025 15:09:09 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?
18-Jun-2025 15:09:09 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?
18-Jun-2025 15:09:09 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?
18-Jun-2025 15:09:09 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?
18-Jun-2025 15:09:09 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?
18-Jun-2025 15:09:09 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?
18-Jun-2025 15:09:15 Clover all over. Instrumented 1103 files (112 packages).
18-Jun-2025 15:09:17
18-Jun-2025 15:09:17 > Task :cloverInstrTests
18-Jun-2025 15:09:17 Clover: About to instrument test files
18-Jun-2025 15:09:17 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
18-Jun-2025 15:09:17 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover.db'.
18-Jun-2025 15:09:17 Processing files at 1.9 source level.
18-Jun-2025 15:09:19 Clover all over. Instrumented 291 files (52 packages).
18-Jun-2025 15:09:19 1594 test methods detected.
18-Jun-2025 15:09:19
18-Jun-2025 15:09:19 > Task :cloverInstr
18-Jun-2025 15:09:21
18-Jun-2025 15:09:21 > Task :compileCloverJava
18-Jun-2025 15:09:21 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
18-Jun-2025 15:09:21   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:21   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:21   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:21 Setting target compatibility to 11
18-Jun-2025 15:09:33 Note: Some input files use or override a deprecated API.
18-Jun-2025 15:09:33 Note: Recompile with -Xlint:deprecation for details.
18-Jun-2025 15:09:33 Note: Some input files use unchecked or unsafe operations.
18-Jun-2025 15:09:33 Note: Recompile with -Xlint:unchecked for details.
18-Jun-2025 15:09:38
18-Jun-2025 15:09:38 > Task :processCloverResources NO-SOURCE
18-Jun-2025 15:09:38 > Task :cloverClasses
18-Jun-2025 15:09:38 > Task :copyHelp
18-Jun-2025 15:09:39 > Task :buildIndices
18-Jun-2025 15:09:39 > Task :copyResources
18-Jun-2025 15:09:39 > Task :copyChannelResources
18-Jun-2025 15:09:39
18-Jun-2025 15:09:39 > Task :createBuildProperties
18-Jun-2025 15:09:39 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
18-Jun-2025 15:09:39   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:39
18-Jun-2025 15:09:39 > Task :buildResources
18-Jun-2025 15:09:39 > Task :copyDocs
18-Jun-2025 15:09:40
18-Jun-2025 15:09:40 > Task :convertMdFiles
18-Jun-2025 15:09:40 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
18-Jun-2025 15:09:40 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/releaseprocess.html
18-Jun-2025 15:09:40 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
18-Jun-2025 15:09:40 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/building.html
18-Jun-2025 15:09:40 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/jalview-projects.html
18-Jun-2025 15:09:40
18-Jun-2025 15:09:40 > Task :releasesTemplates
18-Jun-2025 15:09:40 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
18-Jun-2025 15:09:40   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:40   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:40 Stripping rc/test/etc for TEST
18-Jun-2025 15:09:40 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
18-Jun-2025 15:09:40
18-Jun-2025 15:09:40 > Task :prepare
18-Jun-2025 15:09:42
18-Jun-2025 15:09:42 > Task :compileJava
18-Jun-2025 15:09:42 Setting target compatibility to 11
18-Jun-2025 15:09:46 Note: Some input files use or override a deprecated API.
18-Jun-2025 15:09:46 Note: Recompile with -Xlint:deprecation for details.
18-Jun-2025 15:09:46 Note: Some input files use unchecked or unsafe operations.
18-Jun-2025 15:09:46 Note: Recompile with -Xlint:unchecked for details.
18-Jun-2025 15:09:48
18-Jun-2025 15:09:48 > Task :compileTestJava
18-Jun-2025 15:09:48 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
18-Jun-2025 15:09:48   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:48   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:48 Setting target compatibility to 11
18-Jun-2025 15:09:52 Note: Some input files use or override a deprecated API.
18-Jun-2025 15:09:52 Note: Recompile with -Xlint:deprecation for details.
18-Jun-2025 15:09:52 Note: Some input files use unchecked or unsafe operations.
18-Jun-2025 15:09:52 Note: Recompile with -Xlint:unchecked for details.
18-Jun-2025 15:09:53
18-Jun-2025 15:09:53 > Task :processTestResources
18-Jun-2025 15:09:53 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
18-Jun-2025 15:09:53   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:53   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:53   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:53   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:53   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:53   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:53   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:53   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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.
18-Jun-2025 15:09:53
18-Jun-2025 15:09:53 > Task :testClasses
18-Jun-2025 15:09:55
18-Jun-2025 15:09:55 > Task :testTask0
18-Jun-2025 15:09:55 Running tests WITH clover
18-Jun-2025 15:09:57 WARNING: An illegal reflective access operation has occurred
18-Jun-2025 15:09:57 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
18-Jun-2025 15:09:57 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
18-Jun-2025 15:09:57 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
18-Jun-2025 15:09:57 WARNING: All illegal access operations will be denied in a future release
18-Jun-2025 15:13:34
18-Jun-2025 15:13:34 > Task :testTask1
18-Jun-2025 15:13:34 Running tests WITH clover
18-Jun-2025 15:13:35 WARNING: An illegal reflective access operation has occurred
18-Jun-2025 15:13:35 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
18-Jun-2025 15:13:35 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
18-Jun-2025 15:13:35 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
18-Jun-2025 15:13:35 WARNING: All illegal access operations will be denied in a future release
18-Jun-2025 15:15:08
18-Jun-2025 15:15:08 > Task :testTask2
18-Jun-2025 15:15:08 Running tests WITH clover
18-Jun-2025 15:15:12
18-Jun-2025 15:15:12 > Task :testTask3
18-Jun-2025 15:15:12 Running tests WITH clover
18-Jun-2025 15:15:13 WARNING: An illegal reflective access operation has occurred
18-Jun-2025 15:15:13 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
18-Jun-2025 15:15:13 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
18-Jun-2025 15:15:13 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
18-Jun-2025 15:15:13 WARNING: All illegal access operations will be denied in a future release
18-Jun-2025 15:15:58
18-Jun-2025 15:15:58 > Task :test NO-SOURCE
18-Jun-2025 15:15:58 ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
18-Jun-2025 15:15:58 │jalview:testTask0 results: SUCCESS (1728 tests, 1728 successes, 0 failures, 0 skipped) in 3 minutes, 38.636 seconds│
18-Jun-2025 15:15:58 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask0/index.html│
18-Jun-2025 15:15:58 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
18-Jun-2025 15:15:58 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 34.148 seconds    │
18-Jun-2025 15:15:58 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask1/index.html│
18-Jun-2025 15:15:58 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
18-Jun-2025 15:15:58 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.599 seconds                  │
18-Jun-2025 15:15:58 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask2/index.html│
18-Jun-2025 15:15:58 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
18-Jun-2025 15:15:58 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 47.747 seconds               │
18-Jun-2025 15:15:58 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask3/index.html│
18-Jun-2025 15:15:58 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
18-Jun-2025 15:15:58 │OVERALL: results: SUCCESS (1803 tests, 1803 successes, 0 failures, 0 skipped) in 4 minutes, 124.130 seconds        │
18-Jun-2025 15:15:58 └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
18-Jun-2025 15:15:58
18-Jun-2025 15:15:58 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
18-Jun-2025 15:15:58
18-Jun-2025 15:15:58 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
18-Jun-2025 15:15:58
18-Jun-2025 15:15:58 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
18-Jun-2025 15:15:58
18-Jun-2025 15:15:58 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
18-Jun-2025 15:15:58 Please consult deprecation warnings for more details.
18-Jun-2025 15:15:58
18-Jun-2025 15:15:58 BUILD SUCCESSFUL in 6m 56s
18-Jun-2025 15:15:58 21 actionable tasks: 20 executed, 1 up-to-date
18-Jun-2025 15:15:58 Finished task 'Run tests with openclover under gradle' with result: Success
18-Jun-2025 15:15:58 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
18-Jun-2025 15:15:58 Bamboo Artifactory Plugin version: 2.6.2
18-Jun-2025 15:15:58
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - Clover and Tests #704 (JB-GDB-JOB1-704)'
... 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-GDB-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=main
bamboo_repository_46498240_branch_name=main
bamboo_repository_46498240_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=main
bamboo_repository_revision_number=a07a210e39b574048817742f680ad4bbcebb590c
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB-JOB1-704
bamboo_repository_46498240_git_username=
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-GDB-JOB1
bamboo_planRepository_1_name=Jalview Gitlab
bamboo_buildKey=JB-GDB-JOB1
bamboo_shortPlanName=Gradle Develop Build
bamboo_planRepository_name=Jalview Gitlab
LOGNAME=bamboo
bamboo_buildNumber=704
PWD=/
bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse
bamboo_repository_46498240_previous_revision_number=74108b5332c0b49edc09570b36614c0ada40d3f2
bamboo_shortJobName=Clover and Tests
bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB-JOB1-704
bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
SHELL=/bin/bash
bamboo_agentId=196609
bamboo_planName=Jalview Builds - Gradle Develop Build
bamboo_shortPlanKey=GDB
bamboo_repository_46498240_git_branch=main
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=a07a210e39b574048817742f680ad4bbcebb590c
bamboo_buildTimeStamp=2025-06-18T15:04:26.124+01:00
bamboo_repository_previous_revision_number=74108b5332c0b49edc09570b36614c0ada40d3f2
bamboo_repository_46498240_revision_number=a07a210e39b574048817742f680ad4bbcebb590c
bamboo_planRepository_previousRevision=74108b5332c0b49edc09570b36614c0ada40d3f2
bamboo_repository_git_branch=main
bamboo_buildResultKey=JB-GDB-JOB1-704
bamboo_repository_branch_name=main
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=a07a210e39b574048817742f680ad4bbcebb590c
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
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bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk
bamboo_planRepository_branch=main
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=74108b5332c0b49edc09570b36614c0ada40d3f2
bamboo_planRepository_branchDisplayName=main
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=main
_=/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-7864341
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-GDB-JOB1
bamboo_planKey=JB-GDB
bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_planRepository_username=
bamboo_repository_46498240_name=Jalview Gitlab
HOME=/home/bamboo
bamboo_planRepository_1_branchName=main
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18-Jun-2025 15:15:58 444
18-Jun-2025 15:16:04
18-Jun-2025 15:16:04 > Configure project :
18-Jun-2025 15:16:04 Using properties from file './utils/channels/default/channel_gradle.properties'
18-Jun-2025 15:16:04 JALVIEW_VERSION is set to '2.11.4.1'
18-Jun-2025 15:16:04 HEADLESS BUILD
18-Jun-2025 15:16:04 J2S ENABLED
18-Jun-2025 15:16:04 Using a LOCAL profile.
18-Jun-2025 15:16:05 eclipseDir exists
18-Jun-2025 15:16:07
18-Jun-2025 15:16:07 > Task :cloverHtmlReport
18-Jun-2025 15:16:07 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
18-Jun-2025 15:16:08 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/clover'
18-Jun-2025 15:16:50 Done. Processed 116 packages in 41905ms (361ms per package).
18-Jun-2025 15:16:55
18-Jun-2025 15:16:55 > Task :cloverXmlReport
18-Jun-2025 15:16:55 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
18-Jun-2025 15:16:56 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/clover/clover.xml'
18-Jun-2025 15:16:56
18-Jun-2025 15:16:56 > Task :cloverReport
18-Jun-2025 15:16:56
18-Jun-2025 15:16:56 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
18-Jun-2025 15:16:56
18-Jun-2025 15:16:56 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
18-Jun-2025 15:16:56
18-Jun-2025 15:16:56 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
18-Jun-2025 15:16:56
18-Jun-2025 15:16:56 BUILD SUCCESSFUL in 57s
18-Jun-2025 15:16:56 2 actionable tasks: 2 executed
18-Jun-2025 15:16:56 Finished task 'Clover Report' with result: Success
18-Jun-2025 15:16:56 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
18-Jun-2025 15:16:56 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1...
18-Jun-2025 15:16:56 Finished task 'TestNG Parser' with result: Success
18-Jun-2025 15:16:56 Running post build plugin 'NCover Results Collector'
18-Jun-2025 15:16:56 Running post build plugin 'Artifact Copier'
18-Jun-2025 15:16:56 Publishing an artifact: Clover Report (System)
18-Jun-2025 15:16:59 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.646 s
18-Jun-2025 15:16:59 Publishing an artifact: TestNG report
18-Jun-2025 15:16:59 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/test does not exist.
18-Jun-2025 15:16:59 The artifact hasn't been successfully published after 2.162 ms
18-Jun-2025 15:16:59 Running post build plugin 'Artifactory Release Management Staging'
18-Jun-2025 15:16:59 Running post build plugin 'Artifactory Build Info Copier'
18-Jun-2025 15:16:59 Running post build plugin 'Artifactory Gradle Properties Info Copier'
18-Jun-2025 15:16:59 Running post build plugin 'npm Cache Cleanup'
18-Jun-2025 15:16:59 Running post build plugin 'Clover Results Collector'
18-Jun-2025 15:16:59 Running post build plugin 'Docker Container Cleanup'
18-Jun-2025 15:16:59 Finalising the build...
18-Jun-2025 15:16:59 Stopping timer.
18-Jun-2025 15:16:59 Build JB-GDB-JOB1-704 completed.
18-Jun-2025 15:16:59 Running on server: post build plugin 'NCover Results Collector'
18-Jun-2025 15:16:59 Running on server: post build plugin 'Build Hanging Detection Configuration'
18-Jun-2025 15:16:59 Running on server: post build plugin 'Clover Delta Calculator'
18-Jun-2025 15:16:59 Running on server: post build plugin 'Maven Dependencies Postprocessor'
18-Jun-2025 15:16:59 All post build plugins have finished
18-Jun-2025 15:16:59 Generating build results summary...
18-Jun-2025 15:16:59 Saving build results to disk...
18-Jun-2025 15:16:59 Logging substituted variables...
18-Jun-2025 15:16:59 Indexing build results...
18-Jun-2025 15:16:59 Finished building JB-GDB-JOB1-704.