Build #705

Build and run tests under Java 11

Build: #705 was successful

Job: Clover and Tests was successful

Stages & jobs

  1. Default Stage

Build log

The build generated 285 lines of output. Download or view full build log

17-Sep-2025 10:52:19 Build Jalview Builds - Gradle Develop Build - Clover and Tests #705 (JB-GDB-JOB1-705) started building on agent Default Agent
17-Sep-2025 10:52:19
17-Sep-2025 10:52:19 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1
17-Sep-2025 10:52:19 Executing build Jalview Builds - Gradle Develop Build - Clover and Tests #705 (JB-GDB-JOB1-705)
17-Sep-2025 10:52:19 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
17-Sep-2025 10:52:19 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1
17-Sep-2025 10:52:19 Updating source code to revision: 87afc897f4ab4cf704d7e1c000421e81e0464919
17-Sep-2025 10:52:19 Fetching 'refs/heads/main' from 'https://gitlab.jalview.org/jalview/jalview.git'.
17-Sep-2025 10:52:19 Checking out revision 87afc897f4ab4cf704d7e1c000421e81e0464919.
17-Sep-2025 10:52:19 error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
17-Sep-2025 10:52:19 error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
17-Sep-2025 10:52:19 error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
17-Sep-2025 10:52:19 error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
17-Sep-2025 10:52:19 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
17-Sep-2025 10:52:19    a07a210..87afc89  main       -> origin/main
17-Sep-2025 10:52:19 * [new branch]      bug/JAL-4397_failing_test_on_macos_more_space_display_setting -> origin/bug/JAL-4397_failing_test_on_macos_more_space_display_setting
17-Sep-2025 10:52:19    9ce6176..8291b4c  bug/JAL-4507_Some_exported_annotations_being_reloaded_as_sequences -> origin/bug/JAL-4507_Some_exported_annotations_being_reloaded_as_sequences
17-Sep-2025 10:52:19 * [new branch]      bug/JAL-4530_applescript_to_detect_Applications_symlink -> origin/bug/JAL-4530_applescript_to_detect_Applications_symlink
17-Sep-2025 10:52:19 * [new branch]      bug/JAL-4568_r2_11_4_2_jmol_image_deadlock -> origin/bug/JAL-4568_r2_11_4_2_jmol_image_deadlock
17-Sep-2025 10:52:19 * [new branch]      development/JAL-4107_merge_2115_212 -> origin/development/JAL-4107_merge_2115_212
17-Sep-2025 10:52:19    13316f6..2c0064b  development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch
17-Sep-2025 10:52:19 * [new branch]      feature/JAL-4435_JAL-4509_JAL-4542_JAL-4518_documentation -> origin/feature/JAL-4435_JAL-4509_JAL-4542_JAL-4518_documentation
17-Sep-2025 10:52:19 * [new branch]      feature/JAL-4515_Group_colouring_as_background -> origin/feature/JAL-4515_Group_colouring_as_background
17-Sep-2025 10:52:19 * [new branch]      feature/JAL-4528_check_min_no_annotations_for_tree -> origin/feature/JAL-4528_check_min_no_annotations_for_tree
17-Sep-2025 10:52:19 * [new branch]      feature/JAL-4542_highlight_selected_annot_labels_tree_nodes -> origin/feature/JAL-4542_highlight_selected_annot_labels_tree_nodes
17-Sep-2025 10:52:19 * [new branch]      feature/JAL-4548_show_PDBID_metadata_for_annot_tree -> origin/feature/JAL-4548_show_PDBID_metadata_for_annot_tree
17-Sep-2025 10:52:19 * [new branch]      feature/JAL-4583_incorrect_seq_count_ss_consensus -> origin/feature/JAL-4583_incorrect_seq_count_ss_consensus
17-Sep-2025 10:52:19 * [new branch]      feature/JAL_4542_highlight_selected_annot_labels_tree_nodes -> origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes
17-Sep-2025 10:52:19    f2ebc57..1d05b7e  feature/JAL_4548_show_PDBID_metadata_for_annot_tree -> origin/feature/JAL_4548_show_PDBID_metadata_for_annot_tree
17-Sep-2025 10:52:19 * [new branch]      features/JAL-4219_extended_fasta_rna_ss -> origin/features/JAL-4219_extended_fasta_rna_ss
17-Sep-2025 10:52:19 * [new branch]      features/JAL-4587_colour_group_annotation -> origin/features/JAL-4587_colour_group_annotation
17-Sep-2025 10:52:19 * [new branch]      improvement/JAL-4354_allow_many_structures_to_be_loaded_and_viewed_via_command_line -> origin/improvement/JAL-4354_allow_many_structures_to_be_loaded_and_viewed_via_command_line
17-Sep-2025 10:52:19    19317e1..4a59ca7  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
17-Sep-2025 10:52:19    20d3b89..f0d0210  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
17-Sep-2025 10:52:19 * [new branch]      improvement/JAL-4560_handle_relative_paths_in_jvl_files -> origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files
17-Sep-2025 10:52:19 * [new branch]      improvement/JAL-4570_show_tree_above_alignmentview -> origin/improvement/JAL-4570_show_tree_above_alignmentview
17-Sep-2025 10:52:19 * [new branch]      patch/JAL-3987_pergroup_annotation_consensus -> origin/patch/JAL-3987_pergroup_annotation_consensus
17-Sep-2025 10:52:19 * [new branch]      patch/JAL-4414_for_2_11_5_Branch -> origin/patch/JAL-4414_for_2_11_5_Branch
17-Sep-2025 10:52:19    5b3d6da..d7fbd2a  patch/JAL-4555_sort_by_descr -> origin/patch/JAL-4555_sort_by_descr
17-Sep-2025 10:52:19 * [new branch]      patch/JAL-4590_remove_isBlank_use -> origin/patch/JAL-4590_remove_isBlank_use
17-Sep-2025 10:52:19 * [new branch]      patch_bits/JAL-4590_isBlank_PDB_ChainIssue -> origin/patch_bits/JAL-4590_isBlank_PDB_ChainIssue
17-Sep-2025 10:52:19    dd2df48..147e80c  releases/Release_2_11_4_Branch -> origin/releases/Release_2_11_4_Branch
17-Sep-2025 10:52:19 * [new branch]      releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch
17-Sep-2025 10:52:19 * [new branch]      spike/JAL-4576_ligysis_exploration -> origin/spike/JAL-4576_ligysis_exploration
17-Sep-2025 10:52:19 * [new branch]      update/JAL-4243_biotools_json_record -> origin/update/JAL-4243_biotools_json_record
17-Sep-2025 10:52:19 * [new tag]         Release_2_11_5_0 -> Release_2_11_5_0
17-Sep-2025 10:52:19 error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
17-Sep-2025 10:52:20 Already on 'main'
17-Sep-2025 10:52:20 Your branch is behind 'origin/main' by 378 commits, and can be fast-forwarded.
17-Sep-2025 10:52:20   (use "git pull" to update your local branch)
17-Sep-2025 10:52:20 HEAD is now at 87afc89 Merge tag 'Release_2_11_5_0'
17-Sep-2025 10:52:20 Updated source code to revision: 87afc897f4ab4cf704d7e1c000421e81e0464919
17-Sep-2025 10:52:20 Finished task 'Checkout Default Repository' with result: Success
17-Sep-2025 10:52:20 Running pre-build action: VCS Version Collector
17-Sep-2025 10:52:20 Running pre-build action: Artifactory Release Staging
17-Sep-2025 10:52:20 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
17-Sep-2025 10:52:20 Bamboo Artifactory Plugin version: 2.6.2
17-Sep-2025 10:52:20
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - Clover and Tests #705 (JB-GDB-JOB1-705)'
... 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
... using extra environment variables:
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17-Sep-2025 10:52:20 444
17-Sep-2025 10:52:22
17-Sep-2025 10:52:22 > Configure project :
17-Sep-2025 10:52:22 Using properties from file './utils/channels/default/channel_gradle.properties'
17-Sep-2025 10:52:22 JALVIEW_VERSION is set to '2.11.5.0'
17-Sep-2025 10:52:22 HEADLESS BUILD
17-Sep-2025 10:52:22 J2S ENABLED
17-Sep-2025 10:52:22 Using a LOCAL profile.
17-Sep-2025 10:52:22 eclipseDir exists
17-Sep-2025 10:52:23
17-Sep-2025 10:52:23 > Task :clean
17-Sep-2025 10:52:23 > Task :cleanClover
17-Sep-2025 10:52:23 > Task :cleanTest UP-TO-DATE
17-Sep-2025 10:52:25
17-Sep-2025 10:52:25 > Task :cloverInstrJava
17-Sep-2025 10:52:25 Clover: About to instrument 1106 files
17-Sep-2025 10:52:25 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
17-Sep-2025 10:52:25 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover.db'.
17-Sep-2025 10:52:25 Processing files at 1.9 source level.
17-Sep-2025 10:52:29 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?
17-Sep-2025 10:52:29 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?
17-Sep-2025 10:52:29 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?
17-Sep-2025 10:52:29 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?
17-Sep-2025 10:52:29 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?
17-Sep-2025 10:52:29 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?
17-Sep-2025 10:52:29 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?
17-Sep-2025 10:52:36 Clover all over. Instrumented 1106 files (112 packages).
17-Sep-2025 10:52:38
17-Sep-2025 10:52:38 > Task :cloverInstrTests
17-Sep-2025 10:52:38 Clover: About to instrument test files
17-Sep-2025 10:52:38 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
17-Sep-2025 10:52:38 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover.db'.
17-Sep-2025 10:52:38 Processing files at 1.9 source level.
17-Sep-2025 10:52:41 Clover all over. Instrumented 293 files (52 packages).
17-Sep-2025 10:52:41 1618 test methods detected.
17-Sep-2025 10:52:41
17-Sep-2025 10:52:41 > Task :cloverInstr
17-Sep-2025 10:52:43
17-Sep-2025 10:52:43 > Task :compileCloverJava
17-Sep-2025 10:52:43 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
17-Sep-2025 10:52:43   - 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.
17-Sep-2025 10:52:43   - 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.
17-Sep-2025 10:52:43   - 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.
17-Sep-2025 10:52:43 Setting target compatibility to 11
17-Sep-2025 10:53:03 Note: Some input files use or override a deprecated API.
17-Sep-2025 10:53:03 Note: Recompile with -Xlint:deprecation for details.
17-Sep-2025 10:53:03 Note: Some input files use unchecked or unsafe operations.
17-Sep-2025 10:53:03 Note: Recompile with -Xlint:unchecked for details.
17-Sep-2025 10:53:09
17-Sep-2025 10:53:09 > Task :processCloverResources NO-SOURCE
17-Sep-2025 10:53:09 > Task :cloverClasses
17-Sep-2025 10:53:10 > Task :copyHelp
17-Sep-2025 10:53:11 > Task :buildIndices
17-Sep-2025 10:53:11 > Task :copyResources
17-Sep-2025 10:53:11 > Task :copyChannelResources
17-Sep-2025 10:53:11
17-Sep-2025 10:53:11 > Task :createBuildProperties
17-Sep-2025 10:53:11 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
17-Sep-2025 10:53:11   - 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.
17-Sep-2025 10:53:11
17-Sep-2025 10:53:11 > Task :buildResources
17-Sep-2025 10:53:11 > Task :copyDocs
17-Sep-2025 10:53:11
17-Sep-2025 10:53:11 > Task :convertMdFiles
17-Sep-2025 10:53:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
17-Sep-2025 10:53:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/releaseprocess.html
17-Sep-2025 10:53:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
17-Sep-2025 10:53:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/building.html
17-Sep-2025 10:53:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/jalview-projects.html
17-Sep-2025 10:53:11
17-Sep-2025 10:53:11 > Task :releasesTemplates
17-Sep-2025 10:53:11 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
17-Sep-2025 10:53:11   - 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.
17-Sep-2025 10:53:11   - 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.
17-Sep-2025 10:53:11 Stripping rc/test/etc for TEST
17-Sep-2025 10:53:11 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
17-Sep-2025 10:53:11
17-Sep-2025 10:53:11 > Task :prepare
17-Sep-2025 10:53:13
17-Sep-2025 10:53:13 > Task :compileJava
17-Sep-2025 10:53:13 Setting target compatibility to 11
17-Sep-2025 10:53:20 Note: Some input files use or override a deprecated API.
17-Sep-2025 10:53:20 Note: Recompile with -Xlint:deprecation for details.
17-Sep-2025 10:53:20 Note: Some input files use unchecked or unsafe operations.
17-Sep-2025 10:53:20 Note: Recompile with -Xlint:unchecked for details.
17-Sep-2025 10:53:22
17-Sep-2025 10:53:22 > Task :compileTestJava
17-Sep-2025 10:53:22 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
17-Sep-2025 10:53:22   - 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.
17-Sep-2025 10:53:22   - 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.
17-Sep-2025 10:53:22 Setting target compatibility to 11
17-Sep-2025 10:53:27 Note: Some input files use or override a deprecated API.
17-Sep-2025 10:53:27 Note: Recompile with -Xlint:deprecation for details.
17-Sep-2025 10:53:27 Note: Some input files use unchecked or unsafe operations.
17-Sep-2025 10:53:27 Note: Recompile with -Xlint:unchecked for details.
17-Sep-2025 10:53:28
17-Sep-2025 10:53:28 > Task :processTestResources
17-Sep-2025 10:53:28 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
17-Sep-2025 10:53:28   - 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.
17-Sep-2025 10:53:28   - 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.
17-Sep-2025 10:53:28   - 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.
17-Sep-2025 10:53:28   - 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.
17-Sep-2025 10:53:28   - 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.
17-Sep-2025 10:53:28   - 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.
17-Sep-2025 10:53:28   - 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.
17-Sep-2025 10:53:28   - 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.
17-Sep-2025 10:53:28
17-Sep-2025 10:53:28 > Task :testClasses
17-Sep-2025 10:53:30
17-Sep-2025 10:53:30 > Task :testTask0
17-Sep-2025 10:53:30 Running tests WITH clover
17-Sep-2025 10:53:33 WARNING: An illegal reflective access operation has occurred
17-Sep-2025 10:53:33 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
17-Sep-2025 10:53:33 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
17-Sep-2025 10:53:33 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
17-Sep-2025 10:53:33 WARNING: All illegal access operations will be denied in a future release
17-Sep-2025 10:57:50
17-Sep-2025 10:57:50 > Task :testTask1
17-Sep-2025 10:57:50 Running tests WITH clover
17-Sep-2025 10:57:52 WARNING: An illegal reflective access operation has occurred
17-Sep-2025 10:57:52 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
17-Sep-2025 10:57:52 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
17-Sep-2025 10:57:52 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
17-Sep-2025 10:57:52 WARNING: All illegal access operations will be denied in a future release
17-Sep-2025 11:00:18
17-Sep-2025 11:00:18 > Task :testTask2
17-Sep-2025 11:00:18 Running tests WITH clover
17-Sep-2025 11:00:23
17-Sep-2025 11:00:23 > Task :testTask3
17-Sep-2025 11:00:23 Running tests WITH clover
17-Sep-2025 11:00:24 WARNING: An illegal reflective access operation has occurred
17-Sep-2025 11:00:24 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
17-Sep-2025 11:00:24 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
17-Sep-2025 11:00:24 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
17-Sep-2025 11:00:24 WARNING: All illegal access operations will be denied in a future release
17-Sep-2025 11:01:17
17-Sep-2025 11:01:17 > Task :test NO-SOURCE
17-Sep-2025 11:01:17 ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
17-Sep-2025 11:01:17 │jalview:testTask0 results: SUCCESS (1819 tests, 1819 successes, 0 failures, 0 skipped) in 4 minutes, 19.297 seconds│
17-Sep-2025 11:01:17 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask0/index.html│
17-Sep-2025 11:01:17 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
17-Sep-2025 11:01:17 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 28.129 seconds    │
17-Sep-2025 11:01:17 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask1/index.html│
17-Sep-2025 11:01:17 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
17-Sep-2025 11:01:17 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.026 seconds                  │
17-Sep-2025 11:01:17 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask2/index.html│
17-Sep-2025 11:01:17 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
17-Sep-2025 11:01:17 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 56.473 seconds               │
17-Sep-2025 11:01:17 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask3/index.html│
17-Sep-2025 11:01:17 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
17-Sep-2025 11:01:17 │OVERALL: results: SUCCESS (1907 tests, 1907 successes, 0 failures, 0 skipped) in 6 minutes, 107.925 seconds        │
17-Sep-2025 11:01:17 └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
17-Sep-2025 11:01:17
17-Sep-2025 11:01:17 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
17-Sep-2025 11:01:17
17-Sep-2025 11:01:17 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
17-Sep-2025 11:01:17
17-Sep-2025 11:01:17 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
17-Sep-2025 11:01:17
17-Sep-2025 11:01:17 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
17-Sep-2025 11:01:17 Please consult deprecation warnings for more details.
17-Sep-2025 11:01:17
17-Sep-2025 11:01:17 BUILD SUCCESSFUL in 8m 56s
17-Sep-2025 11:01:17 21 actionable tasks: 20 executed, 1 up-to-date
17-Sep-2025 11:01:18 Finished task 'Run tests with openclover under gradle' with result: Success
17-Sep-2025 11:01:18 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
17-Sep-2025 11:01:18 Bamboo Artifactory Plugin version: 2.6.2
17-Sep-2025 11:01:18
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - Clover and Tests #705 (JB-GDB-JOB1-705)'
... 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
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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=87afc897f4ab4cf704d7e1c000421e81e0464919
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB-JOB1-705
bamboo_repository_46498240_git_username=
JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048
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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=705
PWD=/
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bamboo_repository_46498240_previous_revision_number=a07a210e39b574048817742f680ad4bbcebb590c
bamboo_shortJobName=Clover and Tests
bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB-JOB1-705
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=87afc897f4ab4cf704d7e1c000421e81e0464919
bamboo_buildTimeStamp=2025-09-17T10:49:26.247+01:00
bamboo_repository_previous_revision_number=a07a210e39b574048817742f680ad4bbcebb590c
bamboo_repository_46498240_revision_number=87afc897f4ab4cf704d7e1c000421e81e0464919
bamboo_planRepository_previousRevision=a07a210e39b574048817742f680ad4bbcebb590c
bamboo_repository_git_branch=main
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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=87afc897f4ab4cf704d7e1c000421e81e0464919
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_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=a07a210e39b574048817742f680ad4bbcebb590c
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
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17-Sep-2025 11:01:18 444
17-Sep-2025 11:01:24
17-Sep-2025 11:01:24 > Configure project :
17-Sep-2025 11:01:24 Using properties from file './utils/channels/default/channel_gradle.properties'
17-Sep-2025 11:01:24 JALVIEW_VERSION is set to '2.11.5.0'
17-Sep-2025 11:01:24 HEADLESS BUILD
17-Sep-2025 11:01:24 J2S ENABLED
17-Sep-2025 11:01:25 Using a LOCAL profile.
17-Sep-2025 11:01:26 eclipseDir exists
17-Sep-2025 11:01:29
17-Sep-2025 11:01:29 > Task :cloverHtmlReport
17-Sep-2025 11:01:29 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
17-Sep-2025 11:01:30 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/clover'
17-Sep-2025 11:02:21 Done. Processed 116 packages in 51220ms (441ms per package).
17-Sep-2025 11:02:27
17-Sep-2025 11:02:27 > Task :cloverXmlReport
17-Sep-2025 11:02:27 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
17-Sep-2025 11:02:28 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/clover/clover.xml'
17-Sep-2025 11:02:29
17-Sep-2025 11:02:29 > Task :cloverReport
17-Sep-2025 11:02:29
17-Sep-2025 11:02:29 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
17-Sep-2025 11:02:29
17-Sep-2025 11:02:29 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
17-Sep-2025 11:02:29
17-Sep-2025 11:02:29 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
17-Sep-2025 11:02:29
17-Sep-2025 11:02:29 BUILD SUCCESSFUL in 1m 10s
17-Sep-2025 11:02:29 2 actionable tasks: 2 executed
17-Sep-2025 11:02:29 Finished task 'Clover Report' with result: Success
17-Sep-2025 11:02:29 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
17-Sep-2025 11:02:29 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1...
17-Sep-2025 11:02:30 Finished task 'TestNG Parser' with result: Success
17-Sep-2025 11:02:30 Running post build plugin 'NCover Results Collector'
17-Sep-2025 11:02:30 Running post build plugin 'Artifact Copier'
17-Sep-2025 11:02:30 Publishing an artifact: Clover Report (System)
17-Sep-2025 11:02:32 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.913 s
17-Sep-2025 11:02:32 Publishing an artifact: TestNG report
17-Sep-2025 11:02:32 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.
17-Sep-2025 11:02:32 The artifact hasn't been successfully published after 4.883 ms
17-Sep-2025 11:02:32 Running post build plugin 'Artifactory Release Management Staging'
17-Sep-2025 11:02:32 Running post build plugin 'Artifactory Build Info Copier'
17-Sep-2025 11:02:32 Running post build plugin 'Artifactory Gradle Properties Info Copier'
17-Sep-2025 11:02:32 Running post build plugin 'npm Cache Cleanup'
17-Sep-2025 11:02:32 Running post build plugin 'Clover Results Collector'
17-Sep-2025 11:02:33 Running post build plugin 'Docker Container Cleanup'
17-Sep-2025 11:02:33 Finalising the build...
17-Sep-2025 11:02:33 Stopping timer.
17-Sep-2025 11:02:33 Build JB-GDB-JOB1-705 completed.
17-Sep-2025 11:02:33 Running on server: post build plugin 'NCover Results Collector'
17-Sep-2025 11:02:33 Running on server: post build plugin 'Build Hanging Detection Configuration'
17-Sep-2025 11:02:33 Running on server: post build plugin 'Clover Delta Calculator'
17-Sep-2025 11:02:33 Running on server: post build plugin 'Maven Dependencies Postprocessor'
17-Sep-2025 11:02:33 All post build plugins have finished
17-Sep-2025 11:02:33 Generating build results summary...
17-Sep-2025 11:02:33 Saving build results to disk...
17-Sep-2025 11:02:33 Logging substituted variables...
17-Sep-2025 11:02:33 Indexing build results...
17-Sep-2025 11:02:33 Finished building JB-GDB-JOB1-705.