Build #2

Build: #2 failed

Job: Clover and Tests failed

Stages & jobs

  1. Default Stage

Build log

The build generated 360 lines of output. Download or view full build log

27-May-2026 17:16:24 Build Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #2 (JB-GDB747-JOB1-2) started building on agent Default Agent
27-May-2026 17:16:24
27-May-2026 17:16:24 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1
27-May-2026 17:16:24 Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #2 (JB-GDB747-JOB1-2)
27-May-2026 17:16:24 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
27-May-2026 17:16:24 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1
27-May-2026 17:16:24 Updating source code to revision: 378b2a60f0e594a59de7f5ac31f20b1148702c0a
27-May-2026 17:16:24 Fetching 'refs/heads/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts' from 'https://gitlab.jalview.org/jalview/jalview.git'.
27-May-2026 17:16:24 Checking out revision 378b2a60f0e594a59de7f5ac31f20b1148702c0a.
27-May-2026 17:16:24 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
27-May-2026 17:16:24    0d6f149..378b2a6  patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts -> origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
27-May-2026 17:16:24    b05bef7..4290899  epic/JAL-4320_JAL-4644_refactor_directory_structure -> origin/epic/JAL-4320_JAL-4644_refactor_directory_structure
27-May-2026 17:16:24 * [new branch]      feature/JAL-4478_multimer_pae_import -> origin/feature/JAL-4478_multimer_pae_import
27-May-2026 17:16:24 * [new branch]      patch/JAL-4410_multimers_from_3dbeacons -> origin/patch/JAL-4410_multimers_from_3dbeacons
27-May-2026 17:16:24 * [new branch]      saved/JAL-4320_JAL-4644_refactor_directory_structure-with_nearly_working_openclover -> origin/saved/JAL-4320_JAL-4644_refactor_directory_structure-with_nearly_working_openclover
27-May-2026 17:16:25 Already on 'patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts'
27-May-2026 17:16:25 Your branch is behind 'origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts' by 1 commit, and can be fast-forwarded.
27-May-2026 17:16:25   (use "git pull" to update your local branch)
27-May-2026 17:16:25 HEAD is now at 378b2a6 JAL-4658 first working prototype - 'provider' labels are the sequence IDs when no provider exists for a track - lots of docs and UI changes since many cases still refer to secondary structure in the treeviewer
27-May-2026 17:16:25 Updated source code to revision: 378b2a60f0e594a59de7f5ac31f20b1148702c0a
27-May-2026 17:16:25 Finished task 'Checkout Default Repository' with result: Success
27-May-2026 17:16:25 Running pre-build action: VCS Version Collector
27-May-2026 17:16:25 Running pre-build action: Artifactory Release Staging
27-May-2026 17:16:25 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
27-May-2026 17:16:25 Bamboo Artifactory Plugin version: 2.6.2
27-May-2026 17:16:25
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #2 (JB-GDB747-JOB1-2)'
... running command line:
/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test
... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_repository_revision_number=378b2a60f0e594a59de7f5ac31f20b1148702c0a
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB747-JOB1-2
JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048
bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1
bamboo_planRepository_1_name=Jalview Gitlab
bamboo_buildKey=JB-GDB747-JOB1
bamboo_shortPlanName=patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_planRepository_name=Jalview Gitlab
LOGNAME=bamboo
bamboo_buildNumber=2
PWD=/
bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse
bamboo_shortJobName=Clover and Tests
bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB747-JOB1-2
bamboo_repository_48169034_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
SHELL=/bin/bash
bamboo_agentId=196609
bamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_shortPlanKey=GDB747
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=378b2a60f0e594a59de7f5ac31f20b1148702c0a
bamboo_buildTimeStamp=2026-05-27T17:16:24.074+01:00
bamboo_repository_previous_revision_number=0d6f14957df15006b71decb225c4c15ca80eead6
bamboo_planRepository_previousRevision=0d6f14957df15006b71decb225c4c15ca80eead6
bamboo_repository_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_buildResultKey=JB-GDB747-JOB1-2
bamboo_repository_branch_name=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=378b2a60f0e594a59de7f5ac31f20b1148702c0a
SHLVL=1
bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant
bamboo_repository_48169034_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_repository_name=Jalview Gitlab
JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/
LANG=en_GB.UTF-8
bamboo_buildFailed=false
bamboo_repository_48169034_branch_name=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk
bamboo_planRepository_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609
bamboo_capability_system_git_executable=/bin/git
bamboo_repository_git_username=
bamboo_planRepository_1_previousRevision=0d6f14957df15006b71decb225c4c15ca80eead6
bamboo_planRepository_branchDisplayName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_repository_48169034_name=Jalview Gitlab
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_repository_48169034_previous_revision_number=0d6f14957df15006b71decb225c4c15ca80eead6
_=/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-47972499
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_repository_48169034_revision_number=378b2a60f0e594a59de7f5ac31f20b1148702c0a
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-GDB747-JOB1
bamboo_planKey=JB-GDB747
bamboo_repository_48169034_git_username=
bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_planRepository_username=
HOME=/home/bamboo
bamboo_planRepository_1_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
27-May-2026 17:16:25 2414
27-May-2026 17:16:26 Starting a Gradle Daemon (subsequent builds will be faster)
27-May-2026 17:16:32
27-May-2026 17:16:32 > Configure project :
27-May-2026 17:16:32 Using properties from file './utils/channels/default/channel_gradle.properties'
27-May-2026 17:16:32 JALVIEW_VERSION is set to '2.12.0'
27-May-2026 17:16:32 HEADLESS BUILD
27-May-2026 17:16:32 J2S ENABLED
27-May-2026 17:16:32 Using a LOCAL profile.
27-May-2026 17:16:33 eclipseDir exists
27-May-2026 17:16:34
27-May-2026 17:16:34 > Task :clean
27-May-2026 17:16:34 > Task :cleanClover
27-May-2026 17:16:34 > Task :cleanTest UP-TO-DATE
27-May-2026 17:16:36
27-May-2026 17:16:36 > Task :cloverInstrJava
27-May-2026 17:16:36 Clover: About to instrument 1256 files
27-May-2026 17:16:36 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
27-May-2026 17:16:36 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover.db'.
27-May-2026 17:16:36 Processing files at 1.9 source level.
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:39 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?
27-May-2026 17:16:45 Clover all over. Instrumented 1256 files (133 packages).
27-May-2026 17:16:48
27-May-2026 17:16:48 > Task :cloverInstrTests
27-May-2026 17:16:48 Clover: About to instrument test files
27-May-2026 17:16:48 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
27-May-2026 17:16:48 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover.db'.
27-May-2026 17:16:48 Processing files at 1.9 source level.
27-May-2026 17:16:50 Clover all over. Instrumented 315 files (58 packages).
27-May-2026 17:16:50 1771 test methods detected.
27-May-2026 17:16:50
27-May-2026 17:16:50 > Task :cloverInstr
27-May-2026 17:16:52
27-May-2026 17:16:52 > Task :compileCloverJava
27-May-2026 17:16:52 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
27-May-2026 17:16:52   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:16:52   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:16:52   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:16:52 Setting target compatibility to 11
27-May-2026 17:17:17 Note: Some input files use or override a deprecated API.
27-May-2026 17:17:17 Note: Recompile with -Xlint:deprecation for details.
27-May-2026 17:17:17 Note: Some input files use unchecked or unsafe operations.
27-May-2026 17:17:17 Note: Recompile with -Xlint:unchecked for details.
27-May-2026 17:17:23
27-May-2026 17:17:23 > Task :processCloverResources NO-SOURCE
27-May-2026 17:17:24 > Task :cloverClasses
27-May-2026 17:17:24 > Task :copyHelp
27-May-2026 17:17:25 > Task :buildIndices
27-May-2026 17:17:25 > Task :copyResources
27-May-2026 17:17:25 > Task :copyChannelResources
27-May-2026 17:17:25
27-May-2026 17:17:25 > Task :createBuildProperties
27-May-2026 17:17:25 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
27-May-2026 17:17:25   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:17:25
27-May-2026 17:17:25 > Task :buildResources
27-May-2026 17:17:25 > Task :copyDocs
27-May-2026 17:17:26
27-May-2026 17:17:26 > Task :convertMdFiles
27-May-2026 17:17:26 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
27-May-2026 17:17:26 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/releaseprocess.html
27-May-2026 17:17:26 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
27-May-2026 17:17:26 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
27-May-2026 17:17:26 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/building.html
27-May-2026 17:17:26 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/addingWebClient.html
27-May-2026 17:17:26 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/jalview-projects.html
27-May-2026 17:17:26 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
27-May-2026 17:17:26
27-May-2026 17:17:26 > Task :releasesTemplates
27-May-2026 17:17:26 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
27-May-2026 17:17:26   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:17:26   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:17:26 Stripping rc/test/etc for TEST
27-May-2026 17:17:26 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
27-May-2026 17:17:26
27-May-2026 17:17:26 > Task :prepare
27-May-2026 17:17:28
27-May-2026 17:17:28 > Task :compileJava
27-May-2026 17:17:28 Setting target compatibility to 11
27-May-2026 17:17:35 Note: Some input files use or override a deprecated API.
27-May-2026 17:17:35 Note: Recompile with -Xlint:deprecation for details.
27-May-2026 17:17:35 Note: Some input files use unchecked or unsafe operations.
27-May-2026 17:17:35 Note: Recompile with -Xlint:unchecked for details.
27-May-2026 17:17:39
27-May-2026 17:17:39 > Task :compileTestJava
27-May-2026 17:17:39 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
27-May-2026 17:17:39   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:17:39   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:17:39 Setting target compatibility to 11
27-May-2026 17:17:45 Note: Some input files use or override a deprecated API.
27-May-2026 17:17:45 Note: Recompile with -Xlint:deprecation for details.
27-May-2026 17:17:45 Note: Some input files use unchecked or unsafe operations.
27-May-2026 17:17:45 Note: Recompile with -Xlint:unchecked for details.
27-May-2026 17:17:47
27-May-2026 17:17:47 > Task :processTestResources
27-May-2026 17:17:47 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
27-May-2026 17:17:47   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:17:47   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:17:47   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:17:47   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:17:47   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:17:47   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:17:47   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-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.
27-May-2026 17:17:47
27-May-2026 17:17:47 > Task :testClasses
27-May-2026 17:17:49
27-May-2026 17:17:49 > Task :testTask0
27-May-2026 17:17:49 Running tests WITH clover
27-May-2026 17:17:50 WARNING: An illegal reflective access operation has occurred
27-May-2026 17:17:50 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
27-May-2026 17:17:50 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
27-May-2026 17:17:50 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
27-May-2026 17:17:50 WARNING: All illegal access operations will be denied in a future release
27-May-2026 17:18:37
27-May-2026 17:18:37 Gradle suite > Gradle test > jalview.bin.CommandLineOperations > testHeadlessModeOutputOperations[5](headless -open examples/uniref50.fa,  -svg, test/jalview/bin/test_uniref50_out.svg, false, 4096, 15000, null) FAILED
27-May-2026 17:18:37     java.lang.AssertionError: expected <at least 4096> but was </srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/test/jalview/bin/test_uniref50_out.svg><at least 4096>
27-May-2026 17:18:37         at org.testng.FileAssert.fail(FileAssert.java:263)
27-May-2026 17:18:37         at org.testng.FileAssert.failFile(FileAssert.java:277)
27-May-2026 17:18:37         at org.testng.FileAssert.assertMinLength(FileAssert.java:119)
27-May-2026 17:18:37         at org.testng.FileAssert.assertMinLength(FileAssert.java:129)
27-May-2026 17:18:37         at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:345)
27-May-2026 17:19:42
27-May-2026 17:19:42 Gradle suite > Gradle test > jalview.gui.CalculationChooserTest > testGetApplicableScoreModels FAILED
27-May-2026 17:19:42     java.lang.AssertionError: expected [5] but found [6]
27-May-2026 17:19:42         at org.testng.Assert.fail(Assert.java:110)
27-May-2026 17:19:42         at org.testng.Assert.failNotEquals(Assert.java:1413)
27-May-2026 17:19:42         at org.testng.Assert.assertEqualsImpl(Assert.java:149)
27-May-2026 17:19:42         at org.testng.Assert.assertEquals(Assert.java:131)
27-May-2026 17:19:42         at org.testng.Assert.assertEquals(Assert.java:1240)
27-May-2026 17:19:42         at org.testng.Assert.assertEquals(Assert.java:1274)
27-May-2026 17:19:42         at jalview.gui.CalculationChooserTest.__CLR4_4_1p7y2xs446q(CalculationChooserTest.java:59)
27-May-2026 17:19:42         at jalview.gui.CalculationChooserTest.testGetApplicableScoreModels(CalculationChooserTest.java:48)
27-May-2026 17:20:18 [151.256s][warning][gc,alloc] AWT-EventQueue-0: Retried waiting for GCLocker too often allocating 135080516 words
27-May-2026 17:22:36
27-May-2026 17:22:36 2104 tests completed, 2 failed
27-May-2026 17:22:37 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/tests/testTask0/index.html
27-May-2026 17:22:39
27-May-2026 17:22:39 > Task :testTask1
27-May-2026 17:22:39 Running tests WITH clover
27-May-2026 17:22:40 WARNING: An illegal reflective access operation has occurred
27-May-2026 17:22:40 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
27-May-2026 17:22:40 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
27-May-2026 17:22:40 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
27-May-2026 17:22:40 WARNING: All illegal access operations will be denied in a future release
27-May-2026 17:24:53
27-May-2026 17:24:53 > Task :testTask2
27-May-2026 17:24:53 Running tests WITH clover
27-May-2026 17:24:54 WARNING: An illegal reflective access operation has occurred
27-May-2026 17:24:54 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
27-May-2026 17:24:54 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
27-May-2026 17:24:54 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
27-May-2026 17:24:54 WARNING: All illegal access operations will be denied in a future release
27-May-2026 17:24:58
27-May-2026 17:24:58 > Task :testTask3
27-May-2026 17:24:58 Running tests WITH clover
27-May-2026 17:25:00 WARNING: An illegal reflective access operation has occurred
27-May-2026 17:25:00 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
27-May-2026 17:25:00 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
27-May-2026 17:25:00 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
27-May-2026 17:25:00 WARNING: All illegal access operations will be denied in a future release
27-May-2026 17:25:19
27-May-2026 17:25:19 > Task :test NO-SOURCE
27-May-2026 17:25:19
27-May-2026 17:25:19 FAILURE: Build failed with an exception.
27-May-2026 17:25:19
27-May-2026 17:25:19 * Where:
27-May-2026 17:25:19 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build.gradle' line: 1964
27-May-2026 17:25:19
27-May-2026 17:25:19 * What went wrong:
27-May-2026 17:25:19 Failed tests!
27-May-2026 17:25:19
27-May-2026 17:25:19 * Try:
27-May-2026 17:25:19 > Run with --stacktrace option to get the stack trace.
27-May-2026 17:25:19 > Run with --info or --debug option to get more log output.
27-May-2026 17:25:19 > Run with --scan to get full insights.
27-May-2026 17:25:19
27-May-2026 17:25:19 * Get more help at https://help.gradle.org
27-May-2026 17:25:19
27-May-2026 17:25:19 BUILD FAILED in 8m 53s
27-May-2026 17:25:19 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
27-May-2026 17:25:19 │jalview:testTask0 results: FAILURE (2104 tests, 2102 successes, 2 failures, 0 skipped) in 4 minutes, 48.899 seconds   │
27-May-2026 17:25:19 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/tests/testTask0/index.html│
27-May-2026 17:25:19 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
27-May-2026 17:25:19 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 14.079 seconds       │
27-May-2026 17:25:19 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/tests/testTask1/index.html│
27-May-2026 17:25:19 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
27-May-2026 17:25:19 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 5.226 seconds                     │
27-May-2026 17:25:19 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/tests/testTask2/index.html│
27-May-2026 17:25:19 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
27-May-2026 17:25:19 │jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 22.445 seconds                  │
27-May-2026 17:25:19 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/tests/testTask3/index.html│
27-May-2026 17:25:19 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
27-May-2026 17:25:19 │OVERALL: results: FAILURE (2181 tests, 2178 successes, 2 failures, 1 skipped) in 6 minutes, 90.649 seconds            │
27-May-2026 17:25:19 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
27-May-2026 17:25:19
27-May-2026 17:25:19 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
27-May-2026 17:25:19
27-May-2026 17:25:19 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
27-May-2026 17:25:19
27-May-2026 17:25:19 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
27-May-2026 17:25:19
27-May-2026 17:25:19 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
27-May-2026 17:25:19 Please consult deprecation warnings for more details.
27-May-2026 17:25:19 21 actionable tasks: 20 executed, 1 up-to-date
27-May-2026 17:25:19
27-May-2026 17:25:19 Failing task since return code of [/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test] was 1 while expected 0
27-May-2026 17:25:19 Finished task 'Run tests with openclover under gradle' with result: Failed
27-May-2026 17:25:19 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
27-May-2026 17:25:19 Bamboo Artifactory Plugin version: 2.6.2
27-May-2026 17:25:19
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #2 (JB-GDB747-JOB1-2)'
... running command line:
/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport
... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_repository_revision_number=378b2a60f0e594a59de7f5ac31f20b1148702c0a
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB747-JOB1-2
JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048
bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1
bamboo_planRepository_1_name=Jalview Gitlab
bamboo_buildKey=JB-GDB747-JOB1
bamboo_shortPlanName=patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_planRepository_name=Jalview Gitlab
LOGNAME=bamboo
bamboo_buildNumber=2
PWD=/
bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse
bamboo_shortJobName=Clover and Tests
bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB747-JOB1-2
bamboo_repository_48169034_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
SHELL=/bin/bash
bamboo_agentId=196609
bamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_shortPlanKey=GDB747
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=378b2a60f0e594a59de7f5ac31f20b1148702c0a
bamboo_buildTimeStamp=2026-05-27T17:16:24.074+01:00
bamboo_repository_previous_revision_number=0d6f14957df15006b71decb225c4c15ca80eead6
bamboo_planRepository_previousRevision=0d6f14957df15006b71decb225c4c15ca80eead6
bamboo_repository_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_buildResultKey=JB-GDB747-JOB1-2
bamboo_repository_branch_name=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=378b2a60f0e594a59de7f5ac31f20b1148702c0a
SHLVL=1
bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant
bamboo_repository_48169034_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_repository_name=Jalview Gitlab
bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test
JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/
LANG=en_GB.UTF-8
bamboo_buildFailed=true
bamboo_repository_48169034_branch_name=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk
bamboo_planRepository_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609
bamboo_jobFailed=true
bamboo_capability_system_git_executable=/bin/git
bamboo_repository_git_username=
bamboo_planRepository_1_previousRevision=0d6f14957df15006b71decb225c4c15ca80eead6
bamboo_planRepository_branchDisplayName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_repository_48169034_name=Jalview Gitlab
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
bamboo_repository_48169034_previous_revision_number=0d6f14957df15006b71decb225c4c15ca80eead6
_=/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-47972499
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_repository_48169034_revision_number=378b2a60f0e594a59de7f5ac31f20b1148702c0a
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-GDB747-JOB1
bamboo_planKey=JB-GDB747
bamboo_repository_48169034_git_username=
bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git
bamboo_planRepository_username=
HOME=/home/bamboo
bamboo_planRepository_1_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
27-May-2026 17:25:19 2414
27-May-2026 17:25:25
27-May-2026 17:25:25 > Configure project :
27-May-2026 17:25:25 Using properties from file './utils/channels/default/channel_gradle.properties'
27-May-2026 17:25:25 JALVIEW_VERSION is set to '2.12.0'
27-May-2026 17:25:25 HEADLESS BUILD
27-May-2026 17:25:25 J2S ENABLED
27-May-2026 17:25:25 Using a LOCAL profile.
27-May-2026 17:25:26 eclipseDir exists
27-May-2026 17:25:28
27-May-2026 17:25:28 > Task :cloverHtmlReport
27-May-2026 17:25:28 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
27-May-2026 17:25:30 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/clover'
27-May-2026 17:26:26 Done. Processed 137 packages in 55753ms (406ms per package).
27-May-2026 17:26:32
27-May-2026 17:26:32 > Task :cloverXmlReport
27-May-2026 17:26:32 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
27-May-2026 17:26:33 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/clover/clover.xml'
27-May-2026 17:26:33
27-May-2026 17:26:33 > Task :cloverReport
27-May-2026 17:26:33
27-May-2026 17:26:33 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
27-May-2026 17:26:33
27-May-2026 17:26:33 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
27-May-2026 17:26:33
27-May-2026 17:26:33 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
27-May-2026 17:26:33
27-May-2026 17:26:33 BUILD SUCCESSFUL in 1m 14s
27-May-2026 17:26:33 2 actionable tasks: 2 executed
27-May-2026 17:26:34 Finished task 'Clover Report' with result: Success
27-May-2026 17:26:34 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
27-May-2026 17:26:34 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1...
27-May-2026 17:26:34 Failing task since 2 failing test cases were found.
27-May-2026 17:26:34 Finished task 'TestNG Parser' with result: Failed
27-May-2026 17:26:34 Running post build plugin 'NCover Results Collector'
27-May-2026 17:26:34 Running post build plugin 'Artifact Copier'
27-May-2026 17:26:34 Publishing an artifact: Clover Report (System)
27-May-2026 17:26:36 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.140 s
27-May-2026 17:26:36 Publishing an artifact: TestNG report
27-May-2026 17:26:36 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/tests/test does not exist.
27-May-2026 17:26:36 The artifact hasn't been successfully published after 3.955 ms
27-May-2026 17:26:36 Running post build plugin 'Artifactory Release Management Staging'
27-May-2026 17:26:36 Running post build plugin 'Artifactory Build Info Copier'
27-May-2026 17:26:36 Running post build plugin 'Artifactory Gradle Properties Info Copier'
27-May-2026 17:26:36 Running post build plugin 'npm Cache Cleanup'
27-May-2026 17:26:36 Running post build plugin 'Clover Results Collector'
27-May-2026 17:26:36 Running post build plugin 'Docker Container Cleanup'
27-May-2026 17:26:36 Finalising the build...
27-May-2026 17:26:36 Stopping timer.
27-May-2026 17:26:36 Build JB-GDB747-JOB1-2 completed.
27-May-2026 17:26:36 Running on server: post build plugin 'NCover Results Collector'
27-May-2026 17:26:36 Running on server: post build plugin 'Build Hanging Detection Configuration'
27-May-2026 17:26:36 Running on server: post build plugin 'Clover Delta Calculator'
27-May-2026 17:26:36 Running on server: post build plugin 'Maven Dependencies Postprocessor'
27-May-2026 17:26:36 All post build plugins have finished
27-May-2026 17:26:36 Generating build results summary...
27-May-2026 17:26:36 Saving build results to disk...
27-May-2026 17:26:37 Logging substituted variables...
27-May-2026 17:26:37 Indexing build results...
27-May-2026 17:26:37 Finished building JB-GDB747-JOB1-2.