simple 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 simple 27-May-2026 17:16:24 simple 27-May-2026 17:16:24 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1 simple 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) simple 27-May-2026 17:16:24 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 27-May-2026 17:16:24 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1 simple 27-May-2026 17:16:24 Updating source code to revision: 378b2a60f0e594a59de7f5ac31f20b1148702c0a simple 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'. simple 27-May-2026 17:16:24 Checking out revision 378b2a60f0e594a59de7f5ac31f20b1148702c0a. simple 27-May-2026 17:16:24 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 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 simple 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 simple 27-May-2026 17:16:24 * [new branch] feature/JAL-4478_multimer_pae_import -> origin/feature/JAL-4478_multimer_pae_import simple 27-May-2026 17:16:24 * [new branch] patch/JAL-4410_multimers_from_3dbeacons -> origin/patch/JAL-4410_multimers_from_3dbeacons simple 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 simple 27-May-2026 17:16:25 Already on 'patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts' simple 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. simple 27-May-2026 17:16:25 (use "git pull" to update your local branch) simple 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 simple 27-May-2026 17:16:25 Updated source code to revision: 378b2a60f0e594a59de7f5ac31f20b1148702c0a simple 27-May-2026 17:16:25 Finished task 'Checkout Default Repository' with result: Success simple 27-May-2026 17:16:25 Running pre-build action: VCS Version Collector simple 27-May-2026 17:16:25 Running pre-build action: Artifactory Release Staging simple 27-May-2026 17:16:25 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 27-May-2026 17:16:25 Bamboo Artifactory Plugin version: 2.6.2 command 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)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_repository_revision_number=378b2a60f0e594a59de7f5ac31f20b1148702c0a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB747-JOB1-2\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB747-JOB1\nbamboo_shortPlanName=patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB747-JOB1-2\nbamboo_repository_48169034_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_shortPlanKey=GDB747\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=378b2a60f0e594a59de7f5ac31f20b1148702c0a\nbamboo_buildTimeStamp=2026-05-27T17:16:24.074+01:00\nbamboo_repository_previous_revision_number=0d6f14957df15006b71decb225c4c15ca80eead6\nbamboo_planRepository_previousRevision=0d6f14957df15006b71decb225c4c15ca80eead6\nbamboo_repository_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_buildResultKey=JB-GDB747-JOB1-2\nbamboo_repository_branch_name=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=378b2a60f0e594a59de7f5ac31f20b1148702c0a\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169034_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_repository_48169034_branch_name=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=0d6f14957df15006b71decb225c4c15ca80eead6\nbamboo_planRepository_branchDisplayName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_repository_48169034_name=Jalview Gitlab\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_repository_48169034_previous_revision_number=0d6f14957df15006b71decb225c4c15ca80eead6\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-47972499\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169034_revision_number=378b2a60f0e594a59de7f5ac31f20b1148702c0a\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1\nbamboo_planKey=JB-GDB747\nbamboo_repository_48169034_git_username=\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 27-May-2026 17:16:25 2414 build 27-May-2026 17:16:26 Starting a Gradle Daemon (subsequent builds will be faster) build 27-May-2026 17:16:32 build 27-May-2026 17:16:32 > Configure project : build 27-May-2026 17:16:32 Using properties from file './utils/channels/default/channel_gradle.properties' build 27-May-2026 17:16:32 JALVIEW_VERSION is set to '2.12.0' build 27-May-2026 17:16:32 HEADLESS BUILD build 27-May-2026 17:16:32 J2S ENABLED build 27-May-2026 17:16:32 Using a LOCAL profile. build 27-May-2026 17:16:33 eclipseDir exists build 27-May-2026 17:16:34 build 27-May-2026 17:16:34 > Task :clean build 27-May-2026 17:16:34 > Task :cleanClover build 27-May-2026 17:16:34 > Task :cleanTest UP-TO-DATE build 27-May-2026 17:16:36 build 27-May-2026 17:16:36 > Task :cloverInstrJava build 27-May-2026 17:16:36 Clover: About to instrument 1256 files build 27-May-2026 17:16:36 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 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'. build 27-May-2026 17:16:36 Processing files at 1.9 source level. error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? error 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? build 27-May-2026 17:16:45 Clover all over. Instrumented 1256 files (133 packages). build 27-May-2026 17:16:48 build 27-May-2026 17:16:48 > Task :cloverInstrTests build 27-May-2026 17:16:48 Clover: About to instrument test files build 27-May-2026 17:16:48 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 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'. build 27-May-2026 17:16:48 Processing files at 1.9 source level. build 27-May-2026 17:16:50 Clover all over. Instrumented 315 files (58 packages). build 27-May-2026 17:16:50 1771 test methods detected. build 27-May-2026 17:16:50 build 27-May-2026 17:16:50 > Task :cloverInstr build 27-May-2026 17:16:52 build 27-May-2026 17:16:52 > Task :compileCloverJava build 27-May-2026 17:16:52 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 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. build 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. build 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. build 27-May-2026 17:16:52 Setting target compatibility to 11 error 27-May-2026 17:17:17 Note: Some input files use or override a deprecated API. error 27-May-2026 17:17:17 Note: Recompile with -Xlint:deprecation for details. error 27-May-2026 17:17:17 Note: Some input files use unchecked or unsafe operations. error 27-May-2026 17:17:17 Note: Recompile with -Xlint:unchecked for details. build 27-May-2026 17:17:23 build 27-May-2026 17:17:23 > Task :processCloverResources NO-SOURCE build 27-May-2026 17:17:24 > Task :cloverClasses build 27-May-2026 17:17:24 > Task :copyHelp build 27-May-2026 17:17:25 > Task :buildIndices build 27-May-2026 17:17:25 > Task :copyResources build 27-May-2026 17:17:25 > Task :copyChannelResources build 27-May-2026 17:17:25 build 27-May-2026 17:17:25 > Task :createBuildProperties build 27-May-2026 17:17:25 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 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. build 27-May-2026 17:17:25 build 27-May-2026 17:17:25 > Task :buildResources build 27-May-2026 17:17:25 > Task :copyDocs build 27-May-2026 17:17:26 build 27-May-2026 17:17:26 > Task :convertMdFiles build 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 build 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 build 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 build 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 build 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 build 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 build 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 build 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 build 27-May-2026 17:17:26 build 27-May-2026 17:17:26 > Task :releasesTemplates build 27-May-2026 17:17:26 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 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. build 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. build 27-May-2026 17:17:26 Stripping rc/test/etc for TEST build 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 build 27-May-2026 17:17:26 build 27-May-2026 17:17:26 > Task :prepare build 27-May-2026 17:17:28 build 27-May-2026 17:17:28 > Task :compileJava build 27-May-2026 17:17:28 Setting target compatibility to 11 error 27-May-2026 17:17:35 Note: Some input files use or override a deprecated API. error 27-May-2026 17:17:35 Note: Recompile with -Xlint:deprecation for details. error 27-May-2026 17:17:35 Note: Some input files use unchecked or unsafe operations. error 27-May-2026 17:17:35 Note: Recompile with -Xlint:unchecked for details. build 27-May-2026 17:17:39 build 27-May-2026 17:17:39 > Task :compileTestJava build 27-May-2026 17:17:39 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 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. build 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. build 27-May-2026 17:17:39 Setting target compatibility to 11 error 27-May-2026 17:17:45 Note: Some input files use or override a deprecated API. error 27-May-2026 17:17:45 Note: Recompile with -Xlint:deprecation for details. error 27-May-2026 17:17:45 Note: Some input files use unchecked or unsafe operations. error 27-May-2026 17:17:45 Note: Recompile with -Xlint:unchecked for details. build 27-May-2026 17:17:47 build 27-May-2026 17:17:47 > Task :processTestResources build 27-May-2026 17:17:47 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 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. build 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. build 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. build 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. build 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. build 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. build 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. build 27-May-2026 17:17:47 build 27-May-2026 17:17:47 > Task :testClasses build 27-May-2026 17:17:49 build 27-May-2026 17:17:49 > Task :testTask0 build 27-May-2026 17:17:49 Running tests WITH clover error 27-May-2026 17:17:50 WARNING: An illegal reflective access operation has occurred error 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 error 27-May-2026 17:17:50 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 27-May-2026 17:17:50 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 27-May-2026 17:17:50 WARNING: All illegal access operations will be denied in a future release build 27-May-2026 17:18:37 build 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 build 27-May-2026 17:18:37 java.lang.AssertionError: expected but was build 27-May-2026 17:18:37 at org.testng.FileAssert.fail(FileAssert.java:263) build 27-May-2026 17:18:37 at org.testng.FileAssert.failFile(FileAssert.java:277) build 27-May-2026 17:18:37 at org.testng.FileAssert.assertMinLength(FileAssert.java:119) build 27-May-2026 17:18:37 at org.testng.FileAssert.assertMinLength(FileAssert.java:129) build 27-May-2026 17:18:37 at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:345) build 27-May-2026 17:19:42 build 27-May-2026 17:19:42 Gradle suite > Gradle test > jalview.gui.CalculationChooserTest > testGetApplicableScoreModels FAILED build 27-May-2026 17:19:42 java.lang.AssertionError: expected [5] but found [6] build 27-May-2026 17:19:42 at org.testng.Assert.fail(Assert.java:110) build 27-May-2026 17:19:42 at org.testng.Assert.failNotEquals(Assert.java:1413) build 27-May-2026 17:19:42 at org.testng.Assert.assertEqualsImpl(Assert.java:149) build 27-May-2026 17:19:42 at org.testng.Assert.assertEquals(Assert.java:131) build 27-May-2026 17:19:42 at org.testng.Assert.assertEquals(Assert.java:1240) build 27-May-2026 17:19:42 at org.testng.Assert.assertEquals(Assert.java:1274) build 27-May-2026 17:19:42 at jalview.gui.CalculationChooserTest.__CLR4_4_1p7y2xs446q(CalculationChooserTest.java:59) build 27-May-2026 17:19:42 at jalview.gui.CalculationChooserTest.testGetApplicableScoreModels(CalculationChooserTest.java:48) build 27-May-2026 17:20:18 [151.256s][warning][gc,alloc] AWT-EventQueue-0: Retried waiting for GCLocker too often allocating 135080516 words error 27-May-2026 17:22:36 error 27-May-2026 17:22:36 2104 tests completed, 2 failed build 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 build 27-May-2026 17:22:39 build 27-May-2026 17:22:39 > Task :testTask1 build 27-May-2026 17:22:39 Running tests WITH clover error 27-May-2026 17:22:40 WARNING: An illegal reflective access operation has occurred error 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 error 27-May-2026 17:22:40 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 27-May-2026 17:22:40 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 27-May-2026 17:22:40 WARNING: All illegal access operations will be denied in a future release build 27-May-2026 17:24:53 build 27-May-2026 17:24:53 > Task :testTask2 build 27-May-2026 17:24:53 Running tests WITH clover error 27-May-2026 17:24:54 WARNING: An illegal reflective access operation has occurred error 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 error 27-May-2026 17:24:54 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 27-May-2026 17:24:54 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 27-May-2026 17:24:54 WARNING: All illegal access operations will be denied in a future release build 27-May-2026 17:24:58 build 27-May-2026 17:24:58 > Task :testTask3 build 27-May-2026 17:24:58 Running tests WITH clover error 27-May-2026 17:25:00 WARNING: An illegal reflective access operation has occurred error 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 error 27-May-2026 17:25:00 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 27-May-2026 17:25:00 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 27-May-2026 17:25:00 WARNING: All illegal access operations will be denied in a future release build 27-May-2026 17:25:19 build 27-May-2026 17:25:19 > Task :test NO-SOURCE error 27-May-2026 17:25:19 error 27-May-2026 17:25:19 FAILURE: Build failed with an exception. error 27-May-2026 17:25:19 error 27-May-2026 17:25:19 * Where: error 27-May-2026 17:25:19 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build.gradle' line: 1964 error 27-May-2026 17:25:19 error 27-May-2026 17:25:19 * What went wrong: error 27-May-2026 17:25:19 Failed tests! error 27-May-2026 17:25:19 error 27-May-2026 17:25:19 * Try: error 27-May-2026 17:25:19 > Run with --stacktrace option to get the stack trace. error 27-May-2026 17:25:19 > Run with --info or --debug option to get more log output. error 27-May-2026 17:25:19 > Run with --scan to get full insights. error 27-May-2026 17:25:19 error 27-May-2026 17:25:19 * Get more help at https://help.gradle.org error 27-May-2026 17:25:19 error 27-May-2026 17:25:19 BUILD FAILED in 8m 53s build 27-May-2026 17:25:19 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 27-May-2026 17:25:19 │jalview:testTask0 results: FAILURE (2104 tests, 2102 successes, 2 failures, 0 skipped) in 4 minutes, 48.899 seconds │ build 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│ build 27-May-2026 17:25:19 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 27-May-2026 17:25:19 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 14.079 seconds │ build 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│ build 27-May-2026 17:25:19 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 27-May-2026 17:25:19 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 5.226 seconds │ build 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│ build 27-May-2026 17:25:19 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 27-May-2026 17:25:19 │jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 22.445 seconds │ build 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│ build 27-May-2026 17:25:19 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 27-May-2026 17:25:19 │OVERALL: results: FAILURE (2181 tests, 2178 successes, 2 failures, 1 skipped) in 6 minutes, 90.649 seconds │ build 27-May-2026 17:25:19 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 27-May-2026 17:25:19 build 27-May-2026 17:25:19 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 27-May-2026 17:25:19 build 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. build 27-May-2026 17:25:19 build 27-May-2026 17:25:19 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 27-May-2026 17:25:19 build 27-May-2026 17:25:19 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 27-May-2026 17:25:19 Please consult deprecation warnings for more details. build 27-May-2026 17:25:19 21 actionable tasks: 20 executed, 1 up-to-date simple 27-May-2026 17:25:19 simple 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 simple 27-May-2026 17:25:19 Finished task 'Run tests with openclover under gradle' with result: Failed simple 27-May-2026 17:25:19 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 27-May-2026 17:25:19 Bamboo Artifactory Plugin version: 2.6.2 command 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)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_repository_revision_number=378b2a60f0e594a59de7f5ac31f20b1148702c0a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB747-JOB1-2\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB747-JOB1\nbamboo_shortPlanName=patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB747-JOB1-2\nbamboo_repository_48169034_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_shortPlanKey=GDB747\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=378b2a60f0e594a59de7f5ac31f20b1148702c0a\nbamboo_buildTimeStamp=2026-05-27T17:16:24.074+01:00\nbamboo_repository_previous_revision_number=0d6f14957df15006b71decb225c4c15ca80eead6\nbamboo_planRepository_previousRevision=0d6f14957df15006b71decb225c4c15ca80eead6\nbamboo_repository_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_buildResultKey=JB-GDB747-JOB1-2\nbamboo_repository_branch_name=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=378b2a60f0e594a59de7f5ac31f20b1148702c0a\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169034_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_name=Jalview Gitlab\nbamboo_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\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=true\nbamboo_repository_48169034_branch_name=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=0d6f14957df15006b71decb225c4c15ca80eead6\nbamboo_planRepository_branchDisplayName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_repository_48169034_name=Jalview Gitlab\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nbamboo_repository_48169034_previous_revision_number=0d6f14957df15006b71decb225c4c15ca80eead6\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-47972499\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169034_revision_number=378b2a60f0e594a59de7f5ac31f20b1148702c0a\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1\nbamboo_planKey=JB-GDB747\nbamboo_repository_48169034_git_username=\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 27-May-2026 17:25:19 2414 build 27-May-2026 17:25:25 build 27-May-2026 17:25:25 > Configure project : build 27-May-2026 17:25:25 Using properties from file './utils/channels/default/channel_gradle.properties' build 27-May-2026 17:25:25 JALVIEW_VERSION is set to '2.12.0' build 27-May-2026 17:25:25 HEADLESS BUILD build 27-May-2026 17:25:25 J2S ENABLED build 27-May-2026 17:25:25 Using a LOCAL profile. build 27-May-2026 17:25:26 eclipseDir exists build 27-May-2026 17:25:28 build 27-May-2026 17:25:28 > Task :cloverHtmlReport build 27-May-2026 17:25:28 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 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' build 27-May-2026 17:26:26 Done. Processed 137 packages in 55753ms (406ms per package). build 27-May-2026 17:26:32 build 27-May-2026 17:26:32 > Task :cloverXmlReport build 27-May-2026 17:26:32 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 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' build 27-May-2026 17:26:33 build 27-May-2026 17:26:33 > Task :cloverReport build 27-May-2026 17:26:33 build 27-May-2026 17:26:33 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 27-May-2026 17:26:33 build 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. build 27-May-2026 17:26:33 build 27-May-2026 17:26:33 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 27-May-2026 17:26:33 build 27-May-2026 17:26:33 BUILD SUCCESSFUL in 1m 14s build 27-May-2026 17:26:33 2 actionable tasks: 2 executed simple 27-May-2026 17:26:34 Finished task 'Clover Report' with result: Success simple 27-May-2026 17:26:34 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 27-May-2026 17:26:34 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1... simple 27-May-2026 17:26:34 Failing task since 2 failing test cases were found. simple 27-May-2026 17:26:34 Finished task 'TestNG Parser' with result: Failed simple 27-May-2026 17:26:34 Running post build plugin 'NCover Results Collector' simple 27-May-2026 17:26:34 Running post build plugin 'Artifact Copier' simple 27-May-2026 17:26:34 Publishing an artifact: Clover Report (System) simple 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 simple 27-May-2026 17:26:36 Publishing an artifact: TestNG report error 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. simple 27-May-2026 17:26:36 The artifact hasn't been successfully published after 3.955 ms simple 27-May-2026 17:26:36 Running post build plugin 'Artifactory Release Management Staging' simple 27-May-2026 17:26:36 Running post build plugin 'Artifactory Build Info Copier' simple 27-May-2026 17:26:36 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 27-May-2026 17:26:36 Running post build plugin 'npm Cache Cleanup' simple 27-May-2026 17:26:36 Running post build plugin 'Clover Results Collector' simple 27-May-2026 17:26:36 Running post build plugin 'Docker Container Cleanup' simple 27-May-2026 17:26:36 Finalising the build... simple 27-May-2026 17:26:36 Stopping timer. simple 27-May-2026 17:26:36 Build JB-GDB747-JOB1-2 completed. simple 27-May-2026 17:26:36 Running on server: post build plugin 'NCover Results Collector' simple 27-May-2026 17:26:36 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 27-May-2026 17:26:36 Running on server: post build plugin 'Clover Delta Calculator' simple 27-May-2026 17:26:36 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 27-May-2026 17:26:36 All post build plugins have finished simple 27-May-2026 17:26:36 Generating build results summary... simple 27-May-2026 17:26:36 Saving build results to disk... simple 27-May-2026 17:26:37 Logging substituted variables... simple 27-May-2026 17:26:37 Indexing build results... simple 27-May-2026 17:26:37 Finished building JB-GDB747-JOB1-2.