Build: #1 failed
Job: Clover and Tests failed
Build log
The build generated 237 lines of output. Download or view full build log
| 10-Mar-2026 14:58:14 | Build Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #1 (JB-GDB747-JOB1-1) started building on agent Default Agent |
| 10-Mar-2026 14:58:14 | |
| 10-Mar-2026 14:58:14 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1 |
| 10-Mar-2026 14:58:14 | Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4658_quick_patch_for_clustering_histograms_of_counts - Clover and Tests #1 (JB-GDB747-JOB1-1) |
| 10-Mar-2026 14:58:14 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 10-Mar-2026 14:58:14 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1 |
| 10-Mar-2026 14:58:14 | Updating source code to revision: 0d6f14957df15006b71decb225c4c15ca80eead6 |
| 10-Mar-2026 14:58:14 | Fetching 'refs/heads/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 10-Mar-2026 14:58:14 | Checking out revision 0d6f14957df15006b71decb225c4c15ca80eead6. |
| 10-Mar-2026 14:58:14 | Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/.git'. |
| 10-Mar-2026 14:58:14 | Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1'... |
| 10-Mar-2026 14:58:14 | done. |
| 10-Mar-2026 14:58:21 | Branch patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts set up to track remote branch patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts from origin. |
| 10-Mar-2026 14:58:21 | Switched to a new branch 'patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts' |
| 10-Mar-2026 14:58:21 | Updated source code to revision: 0d6f14957df15006b71decb225c4c15ca80eead6 |
| 10-Mar-2026 14:58:21 | Finished task 'Checkout Default Repository' with result: Success |
| 10-Mar-2026 14:58:21 | Running pre-build action: VCS Version Collector |
| 10-Mar-2026 14:58:21 | Running pre-build action: Artifactory Release Staging |
| 10-Mar-2026 14:58:21 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 10-Mar-2026 14:58:21 | Bamboo Artifactory Plugin version: 2.6.2 |
| 10-Mar-2026 14:58:21 | 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 #1 (JB-GDB747-JOB1-1)' ... 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=0d6f14957df15006b71decb225c4c15ca80eead6 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB747-JOB1-1 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=1 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-JOB1-1 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=0d6f14957df15006b71decb225c4c15ca80eead6 bamboo_buildTimeStamp=2026-03-10T14:58:14.165Z bamboo_repository_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts bamboo_buildResultKey=JB-GDB747-JOB1-1 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=0d6f14957df15006b71decb225c4c15ca80eead6 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_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 _=/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=0d6f14957df15006b71decb225c4c15ca80eead6 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 |
| 10-Mar-2026 14:58:21 | 2414 |
| 10-Mar-2026 14:58:22 | Starting a Gradle Daemon (subsequent builds will be faster) |
| 10-Mar-2026 14:58:28 | |
| 10-Mar-2026 14:58:28 | > Configure project : |
| 10-Mar-2026 14:58:28 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 10-Mar-2026 14:58:28 | JALVIEW_VERSION is set to '2.12.0' |
| 10-Mar-2026 14:58:28 | HEADLESS BUILD |
| 10-Mar-2026 14:58:28 | J2S ENABLED |
| 10-Mar-2026 14:58:29 | Using a LOCAL profile. |
| 10-Mar-2026 14:58:29 | eclipseDir exists |
| 10-Mar-2026 14:58:30 | |
| 10-Mar-2026 14:58:30 | > Task :clean |
| 10-Mar-2026 14:58:30 | > Task :cleanClover |
| 10-Mar-2026 14:58:30 | > Task :cleanTest UP-TO-DATE |
| 10-Mar-2026 14:58:32 | |
| 10-Mar-2026 14:58:32 | > Task :cloverInstrJava |
| 10-Mar-2026 14:58:32 | Clover: About to instrument 1255 files |
| 10-Mar-2026 14:58:32 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 10-Mar-2026 14:58:32 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover.db'. |
| 10-Mar-2026 14:58:32 | Processing files at 1.9 source level. |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:36 | 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? |
| 10-Mar-2026 14:58:37 | 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? |
| 10-Mar-2026 14:58:37 | 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? |
| 10-Mar-2026 14:58:37 | 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? |
| 10-Mar-2026 14:58:37 | 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? |
| 10-Mar-2026 14:58:37 | 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? |
| 10-Mar-2026 14:58:37 | 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? |
| 10-Mar-2026 14:58:37 | 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? |
| 10-Mar-2026 14:58:37 | 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? |
| 10-Mar-2026 14:58:37 | 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? |
| 10-Mar-2026 14:58:37 | 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? |
| 10-Mar-2026 14:58:37 | 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? |
| 10-Mar-2026 14:58:37 | 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? |
| 10-Mar-2026 14:58:42 | Clover all over. Instrumented 1255 files (133 packages). |
| 10-Mar-2026 14:58:45 | |
| 10-Mar-2026 14:58:45 | > Task :cloverInstrTests |
| 10-Mar-2026 14:58:45 | Clover: About to instrument test files |
| 10-Mar-2026 14:58:45 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 10-Mar-2026 14:58:45 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover.db'. |
| 10-Mar-2026 14:58:45 | Processing files at 1.9 source level. |
| 10-Mar-2026 14:58:47 | Clover all over. Instrumented 315 files (58 packages). |
| 10-Mar-2026 14:58:47 | 1771 test methods detected. |
| 10-Mar-2026 14:58:48 | |
| 10-Mar-2026 14:58:48 | > Task :cloverInstr |
| 10-Mar-2026 14:58:51 | |
| 10-Mar-2026 14:58:51 | > Task :compileCloverJava |
| 10-Mar-2026 14:58:51 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 10-Mar-2026 14:58:51 | - 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. |
| 10-Mar-2026 14:58:51 | - 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. |
| 10-Mar-2026 14:58:51 | - 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. |
| 10-Mar-2026 14:58:51 | Setting target compatibility to 11 |
| 10-Mar-2026 14:58:56 | /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-instr/jalview/gui/CalculationChooser.java:62: error: cannot find symbol |
| 10-Mar-2026 14:58:56 | import jalview.analysis.scoremodels.ValueAnnotationDistanceModel; |
| 10-Mar-2026 14:58:56 | ^ |
| 10-Mar-2026 14:58:56 | symbol: class ValueAnnotationDistanceModel |
| 10-Mar-2026 14:58:56 | location: package jalview.analysis.scoremodels |
| 10-Mar-2026 14:59:01 | /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-instr/jalview/gui/CalculationChooser.java:744: error: cannot find symbol |
| 10-Mar-2026 14:59:01 | || sm.isSecondaryStructure() && ssPresent || sm instanceof ValueAnnotationDistanceModel))&&(__CLR4_4_11w671w67mmkqjcvr.R.iget(88621)!=0|true))||(__CLR4_4_11w671w67mmkqjcvr.R.iget(88622)==0&false))) |
| 10-Mar-2026 14:59:01 | ^ |
| 10-Mar-2026 14:59:01 | symbol: class ValueAnnotationDistanceModel |
| 10-Mar-2026 14:59:01 | location: class CalculationChooser |
| 10-Mar-2026 14:59:08 | /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/clover/clover-instr/jalview/analysis/scoremodels/ScoreModels.java:86: error: cannot find symbol |
| 10-Mar-2026 14:59:08 | __CLR4_4_13hv23hv2mmkqjfj1.R.inc(163129);registerScoreModel(new ValueAnnotationDistanceModel()); |
| 10-Mar-2026 14:59:08 | ^ |
| 10-Mar-2026 14:59:08 | symbol: class ValueAnnotationDistanceModel |
| 10-Mar-2026 14:59:08 | location: class ScoreModels |
| 10-Mar-2026 14:59:09 | |
| 10-Mar-2026 14:59:09 | > Task :compileCloverJava FAILED |
| 10-Mar-2026 14:59:09 | Note: Some input files use or override a deprecated API. |
| 10-Mar-2026 14:59:09 | Note: Recompile with -Xlint:deprecation for details. |
| 10-Mar-2026 14:59:09 | Note: Some input files use unchecked or unsafe operations. |
| 10-Mar-2026 14:59:09 | Note: Recompile with -Xlint:unchecked for details. |
| 10-Mar-2026 14:59:09 | 3 errors |
| 10-Mar-2026 14:59:09 | |
| 10-Mar-2026 14:59:09 | FAILURE: Build failed with an exception. |
| 10-Mar-2026 14:59:09 | |
| 10-Mar-2026 14:59:09 | * What went wrong: |
| 10-Mar-2026 14:59:09 | Execution failed for task ':compileCloverJava'. |
| 10-Mar-2026 14:59:09 | > Compilation failed; see the compiler error output for details. |
| 10-Mar-2026 14:59:09 | |
| 10-Mar-2026 14:59:09 | * Try: |
| 10-Mar-2026 14:59:09 | > Run with --stacktrace option to get the stack trace. |
| 10-Mar-2026 14:59:09 | > Run with --info or --debug option to get more log output. |
| 10-Mar-2026 14:59:09 | > Run with --scan to get full insights. |
| 10-Mar-2026 14:59:09 | |
| 10-Mar-2026 14:59:09 | |
| 10-Mar-2026 14:59:09 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 10-Mar-2026 14:59:09 | |
| 10-Mar-2026 14:59:09 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 10-Mar-2026 14:59:09 | |
| 10-Mar-2026 14:59:09 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 10-Mar-2026 14:59:09 | |
| 10-Mar-2026 14:59:09 | Execution optimizations have been disabled for 1 invalid unit(s) of work during this build to ensure correctness. |
| 10-Mar-2026 14:59:09 | Please consult deprecation warnings for more details. |
| 10-Mar-2026 14:59:09 | 6 actionable tasks: 5 executed, 1 up-to-date |
| 10-Mar-2026 14:59:09 | * Get more help at https://help.gradle.org |
| 10-Mar-2026 14:59:09 | |
| 10-Mar-2026 14:59:09 | BUILD FAILED in 48s |
| 10-Mar-2026 14:59:10 | |
| 10-Mar-2026 14:59:10 | 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 |
| 10-Mar-2026 14:59:10 | Finished task 'Run tests with openclover under gradle' with result: Failed |
| 10-Mar-2026 14:59:10 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 10-Mar-2026 14:59:10 | Bamboo Artifactory Plugin version: 2.6.2 |
| 10-Mar-2026 14:59:10 | 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 #1 (JB-GDB747-JOB1-1)' ... 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=0d6f14957df15006b71decb225c4c15ca80eead6 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB747-JOB1-1 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=1 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-JOB1-1 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=0d6f14957df15006b71decb225c4c15ca80eead6 bamboo_buildTimeStamp=2026-03-10T14:58:14.165Z bamboo_repository_git_branch=patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts bamboo_buildResultKey=JB-GDB747-JOB1-1 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=0d6f14957df15006b71decb225c4c15ca80eead6 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_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 _=/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=0d6f14957df15006b71decb225c4c15ca80eead6 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 |
| 10-Mar-2026 14:59:10 | 2414 |
| 10-Mar-2026 14:59:15 | |
| 10-Mar-2026 14:59:15 | > Configure project : |
| 10-Mar-2026 14:59:15 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 10-Mar-2026 14:59:15 | JALVIEW_VERSION is set to '2.12.0' |
| 10-Mar-2026 14:59:15 | HEADLESS BUILD |
| 10-Mar-2026 14:59:15 | J2S ENABLED |
| 10-Mar-2026 14:59:15 | Using a LOCAL profile. |
| 10-Mar-2026 14:59:16 | eclipseDir exists |
| 10-Mar-2026 14:59:18 | |
| 10-Mar-2026 14:59:18 | > Task :cloverHtmlReport |
| 10-Mar-2026 14:59:18 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 10-Mar-2026 14:59:18 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/clover' |
| 10-Mar-2026 14:59:28 | Done. Processed 137 packages in 11278ms (82ms per package). |
| 10-Mar-2026 14:59:32 | |
| 10-Mar-2026 14:59:32 | > Task :cloverXmlReport |
| 10-Mar-2026 14:59:32 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 10-Mar-2026 14:59:32 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1/build/reports/clover/clover.xml' |
| 10-Mar-2026 14:59:32 | |
| 10-Mar-2026 14:59:32 | > Task :cloverReport |
| 10-Mar-2026 14:59:32 | |
| 10-Mar-2026 14:59:32 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 10-Mar-2026 14:59:32 | |
| 10-Mar-2026 14:59:32 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 10-Mar-2026 14:59:32 | |
| 10-Mar-2026 14:59:32 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 10-Mar-2026 14:59:32 | |
| 10-Mar-2026 14:59:32 | BUILD SUCCESSFUL in 22s |
| 10-Mar-2026 14:59:32 | 2 actionable tasks: 2 executed |
| 10-Mar-2026 14:59:32 | Finished task 'Clover Report' with result: Success |
| 10-Mar-2026 14:59:32 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 10-Mar-2026 14:59:32 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB747-JOB1... |
| 10-Mar-2026 14:59:32 | Failing task since test cases were expected but none were found. |
| 10-Mar-2026 14:59:32 | Finished task 'TestNG Parser' with result: Failed |
| 10-Mar-2026 14:59:32 | Running post build plugin 'NCover Results Collector' |
| 10-Mar-2026 14:59:32 | Running post build plugin 'Artifact Copier' |
| 10-Mar-2026 14:59:32 | Publishing an artifact: Clover Report (System) |
| 10-Mar-2026 14:59:33 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.158 s |
| 10-Mar-2026 14:59:33 | Publishing an artifact: TestNG report |
| 10-Mar-2026 14:59:33 | 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. |
| 10-Mar-2026 14:59:33 | The artifact hasn't been successfully published after 2.274 ms |
| 10-Mar-2026 14:59:33 | Running post build plugin 'Artifactory Release Management Staging' |
| 10-Mar-2026 14:59:33 | Running post build plugin 'Artifactory Build Info Copier' |
| 10-Mar-2026 14:59:33 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 10-Mar-2026 14:59:33 | Running post build plugin 'npm Cache Cleanup' |
| 10-Mar-2026 14:59:33 | Running post build plugin 'Clover Results Collector' |
| 10-Mar-2026 14:59:33 | Running post build plugin 'Docker Container Cleanup' |
| 10-Mar-2026 14:59:33 | Finalising the build... |
| 10-Mar-2026 14:59:33 | Stopping timer. |
| 10-Mar-2026 14:59:33 | Build JB-GDB747-JOB1-1 completed. |
| 10-Mar-2026 14:59:33 | Running on server: post build plugin 'NCover Results Collector' |
| 10-Mar-2026 14:59:33 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 10-Mar-2026 14:59:33 | Running on server: post build plugin 'Clover Delta Calculator' |
| 10-Mar-2026 14:59:33 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 10-Mar-2026 14:59:33 | All post build plugins have finished |
| 10-Mar-2026 14:59:33 | Generating build results summary... |
| 10-Mar-2026 14:59:33 | Saving build results to disk... |
| 10-Mar-2026 14:59:33 | Logging substituted variables... |
| 10-Mar-2026 14:59:33 | Indexing build results... |
| 10-Mar-2026 14:59:33 | Finished building JB-GDB747-JOB1-1. |