Build: #10 failed
Job: Clover and Tests failed
Build log
The build generated 353 lines of output. Download or view full build log
| 04-Jun-2026 14:16:23 | Build Jalview Builds - Gradle Develop Build - spike-na_hack_JAL-4673 - Clover and Tests #10 (JB-GDB752-JOB1-10) started building on agent Default Agent |
| 04-Jun-2026 14:16:23 | |
| 04-Jun-2026 14:16:23 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1 |
| 04-Jun-2026 14:16:23 | Executing build Jalview Builds - Gradle Develop Build - spike-na_hack_JAL-4673 - Clover and Tests #10 (JB-GDB752-JOB1-10) |
| 04-Jun-2026 14:16:23 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 04-Jun-2026 14:16:23 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1 |
| 04-Jun-2026 14:16:23 | Updating source code to revision: c69120010d6eb381a3001a73f16bd0f52af272b4 |
| 04-Jun-2026 14:16:23 | Fetching 'refs/heads/spike/na_hack_JAL-4673' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 04-Jun-2026 14:16:23 | Checking out revision c69120010d6eb381a3001a73f16bd0f52af272b4. |
| 04-Jun-2026 14:16:23 | From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 |
| 04-Jun-2026 14:16:23 | be35cec..c691200 spike/na_hack_JAL-4673 -> origin/spike/na_hack_JAL-4673 |
| 04-Jun-2026 14:16:23 | Already on 'spike/na_hack_JAL-4673' |
| 04-Jun-2026 14:16:23 | Your branch is behind 'origin/spike/na_hack_JAL-4673' by 1 commit, and can be fast-forwarded. |
| 04-Jun-2026 14:16:23 | (use "git pull" to update your local branch) |
| 04-Jun-2026 14:16:23 | HEAD is now at c691200 JAL-4678 try several times to look for mappings. |
| 04-Jun-2026 14:16:23 | Updated source code to revision: c69120010d6eb381a3001a73f16bd0f52af272b4 |
| 04-Jun-2026 14:16:23 | Finished task 'Checkout Default Repository' with result: Success |
| 04-Jun-2026 14:16:23 | Running pre-build action: VCS Version Collector |
| 04-Jun-2026 14:16:23 | Running pre-build action: Artifactory Release Staging |
| 04-Jun-2026 14:16:23 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 04-Jun-2026 14:16:23 | Bamboo Artifactory Plugin version: 2.6.2 |
| 04-Jun-2026 14:16:23 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-na_hack_JAL-4673 - Clover and Tests #10 (JB-GDB752-JOB1-10)' ... 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-GDB752-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=spike/na_hack_JAL-4673 bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_repository_48169057_git_username= CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=spike/na_hack_JAL-4673 bamboo_repository_revision_number=c69120010d6eb381a3001a73f16bd0f52af272b4 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB752-JOB1-10 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_repository_48169057_previous_revision_number=be35cec3b9c3763f923ff0ead2b3f6665d8a3fa9 bamboo_repository_48169057_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB752-JOB1 bamboo_shortPlanName=spike-na_hack_JAL-4673 bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=10 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_48169057_git_branch=spike/na_hack_JAL-4673 bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB752-JOB1-10 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - spike-na_hack_JAL-4673 bamboo_shortPlanKey=GDB752 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=c69120010d6eb381a3001a73f16bd0f52af272b4 bamboo_buildTimeStamp=2026-06-04T14:16:23.236+01:00 bamboo_repository_previous_revision_number=be35cec3b9c3763f923ff0ead2b3f6665d8a3fa9 bamboo_planRepository_previousRevision=be35cec3b9c3763f923ff0ead2b3f6665d8a3fa9 bamboo_repository_git_branch=spike/na_hack_JAL-4673 bamboo_buildResultKey=JB-GDB752-JOB1-10 bamboo_repository_branch_name=spike/na_hack_JAL-4673 bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-na_hack_JAL-4673 - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=c69120010d6eb381a3001a73f16bd0f52af272b4 SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Gitlab JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ bamboo_repository_48169057_branch_name=spike/na_hack_JAL-4673 LANG=en_GB.UTF-8 bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_repository_48169057_name=Jalview Gitlab bamboo_planRepository_branch=spike/na_hack_JAL-4673 bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_48169057_revision_number=c69120010d6eb381a3001a73f16bd0f52af272b4 bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=be35cec3b9c3763f923ff0ead2b3f6665d8a3fa9 bamboo_planRepository_branchDisplayName=spike/na_hack_JAL-4673 bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=spike/na_hack_JAL-4673 _=/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-47972545 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1 bamboo_planKey=JB-GDB752 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=spike/na_hack_JAL-4673 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 04-Jun-2026 14:16:23 | 2414 |
| 04-Jun-2026 14:16:24 | |
| 04-Jun-2026 14:16:24 | > Configure project : |
| 04-Jun-2026 14:16:24 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 04-Jun-2026 14:16:24 | JALVIEW_VERSION is set to '2.12.0' |
| 04-Jun-2026 14:16:24 | HEADLESS BUILD |
| 04-Jun-2026 14:16:24 | J2S ENABLED |
| 04-Jun-2026 14:16:24 | Using a LOCAL profile. |
| 04-Jun-2026 14:16:24 | eclipseDir exists |
| 04-Jun-2026 14:16:25 | |
| 04-Jun-2026 14:16:25 | > Task :clean |
| 04-Jun-2026 14:16:25 | > Task :cleanClover |
| 04-Jun-2026 14:16:25 | > Task :cleanTest UP-TO-DATE |
| 04-Jun-2026 14:16:27 | |
| 04-Jun-2026 14:16:27 | > Task :cloverInstrJava |
| 04-Jun-2026 14:16:27 | Clover: About to instrument 1259 files |
| 04-Jun-2026 14:16:27 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 04-Jun-2026 14:16:27 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/clover/clover.db'. |
| 04-Jun-2026 14:16:27 | Processing files at 1.9 source level. |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:30 | 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? |
| 04-Jun-2026 14:16:31 | 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? |
| 04-Jun-2026 14:16:31 | 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? |
| 04-Jun-2026 14:16:31 | 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? |
| 04-Jun-2026 14:16:31 | 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? |
| 04-Jun-2026 14:16:31 | 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? |
| 04-Jun-2026 14:16:31 | 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? |
| 04-Jun-2026 14:16:31 | 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? |
| 04-Jun-2026 14:16:31 | 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? |
| 04-Jun-2026 14:16:31 | 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? |
| 04-Jun-2026 14:16:31 | 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? |
| 04-Jun-2026 14:16:31 | 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? |
| 04-Jun-2026 14:16:31 | 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? |
| 04-Jun-2026 14:16:37 | Clover all over. Instrumented 1259 files (134 packages). |
| 04-Jun-2026 14:16:39 | |
| 04-Jun-2026 14:16:39 | > Task :cloverInstrTests |
| 04-Jun-2026 14:16:39 | Clover: About to instrument test files |
| 04-Jun-2026 14:16:39 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 04-Jun-2026 14:16:39 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/clover/clover.db'. |
| 04-Jun-2026 14:16:39 | Processing files at 1.9 source level. |
| 04-Jun-2026 14:16:42 | Clover all over. Instrumented 316 files (58 packages). |
| 04-Jun-2026 14:16:42 | 1774 test methods detected. |
| 04-Jun-2026 14:16:42 | |
| 04-Jun-2026 14:16:42 | > Task :cloverInstr |
| 04-Jun-2026 14:16:44 | |
| 04-Jun-2026 14:16:44 | > Task :compileCloverJava |
| 04-Jun-2026 14:16:44 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 04-Jun-2026 14:16:44 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:16:44 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:16:44 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:16:44 | Setting target compatibility to 11 |
| 04-Jun-2026 14:16:57 | Note: Some input files use or override a deprecated API. |
| 04-Jun-2026 14:16:57 | Note: Recompile with -Xlint:deprecation for details. |
| 04-Jun-2026 14:16:57 | Note: Some input files use unchecked or unsafe operations. |
| 04-Jun-2026 14:16:57 | Note: Recompile with -Xlint:unchecked for details. |
| 04-Jun-2026 14:17:03 | |
| 04-Jun-2026 14:17:03 | > Task :processCloverResources NO-SOURCE |
| 04-Jun-2026 14:17:03 | > Task :cloverClasses |
| 04-Jun-2026 14:17:03 | > Task :copyHelp |
| 04-Jun-2026 14:17:04 | > Task :buildIndices |
| 04-Jun-2026 14:17:04 | > Task :copyResources |
| 04-Jun-2026 14:17:04 | > Task :copyChannelResources |
| 04-Jun-2026 14:17:04 | |
| 04-Jun-2026 14:17:04 | > Task :createBuildProperties |
| 04-Jun-2026 14:17:04 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 04-Jun-2026 14:17:04 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:17:04 | |
| 04-Jun-2026 14:17:04 | > Task :buildResources |
| 04-Jun-2026 14:17:04 | > Task :copyDocs |
| 04-Jun-2026 14:17:04 | |
| 04-Jun-2026 14:17:04 | > Task :convertMdFiles |
| 04-Jun-2026 14:17:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 04-Jun-2026 14:17:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 04-Jun-2026 14:17:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 04-Jun-2026 14:17:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/resources/doc_build/doc/JalviewJS-API.html |
| 04-Jun-2026 14:17:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/resources/doc_build/doc/building.html |
| 04-Jun-2026 14:17:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/resources/doc_build/doc/addingWebClient.html |
| 04-Jun-2026 14:17:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 04-Jun-2026 14:17:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html |
| 04-Jun-2026 14:17:05 | |
| 04-Jun-2026 14:17:05 | > Task :releasesTemplates |
| 04-Jun-2026 14:17:05 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 04-Jun-2026 14:17:05 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:17:05 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:17:05 | Stripping rc/test/etc for TEST |
| 04-Jun-2026 14:17:05 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/help/markdown/whatsnew/whatsnew-TEST.md |
| 04-Jun-2026 14:17:05 | |
| 04-Jun-2026 14:17:05 | > Task :prepare |
| 04-Jun-2026 14:17:07 | |
| 04-Jun-2026 14:17:07 | > Task :compileJava |
| 04-Jun-2026 14:17:07 | Setting target compatibility to 11 |
| 04-Jun-2026 14:17:12 | Note: Some input files use or override a deprecated API. |
| 04-Jun-2026 14:17:12 | Note: Recompile with -Xlint:deprecation for details. |
| 04-Jun-2026 14:17:12 | Note: Some input files use unchecked or unsafe operations. |
| 04-Jun-2026 14:17:12 | Note: Recompile with -Xlint:unchecked for details. |
| 04-Jun-2026 14:17:15 | |
| 04-Jun-2026 14:17:15 | > Task :compileTestJava |
| 04-Jun-2026 14:17:15 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
| 04-Jun-2026 14:17:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:17:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:17:15 | Setting target compatibility to 11 |
| 04-Jun-2026 14:17:20 | Note: Some input files use or override a deprecated API. |
| 04-Jun-2026 14:17:20 | Note: Recompile with -Xlint:deprecation for details. |
| 04-Jun-2026 14:17:20 | Note: Some input files use unchecked or unsafe operations. |
| 04-Jun-2026 14:17:20 | Note: Recompile with -Xlint:unchecked for details. |
| 04-Jun-2026 14:17:21 | |
| 04-Jun-2026 14:17:21 | > Task :processTestResources |
| 04-Jun-2026 14:17:21 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
| 04-Jun-2026 14:17:21 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 04-Jun-2026 14:17:21 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:17:21 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:17:21 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:17:21 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:17:21 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:17:21 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:17:21 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-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. |
| 04-Jun-2026 14:17:21 | |
| 04-Jun-2026 14:17:21 | > Task :testClasses |
| 04-Jun-2026 14:17:23 | |
| 04-Jun-2026 14:17:23 | > Task :testTask0 |
| 04-Jun-2026 14:17:23 | Running tests WITH clover |
| 04-Jun-2026 14:17:25 | WARNING: An illegal reflective access operation has occurred |
| 04-Jun-2026 14:17:25 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 04-Jun-2026 14:17:25 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 04-Jun-2026 14:17:25 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 04-Jun-2026 14:17:25 | WARNING: All illegal access operations will be denied in a future release |
| 04-Jun-2026 14:19:25 | |
| 04-Jun-2026 14:19:25 | Gradle suite > Gradle test > jalview.gui.StructureChooserTest > openStructureFileForSequenceMultiChainTest[0](examples/testdata/9CFN.lbn, 9CFN|A[1_555], examples/testdata/9CFN.cif, Default, [Ljava.lang.String;@fdc3b84, null, true, false, JMOL, 2, 16, 1, null) FAILED |
| 04-Jun-2026 14:19:25 | java.lang.AssertionError: |
| 04-Jun-2026 14:19:25 | at org.testng.AssertJUnit.fail(AssertJUnit.java:65) |
| 04-Jun-2026 14:19:25 | at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:23) |
| 04-Jun-2026 14:19:25 | at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:33) |
| 04-Jun-2026 14:19:25 | at jalview.gui.StructureChooserTest.__CLR4_4_1jb8ksh43o7(StructureChooserTest.java:384) |
| 04-Jun-2026 14:19:25 | at jalview.gui.StructureChooserTest.openStructureFileForSequenceMultiChainTest(StructureChooserTest.java:341) |
| 04-Jun-2026 14:19:26 | |
| 04-Jun-2026 14:19:26 | Gradle suite > Gradle test > jalview.gui.StructureChooserTest > openStructureFileForSequenceMultiChainTest[1](examples/testdata/9CFN.lbn, 9CFN|B[1_555], examples/testdata/9CFN.cif, Default, [Ljava.lang.String;@5ff65505, null, true, false, JMOL, 2, 16, 1, null) FAILED |
| 04-Jun-2026 14:19:26 | java.lang.AssertionError: |
| 04-Jun-2026 14:19:26 | at org.testng.AssertJUnit.fail(AssertJUnit.java:65) |
| 04-Jun-2026 14:19:26 | at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:23) |
| 04-Jun-2026 14:19:26 | at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:33) |
| 04-Jun-2026 14:19:26 | at jalview.gui.StructureChooserTest.OSFforSeqValidate(StructureChooserTest.java:463) |
| 04-Jun-2026 14:19:26 | at jalview.gui.StructureChooserTest.__CLR4_4_1jb8ksh43o7(StructureChooserTest.java:370) |
| 04-Jun-2026 14:19:26 | at jalview.gui.StructureChooserTest.openStructureFileForSequenceMultiChainTest(StructureChooserTest.java:341) |
| 04-Jun-2026 14:22:33 | |
| 04-Jun-2026 14:22:33 | 2108 tests completed, 2 failed |
| 04-Jun-2026 14:22:33 | There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/reports/tests/testTask0/index.html |
| 04-Jun-2026 14:22:35 | |
| 04-Jun-2026 14:22:35 | > Task :testTask1 |
| 04-Jun-2026 14:22:35 | Running tests WITH clover |
| 04-Jun-2026 14:22:36 | WARNING: An illegal reflective access operation has occurred |
| 04-Jun-2026 14:22:36 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 04-Jun-2026 14:22:36 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 04-Jun-2026 14:22:36 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 04-Jun-2026 14:22:36 | WARNING: All illegal access operations will be denied in a future release |
| 04-Jun-2026 14:24:45 | |
| 04-Jun-2026 14:24:45 | > Task :testTask2 |
| 04-Jun-2026 14:24:45 | Running tests WITH clover |
| 04-Jun-2026 14:24:46 | WARNING: An illegal reflective access operation has occurred |
| 04-Jun-2026 14:24:46 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 04-Jun-2026 14:24:46 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 04-Jun-2026 14:24:46 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 04-Jun-2026 14:24:46 | WARNING: All illegal access operations will be denied in a future release |
| 04-Jun-2026 14:24:50 | |
| 04-Jun-2026 14:24:50 | > Task :testTask3 |
| 04-Jun-2026 14:24:50 | Running tests WITH clover |
| 04-Jun-2026 14:24:51 | WARNING: An illegal reflective access operation has occurred |
| 04-Jun-2026 14:24:51 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 04-Jun-2026 14:24:51 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 04-Jun-2026 14:24:51 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 04-Jun-2026 14:24:51 | WARNING: All illegal access operations will be denied in a future release |
| 04-Jun-2026 14:25:10 | |
| 04-Jun-2026 14:25:10 | FAILURE: Build failed with an exception. |
| 04-Jun-2026 14:25:10 | |
| 04-Jun-2026 14:25:10 | * Where: |
| 04-Jun-2026 14:25:10 | Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build.gradle' line: 1964 |
| 04-Jun-2026 14:25:10 | |
| 04-Jun-2026 14:25:10 | * What went wrong: |
| 04-Jun-2026 14:25:10 | Failed tests! |
| 04-Jun-2026 14:25:10 | |
| 04-Jun-2026 14:25:10 | * Try: |
| 04-Jun-2026 14:25:10 | > Run with --stacktrace option to get the stack trace. |
| 04-Jun-2026 14:25:10 | > Run with --info or --debug option to get more log output. |
| 04-Jun-2026 14:25:10 | > Run with --scan to get full insights. |
| 04-Jun-2026 14:25:10 | |
| 04-Jun-2026 14:25:10 | * Get more help at https://help.gradle.org |
| 04-Jun-2026 14:25:10 | |
| 04-Jun-2026 14:25:10 | BUILD FAILED in 8m 46s |
| 04-Jun-2026 14:25:10 | |
| 04-Jun-2026 14:25:10 | > Task :test NO-SOURCE |
| 04-Jun-2026 14:25:10 | ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ |
| 04-Jun-2026 14:25:10 | │jalview:testTask0 results: FAILURE (2108 tests, 2106 successes, 2 failures, 0 skipped) in 5 minutes, 11.331 seconds │ |
| 04-Jun-2026 14:25:10 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/reports/tests/testTask0/index.html│ |
| 04-Jun-2026 14:25:10 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 04-Jun-2026 14:25:10 | │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 9.788 seconds │ |
| 04-Jun-2026 14:25:10 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/reports/tests/testTask1/index.html│ |
| 04-Jun-2026 14:25:10 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 04-Jun-2026 14:25:10 | │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 5.042 seconds │ |
| 04-Jun-2026 14:25:10 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/reports/tests/testTask2/index.html│ |
| 04-Jun-2026 14:25:10 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 04-Jun-2026 14:25:10 | │jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 21.931 seconds │ |
| 04-Jun-2026 14:25:10 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/reports/tests/testTask3/index.html│ |
| 04-Jun-2026 14:25:10 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 04-Jun-2026 14:25:10 | │OVERALL: results: FAILURE (2185 tests, 2182 successes, 2 failures, 1 skipped) in 7 minutes, 48.092 seconds │ |
| 04-Jun-2026 14:25:10 | └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ |
| 04-Jun-2026 14:25:10 | |
| 04-Jun-2026 14:25:10 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 04-Jun-2026 14:25:10 | |
| 04-Jun-2026 14:25:10 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 04-Jun-2026 14:25:10 | |
| 04-Jun-2026 14:25:10 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 04-Jun-2026 14:25:10 | |
| 04-Jun-2026 14:25:10 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 04-Jun-2026 14:25:10 | Please consult deprecation warnings for more details. |
| 04-Jun-2026 14:25:10 | 21 actionable tasks: 20 executed, 1 up-to-date |
| 04-Jun-2026 14:25:10 | |
| 04-Jun-2026 14:25:10 | 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 |
| 04-Jun-2026 14:25:10 | Finished task 'Run tests with openclover under gradle' with result: Failed |
| 04-Jun-2026 14:25:10 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 04-Jun-2026 14:25:10 | Bamboo Artifactory Plugin version: 2.6.2 |
| 04-Jun-2026 14:25:10 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-na_hack_JAL-4673 - Clover and Tests #10 (JB-GDB752-JOB1-10)' ... 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-GDB752-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=spike/na_hack_JAL-4673 bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_repository_48169057_git_username= CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=spike/na_hack_JAL-4673 bamboo_repository_revision_number=c69120010d6eb381a3001a73f16bd0f52af272b4 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB752-JOB1-10 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_repository_48169057_previous_revision_number=be35cec3b9c3763f923ff0ead2b3f6665d8a3fa9 bamboo_repository_48169057_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB752-JOB1 bamboo_shortPlanName=spike-na_hack_JAL-4673 bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=10 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_48169057_git_branch=spike/na_hack_JAL-4673 bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB752-JOB1-10 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - spike-na_hack_JAL-4673 bamboo_shortPlanKey=GDB752 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=c69120010d6eb381a3001a73f16bd0f52af272b4 bamboo_buildTimeStamp=2026-06-04T14:16:23.236+01:00 bamboo_repository_previous_revision_number=be35cec3b9c3763f923ff0ead2b3f6665d8a3fa9 bamboo_planRepository_previousRevision=be35cec3b9c3763f923ff0ead2b3f6665d8a3fa9 bamboo_repository_git_branch=spike/na_hack_JAL-4673 bamboo_buildResultKey=JB-GDB752-JOB1-10 bamboo_repository_branch_name=spike/na_hack_JAL-4673 bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-na_hack_JAL-4673 - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=c69120010d6eb381a3001a73f16bd0f52af272b4 SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Gitlab bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ bamboo_repository_48169057_branch_name=spike/na_hack_JAL-4673 LANG=en_GB.UTF-8 bamboo_buildFailed=true bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_repository_48169057_name=Jalview Gitlab bamboo_planRepository_branch=spike/na_hack_JAL-4673 bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_jobFailed=true bamboo_capability_system_git_executable=/bin/git bamboo_repository_48169057_revision_number=c69120010d6eb381a3001a73f16bd0f52af272b4 bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=be35cec3b9c3763f923ff0ead2b3f6665d8a3fa9 bamboo_planRepository_branchDisplayName=spike/na_hack_JAL-4673 bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=spike/na_hack_JAL-4673 _=/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-47972545 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1 bamboo_planKey=JB-GDB752 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=spike/na_hack_JAL-4673 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 04-Jun-2026 14:25:10 | 2414 |
| 04-Jun-2026 14:25:16 | |
| 04-Jun-2026 14:25:16 | > Configure project : |
| 04-Jun-2026 14:25:16 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 04-Jun-2026 14:25:17 | JALVIEW_VERSION is set to '2.12.0' |
| 04-Jun-2026 14:25:17 | HEADLESS BUILD |
| 04-Jun-2026 14:25:17 | J2S ENABLED |
| 04-Jun-2026 14:25:17 | Using a LOCAL profile. |
| 04-Jun-2026 14:25:18 | eclipseDir exists |
| 04-Jun-2026 14:25:20 | |
| 04-Jun-2026 14:25:20 | > Task :cloverHtmlReport |
| 04-Jun-2026 14:25:20 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 04-Jun-2026 14:25:22 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/reports/clover' |
| 04-Jun-2026 14:26:19 | Done. Processed 138 packages in 56880ms (412ms per package). |
| 04-Jun-2026 14:26:26 | |
| 04-Jun-2026 14:26:26 | > Task :cloverXmlReport |
| 04-Jun-2026 14:26:26 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 04-Jun-2026 14:26:28 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/reports/clover/clover.xml' |
| 04-Jun-2026 14:26:28 | |
| 04-Jun-2026 14:26:28 | > Task :cloverReport |
| 04-Jun-2026 14:26:28 | |
| 04-Jun-2026 14:26:28 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 04-Jun-2026 14:26:28 | |
| 04-Jun-2026 14:26:28 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 04-Jun-2026 14:26:28 | |
| 04-Jun-2026 14:26:28 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 04-Jun-2026 14:26:28 | |
| 04-Jun-2026 14:26:28 | BUILD SUCCESSFUL in 1m 17s |
| 04-Jun-2026 14:26:28 | 2 actionable tasks: 2 executed |
| 04-Jun-2026 14:26:28 | Finished task 'Clover Report' with result: Success |
| 04-Jun-2026 14:26:28 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 04-Jun-2026 14:26:28 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1... |
| 04-Jun-2026 14:26:28 | Failing task since 2 failing test cases were found. |
| 04-Jun-2026 14:26:28 | Finished task 'TestNG Parser' with result: Failed |
| 04-Jun-2026 14:26:28 | Running post build plugin 'NCover Results Collector' |
| 04-Jun-2026 14:26:28 | Running post build plugin 'Artifact Copier' |
| 04-Jun-2026 14:26:28 | Publishing an artifact: Clover Report (System) |
| 04-Jun-2026 14:26:31 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.108 s |
| 04-Jun-2026 14:26:31 | Publishing an artifact: TestNG report |
| 04-Jun-2026 14:26:31 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB752-JOB1/build/reports/tests/test does not exist. |
| 04-Jun-2026 14:26:31 | The artifact hasn't been successfully published after 3.204 ms |
| 04-Jun-2026 14:26:31 | Running post build plugin 'Artifactory Release Management Staging' |
| 04-Jun-2026 14:26:31 | Running post build plugin 'Artifactory Build Info Copier' |
| 04-Jun-2026 14:26:31 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 04-Jun-2026 14:26:31 | Running post build plugin 'npm Cache Cleanup' |
| 04-Jun-2026 14:26:31 | Running post build plugin 'Clover Results Collector' |
| 04-Jun-2026 14:26:31 | Running post build plugin 'Docker Container Cleanup' |
| 04-Jun-2026 14:26:31 | Finalising the build... |
| 04-Jun-2026 14:26:31 | Stopping timer. |
| 04-Jun-2026 14:26:31 | Build JB-GDB752-JOB1-10 completed. |
| 04-Jun-2026 14:26:31 | Running on server: post build plugin 'NCover Results Collector' |
| 04-Jun-2026 14:26:31 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 04-Jun-2026 14:26:31 | Running on server: post build plugin 'Clover Delta Calculator' |
| 04-Jun-2026 14:26:31 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 04-Jun-2026 14:26:31 | All post build plugins have finished |
| 04-Jun-2026 14:26:31 | Generating build results summary... |
| 04-Jun-2026 14:26:31 | Saving build results to disk... |
| 04-Jun-2026 14:26:31 | Logging substituted variables... |
| 04-Jun-2026 14:26:31 | Indexing build results... |
| 04-Jun-2026 14:26:31 | Finished building JB-GDB752-JOB1-10. |