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Job: Clover and Tests did not complete
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| 05-Jan-2026 03:03:22 | Build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6) started building on agent Default Agent |
| 05-Jan-2026 03:03:22 | |
| 05-Jan-2026 03:03:22 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1 |
| 05-Jan-2026 03:03:22 | Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6) |
| 05-Jan-2026 03:03:22 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 05-Jan-2026 03:03:22 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1 |
| 05-Jan-2026 03:03:22 | Updating source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 |
| 05-Jan-2026 03:03:22 | Fetching 'refs/heads/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 05-Jan-2026 03:03:23 | Checking out revision b6ff7e553d3ba8b32e1d2650df7860706b2a37d5. |
| 05-Jan-2026 03:03:23 | From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 |
| 05-Jan-2026 03:03:23 | 5857fe7..b6ff7e5 bug/JAL-4107_jalviewjs_fixes_on_2_12_branch -> origin/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch |
| 05-Jan-2026 03:03:23 | Already on 'bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' |
| 05-Jan-2026 03:03:23 | Your branch is behind 'origin/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' by 1 commit, and can be fast-forwarded. |
| 05-Jan-2026 03:03:23 | (use "git pull" to update your local branch) |
| 05-Jan-2026 03:03:23 | HEAD is now at b6ff7e5 JAL-4107 reinstate Console output of DESKTOP CREATED so jalviewjsHeadlessTest passes |
| 05-Jan-2026 03:03:23 | Updated source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 |
| 05-Jan-2026 03:03:23 | Finished task 'Checkout Default Repository' with result: Success |
| 05-Jan-2026 03:03:23 | Running pre-build action: VCS Version Collector |
| 05-Jan-2026 03:03:23 | Running pre-build action: Artifactory Release Staging |
| 05-Jan-2026 03:03:23 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 05-Jan-2026 03:03:23 | Bamboo Artifactory Plugin version: 2.6.2 |
| 05-Jan-2026 03:03:23 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6)' ... 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-GDB734-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_repository_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-JOB1-6 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-GDB734-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB734-JOB1 bamboo_repository_46498616_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_repository_46498616_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 bamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=6 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-GDB734-JOB1-6 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - 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| 05-Jan-2026 03:03:23 | 2414 |
| 05-Jan-2026 03:03:24 | |
| 05-Jan-2026 03:03:24 | > Configure project : |
| 05-Jan-2026 03:03:24 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 05-Jan-2026 03:03:24 | JALVIEW_VERSION is set to '2.12.0' |
| 05-Jan-2026 03:03:24 | HEADLESS BUILD |
| 05-Jan-2026 03:03:24 | J2S ENABLED |
| 05-Jan-2026 03:03:24 | Using a LOCAL profile. |
| 05-Jan-2026 03:03:24 | eclipseDir exists |
| 05-Jan-2026 03:03:25 | |
| 05-Jan-2026 03:03:25 | > Task :clean |
| 05-Jan-2026 03:03:25 | > Task :cleanClover |
| 05-Jan-2026 03:03:25 | > Task :cleanTest UP-TO-DATE |
| 05-Jan-2026 03:03:27 | |
| 05-Jan-2026 03:03:27 | > Task :cloverInstrJava |
| 05-Jan-2026 03:03:27 | Clover: About to instrument 1253 files |
| 05-Jan-2026 03:03:27 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 05-Jan-2026 03:03:27 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'. |
| 05-Jan-2026 03:03:27 | Processing files at 1.9 source level. |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:30 | 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? |
| 05-Jan-2026 03:03:36 | Clover all over. Instrumented 1253 files (133 packages). |
| 05-Jan-2026 03:03:38 | |
| 05-Jan-2026 03:03:38 | > Task :cloverInstrTests |
| 05-Jan-2026 03:03:38 | Clover: About to instrument test files |
| 05-Jan-2026 03:03:38 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 05-Jan-2026 03:03:38 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'. |
| 05-Jan-2026 03:03:38 | Processing files at 1.9 source level. |
| 05-Jan-2026 03:03:40 | Clover all over. Instrumented 315 files (58 packages). |
| 05-Jan-2026 03:03:40 | 1770 test methods detected. |
| 05-Jan-2026 03:03:41 | |
| 05-Jan-2026 03:03:41 | > Task :cloverInstr |
| 05-Jan-2026 03:03:43 | |
| 05-Jan-2026 03:03:43 | > Task :compileCloverJava |
| 05-Jan-2026 03:03:43 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 05-Jan-2026 03:03:43 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:03:43 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:03:43 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:03:43 | Setting target compatibility to 11 |
| 05-Jan-2026 03:03:56 | Note: Some input files use or override a deprecated API. |
| 05-Jan-2026 03:03:56 | Note: Recompile with -Xlint:deprecation for details. |
| 05-Jan-2026 03:03:56 | Note: Some input files use unchecked or unsafe operations. |
| 05-Jan-2026 03:03:56 | Note: Recompile with -Xlint:unchecked for details. |
| 05-Jan-2026 03:04:01 | |
| 05-Jan-2026 03:04:01 | > Task :processCloverResources NO-SOURCE |
| 05-Jan-2026 03:04:01 | > Task :cloverClasses |
| 05-Jan-2026 03:04:01 | > Task :copyHelp |
| 05-Jan-2026 03:04:02 | > Task :buildIndices |
| 05-Jan-2026 03:04:02 | > Task :copyResources |
| 05-Jan-2026 03:04:02 | > Task :copyChannelResources |
| 05-Jan-2026 03:04:02 | |
| 05-Jan-2026 03:04:02 | > Task :createBuildProperties |
| 05-Jan-2026 03:04:02 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 05-Jan-2026 03:04:02 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:04:02 | |
| 05-Jan-2026 03:04:02 | > Task :buildResources |
| 05-Jan-2026 03:04:02 | > Task :copyDocs |
| 05-Jan-2026 03:04:02 | |
| 05-Jan-2026 03:04:02 | > Task :convertMdFiles |
| 05-Jan-2026 03:04:02 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 05-Jan-2026 03:04:02 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 05-Jan-2026 03:04:02 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 05-Jan-2026 03:04:02 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-API.html |
| 05-Jan-2026 03:04:02 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/building.html |
| 05-Jan-2026 03:04:02 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/addingWebClient.html |
| 05-Jan-2026 03:04:02 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 05-Jan-2026 03:04:02 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html |
| 05-Jan-2026 03:04:03 | |
| 05-Jan-2026 03:04:03 | > Task :releasesTemplates |
| 05-Jan-2026 03:04:03 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 05-Jan-2026 03:04:03 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:04:03 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:04:03 | Stripping rc/test/etc for TEST |
| 05-Jan-2026 03:04:03 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/help/markdown/whatsnew/whatsnew-TEST.md |
| 05-Jan-2026 03:04:03 | |
| 05-Jan-2026 03:04:03 | > Task :prepare |
| 05-Jan-2026 03:04:05 | |
| 05-Jan-2026 03:04:05 | > Task :compileJava |
| 05-Jan-2026 03:04:05 | Setting target compatibility to 11 |
| 05-Jan-2026 03:04:09 | Note: Some input files use or override a deprecated API. |
| 05-Jan-2026 03:04:09 | Note: Recompile with -Xlint:deprecation for details. |
| 05-Jan-2026 03:04:09 | Note: Some input files use unchecked or unsafe operations. |
| 05-Jan-2026 03:04:09 | Note: Recompile with -Xlint:unchecked for details. |
| 05-Jan-2026 03:04:12 | |
| 05-Jan-2026 03:04:12 | > Task :compileTestJava |
| 05-Jan-2026 03:04:12 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
| 05-Jan-2026 03:04:12 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:04:12 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:04:12 | Setting target compatibility to 11 |
| 05-Jan-2026 03:04:16 | Note: Some input files use or override a deprecated API. |
| 05-Jan-2026 03:04:16 | Note: Recompile with -Xlint:deprecation for details. |
| 05-Jan-2026 03:04:16 | Note: Some input files use unchecked or unsafe operations. |
| 05-Jan-2026 03:04:16 | Note: Recompile with -Xlint:unchecked for details. |
| 05-Jan-2026 03:04:18 | |
| 05-Jan-2026 03:04:18 | > Task :processTestResources |
| 05-Jan-2026 03:04:18 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
| 05-Jan-2026 03:04:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:04:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:04:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:04:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:04:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:04:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:04:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:04:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 03:04:18 | |
| 05-Jan-2026 03:04:18 | > Task :testClasses |
| 05-Jan-2026 03:04:20 | |
| 05-Jan-2026 03:04:20 | > Task :testTask0 |
| 05-Jan-2026 03:04:20 | Running tests WITH clover |
| 05-Jan-2026 03:04:21 | WARNING: An illegal reflective access operation has occurred |
| 05-Jan-2026 03:04:21 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 05-Jan-2026 03:04:21 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 05-Jan-2026 03:04:21 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 05-Jan-2026 03:04:21 | WARNING: All illegal access operations will be denied in a future release |
| 05-Jan-2026 03:05:09 | |
| 05-Jan-2026 03:05:09 | Gradle suite > Gradle test > jalview.bin.CommandLineOperations > testHeadlessModeOutputOperations[7](headless -open examples/uniref50.fa, -html, test/jalview/bin/test_uniref50_out.html, true, 4096, 15000, null) FAILED |
| 05-Jan-2026 03:05:09 | java.lang.AssertionError: Didn't create an output -html file.[headless -open examples/uniref50.fa] expected [true] but found [false] |
| 05-Jan-2026 03:05:09 | at org.testng.Assert.fail(Assert.java:110) |
| 05-Jan-2026 03:05:09 | at org.testng.Assert.failNotEquals(Assert.java:1413) |
| 05-Jan-2026 03:05:09 | at org.testng.Assert.assertTrue(Assert.java:56) |
| 05-Jan-2026 03:05:09 | at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:343) |
| 05-Jan-2026 03:09:04 | There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask0/index.html |
| 05-Jan-2026 03:09:04 | |
| 05-Jan-2026 03:09:04 | 2102 tests completed, 1 failed |
| 05-Jan-2026 03:09:06 | |
| 05-Jan-2026 03:09:06 | > Task :testTask1 |
| 05-Jan-2026 03:09:06 | Running tests WITH clover |
| 05-Jan-2026 03:09:07 | WARNING: An illegal reflective access operation has occurred |
| 05-Jan-2026 03:09:07 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 05-Jan-2026 03:09:07 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 05-Jan-2026 03:09:07 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 05-Jan-2026 03:09:07 | WARNING: All illegal access operations will be denied in a future release |
| 05-Jan-2026 03:11:09 | |
| 05-Jan-2026 03:11:09 | > Task :testTask2 |
| 05-Jan-2026 03:11:09 | Running tests WITH clover |
| 05-Jan-2026 03:11:10 | WARNING: An illegal reflective access operation has occurred |
| 05-Jan-2026 03:11:10 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 05-Jan-2026 03:11:10 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 05-Jan-2026 03:11:10 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 05-Jan-2026 03:11:10 | WARNING: All illegal access operations will be denied in a future release |
| 05-Jan-2026 03:11:14 | |
| 05-Jan-2026 03:11:14 | > Task :testTask3 |
| 05-Jan-2026 03:11:14 | Running tests WITH clover |
| 05-Jan-2026 03:11:15 | WARNING: An illegal reflective access operation has occurred |
| 05-Jan-2026 03:11:15 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 05-Jan-2026 03:11:15 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 05-Jan-2026 03:11:15 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 05-Jan-2026 03:11:15 | WARNING: All illegal access operations will be denied in a future release |
| 05-Jan-2026 03:11:33 | |
| 05-Jan-2026 03:11:33 | > Task :test NO-SOURCE |
| 05-Jan-2026 03:11:33 | ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ |
| 05-Jan-2026 03:11:33 | │jalview:testTask0 results: FAILURE (2102 tests, 2101 successes, 1 failures, 0 skipped) in 4 minutes, 46.257 seconds │ |
| 05-Jan-2026 03:11:33 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask0/index.html│ |
| 05-Jan-2026 03:11:33 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 05-Jan-2026 03:11:33 | │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 2.841 seconds │ |
| 05-Jan-2026 03:11:33 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask1/index.html│ |
| 05-Jan-2026 03:11:33 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 05-Jan-2026 03:11:33 | │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.432 seconds │ |
| 05-Jan-2026 03:11:33 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask2/index.html│ |
| 05-Jan-2026 03:11:33 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 05-Jan-2026 03:11:33 | │jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 20.783 seconds │ |
| 05-Jan-2026 03:11:33 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask3/index.html│ |
| 05-Jan-2026 03:11:33 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 05-Jan-2026 03:11:33 | │OVERALL: results: FAILURE (2179 tests, 2177 successes, 1 failures, 1 skipped) in 6 minutes, 74.313 seconds │ |
| 05-Jan-2026 03:11:33 | └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ |
| 05-Jan-2026 03:11:33 | |
| 05-Jan-2026 03:11:33 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 05-Jan-2026 03:11:33 | |
| 05-Jan-2026 03:11:33 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 05-Jan-2026 03:11:33 | |
| 05-Jan-2026 03:11:33 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 05-Jan-2026 03:11:33 | |
| 05-Jan-2026 03:11:33 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 05-Jan-2026 03:11:33 | Please consult deprecation warnings for more details. |
| 05-Jan-2026 03:11:33 | |
| 05-Jan-2026 03:11:33 | FAILURE: Build failed with an exception. |
| 05-Jan-2026 03:11:33 | |
| 05-Jan-2026 03:11:33 | * Where: |
| 05-Jan-2026 03:11:33 | Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build.gradle' line: 1964 |
| 05-Jan-2026 03:11:33 | |
| 05-Jan-2026 03:11:33 | * What went wrong: |
| 05-Jan-2026 03:11:33 | Failed tests! |
| 05-Jan-2026 03:11:33 | |
| 05-Jan-2026 03:11:33 | * Try: |
| 05-Jan-2026 03:11:33 | > Run with --stacktrace option to get the stack trace. |
| 05-Jan-2026 03:11:33 | > Run with --info or --debug option to get more log output. |
| 05-Jan-2026 03:11:33 | > Run with --scan to get full insights. |
| 05-Jan-2026 03:11:33 | |
| 05-Jan-2026 03:11:33 | * Get more help at https://help.gradle.org |
| 05-Jan-2026 03:11:33 | |
| 05-Jan-2026 03:11:33 | BUILD FAILED in 8m 9s |
| 05-Jan-2026 03:11:33 | 21 actionable tasks: 20 executed, 1 up-to-date |
| 05-Jan-2026 03:11:33 | |
| 05-Jan-2026 03:11:33 | 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 |
| 05-Jan-2026 03:11:33 | Finished task 'Run tests with openclover under gradle' with result: Failed |
| 05-Jan-2026 03:11:33 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 05-Jan-2026 03:11:33 | Bamboo Artifactory Plugin version: 2.6.2 |
| 05-Jan-2026 03:11:33 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6)' ... 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-GDB734-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_repository_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-JOB1-6 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-GDB734-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB734-JOB1 bamboo_repository_46498616_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_repository_46498616_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 bamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=6 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-GDB734-JOB1-6 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_shortPlanKey=GDB734 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 bamboo_buildTimeStamp=2026-01-05T03:03:22.820Z bamboo_repository_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7 bamboo_planRepository_previousRevision=5857fe763e55a89397fc3bb157f282726c22b1a7 bamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_buildResultKey=JB-GDB734-JOB1-6 bamboo_repository_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 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_46498616_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch LANG=en_GB.UTF-8 bamboo_buildFailed=true bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_jobFailed=true bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=5857fe763e55a89397fc3bb157f282726c22b1a7 bamboo_planRepository_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch _=/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-46302801 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-GDB734-JOB1 bamboo_planKey=JB-GDB734 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= bamboo_repository_46498616_git_username= bamboo_repository_46498616_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7 bamboo_repository_46498616_name=Jalview Gitlab HOME=/home/bamboo bamboo_planRepository_1_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_repository_46498616_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 05-Jan-2026 03:11:33 | 2414 |
| 05-Jan-2026 03:11:38 | |
| 05-Jan-2026 03:11:38 | > Configure project : |
| 05-Jan-2026 03:11:38 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 05-Jan-2026 03:11:38 | JALVIEW_VERSION is set to '2.12.0' |
| 05-Jan-2026 03:11:38 | HEADLESS BUILD |
| 05-Jan-2026 03:11:38 | J2S ENABLED |
| 05-Jan-2026 03:11:39 | Using a LOCAL profile. |
| 05-Jan-2026 03:11:39 | eclipseDir exists |
| 05-Jan-2026 03:11:42 | |
| 05-Jan-2026 03:11:42 | > Task :cloverHtmlReport |
| 05-Jan-2026 03:11:42 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 05-Jan-2026 03:11:43 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover' |
| 05-Jan-2026 03:12:31 | ERROR: Invalid Java source found or Clover failed to parse it: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/src/jalview/analysis/AlignmentUtils.java |
| 05-Jan-2026 03:12:37 | Done. Processed 137 packages in 53579ms (391ms per package). |
| 05-Jan-2026 03:12:42 | |
| 05-Jan-2026 03:12:42 | > Task :cloverXmlReport |
| 05-Jan-2026 03:12:42 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 05-Jan-2026 03:12:42 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover/clover.xml' |
| 05-Jan-2026 03:12:43 | |
| 05-Jan-2026 03:12:43 | > Task :cloverReport |
| 05-Jan-2026 03:12:43 | |
| 05-Jan-2026 03:12:43 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 05-Jan-2026 03:12:43 | |
| 05-Jan-2026 03:12:43 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 05-Jan-2026 03:12:43 | |
| 05-Jan-2026 03:12:43 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 05-Jan-2026 03:12:43 | |
| 05-Jan-2026 03:12:43 | BUILD SUCCESSFUL in 1m 9s |
| 05-Jan-2026 03:12:43 | 2 actionable tasks: 2 executed |
| 05-Jan-2026 03:12:43 | Finished task 'Clover Report' with result: Success |
| 05-Jan-2026 03:12:43 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 05-Jan-2026 03:12:43 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1... |
| 05-Jan-2026 03:12:43 | Failing task since 1 failing test cases were found. |
| 05-Jan-2026 03:12:43 | Finished task 'TestNG Parser' with result: Failed |
| 05-Jan-2026 03:12:43 | Running post build plugin 'NCover Results Collector' |
| 05-Jan-2026 03:12:43 | Running post build plugin 'Artifact Copier' |
| 05-Jan-2026 03:12:43 | Publishing an artifact: Clover Report (System) |
| 05-Jan-2026 03:12:45 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.048 s |
| 05-Jan-2026 03:12:45 | Publishing an artifact: TestNG report |
| 05-Jan-2026 03:12:45 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/test does not exist. |
| 05-Jan-2026 03:12:45 | The artifact hasn't been successfully published after 80.75 μs |
| 05-Jan-2026 03:12:45 | Running post build plugin 'Artifactory Release Management Staging' |
| 05-Jan-2026 03:12:45 | Running post build plugin 'Artifactory Build Info Copier' |
| 05-Jan-2026 03:12:45 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 05-Jan-2026 03:12:45 | Running post build plugin 'npm Cache Cleanup' |
| 05-Jan-2026 03:12:45 | Running post build plugin 'Clover Results Collector' |
| 05-Jan-2026 03:12:45 | Running post build plugin 'Docker Container Cleanup' |
| 05-Jan-2026 03:12:45 | Finalising the build... |
| 05-Jan-2026 03:12:45 | Stopping timer. |
| 05-Jan-2026 03:12:45 | Build JB-GDB734-JOB1-6 completed. |
| 05-Jan-2026 03:12:45 | Running on server: post build plugin 'NCover Results Collector' |
| 05-Jan-2026 03:12:45 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 05-Jan-2026 03:12:45 | Running on server: post build plugin 'Clover Delta Calculator' |
| 05-Jan-2026 03:12:45 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 05-Jan-2026 03:12:45 | All post build plugins have finished |
| 05-Jan-2026 03:12:45 | Generating build results summary... |
| 05-Jan-2026 03:12:45 | Saving build results to disk... |
| 05-Jan-2026 03:12:45 | Logging substituted variables... |
| 05-Jan-2026 03:12:45 | Indexing build results... |
| 05-Jan-2026 03:12:45 | Finished building JB-GDB734-JOB1-6. |
| 05-Jan-2026 05:00:18 | Build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6) started building on agent Default Agent |
| 05-Jan-2026 05:00:18 | |
| 05-Jan-2026 05:00:18 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1 |
| 05-Jan-2026 05:00:18 | Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6) |
| 05-Jan-2026 05:00:18 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 05-Jan-2026 05:00:18 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1 |
| 05-Jan-2026 05:00:18 | Updating source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 |
| 05-Jan-2026 05:00:18 | Fetching 'refs/heads/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 05-Jan-2026 05:00:18 | Checking out revision b6ff7e553d3ba8b32e1d2650df7860706b2a37d5. |
| 05-Jan-2026 05:00:18 | Already on 'bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' |
| 05-Jan-2026 05:00:18 | Updated source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 |
| 05-Jan-2026 05:00:18 | Finished task 'Checkout Default Repository' with result: Success |
| 05-Jan-2026 05:00:18 | Running pre-build action: VCS Version Collector |
| 05-Jan-2026 05:00:18 | Running pre-build action: Artifactory Release Staging |
| 05-Jan-2026 05:00:18 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 05-Jan-2026 05:00:18 | Bamboo Artifactory Plugin version: 2.6.2 |
| 05-Jan-2026 05:00:18 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6)' ... 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-GDB734-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_planRepository_1_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_repository_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 bamboo_CLOVER_CLASSES=1607 bamboo_buildKey=JB-GDB734-JOB1 bamboo_CLOVER_COVERED_CONDITIONALS=16926 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-GDB734-JOB1-6 bamboo_CLOVER_STATEMENTS=121136 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_agentId=196609 bamboo_CLOVER_NCLOC=290874 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 bamboo_planRepository_previousRevision=5857fe763e55a89397fc3bb157f282726c22b1a7 bamboo_CLOVER_CONDITIONALS=45046 bamboo_repository_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ bamboo_repository_46498616_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_CLOVER_PACKAGES=135 bamboo_planRepository_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch _=/usr/bin/java bamboo_CLOVER_COVERAGE_DELTA=-0.1 bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr 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 bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_ManualBuildTriggerReason_userName=jprocter 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_planKey=JB-GDB734 bamboo_planRepository_username= bamboo_repository_46498616_git_username= bamboo_repository_46498616_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7 bamboo_planRepository_1_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_CLOVER_ELEMENTS=184000 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-JOB1-6 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_CLOVER_BUILD_COVERAGE=40.8 bamboo_CLOVER_METHODS=17818 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_CLOVER_COVERED_STATEMENTS=50445 bamboo_repository_46498616_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_repository_46498616_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 bamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=6 SHELL=/bin/bash bamboo_ManualBuildTriggerReason_stageName=Default Stage bamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_shortPlanKey=GDB734 bamboo_shortJobKey=JOB1 bamboo_buildTimeStamp=2026-01-05T05:00:18.274Z bamboo_repository_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7 bamboo_CLOVER_COVERED_METHODS=7764 bamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_buildResultKey=JB-GDB734-JOB1-6 bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests bamboo_planRepository_1_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_4=/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport 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 LANG=en_GB.UTF-8 bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=5857fe763e55a89397fc3bb157f282726c22b1a7 bamboo_planRepository_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_plan_storageTag=plan-46302801 bamboo_CLOVER_LOC=460432 bamboo_CLOVER_FILES=1270 USER=bamboo bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_CLOVER_COVERED_ELEMENTS=75135 bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1 bamboo_RerunBuildTriggerReason_noOfRetries=1 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_repository_46498616_name=Jalview Gitlab HOME=/home/bamboo bamboo_repository_46498616_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 05-Jan-2026 05:00:18 | 2414 |
| 05-Jan-2026 05:00:20 | |
| 05-Jan-2026 05:00:20 | > Configure project : |
| 05-Jan-2026 05:00:20 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 05-Jan-2026 05:00:20 | JALVIEW_VERSION is set to '2.12.0' |
| 05-Jan-2026 05:00:20 | HEADLESS BUILD |
| 05-Jan-2026 05:00:20 | J2S ENABLED |
| 05-Jan-2026 05:00:20 | Using a LOCAL profile. |
| 05-Jan-2026 05:00:20 | eclipseDir exists |
| 05-Jan-2026 05:00:21 | |
| 05-Jan-2026 05:00:21 | > Task :clean |
| 05-Jan-2026 05:00:21 | > Task :cleanClover |
| 05-Jan-2026 05:00:21 | > Task :cleanTest UP-TO-DATE |
| 05-Jan-2026 05:00:23 | |
| 05-Jan-2026 05:00:23 | > Task :cloverInstrJava |
| 05-Jan-2026 05:00:23 | Clover: About to instrument 1253 files |
| 05-Jan-2026 05:00:23 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 05-Jan-2026 05:00:23 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'. |
| 05-Jan-2026 05:00:23 | Processing files at 1.9 source level. |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:25 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:26 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:26 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:26 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:26 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:26 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:26 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:26 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:26 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:26 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:26 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:26 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:26 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 05-Jan-2026 05:00:31 | Clover all over. Instrumented 1253 files (133 packages). |
| 05-Jan-2026 05:00:33 | |
| 05-Jan-2026 05:00:33 | > Task :cloverInstrTests |
| 05-Jan-2026 05:00:33 | Clover: About to instrument test files |
| 05-Jan-2026 05:00:33 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 05-Jan-2026 05:00:33 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'. |
| 05-Jan-2026 05:00:33 | Processing files at 1.9 source level. |
| 05-Jan-2026 05:00:36 | Clover all over. Instrumented 315 files (58 packages). |
| 05-Jan-2026 05:00:36 | 1770 test methods detected. |
| 05-Jan-2026 05:00:36 | |
| 05-Jan-2026 05:00:36 | > Task :cloverInstr |
| 05-Jan-2026 05:00:38 | |
| 05-Jan-2026 05:00:38 | > Task :compileCloverJava |
| 05-Jan-2026 05:00:38 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 05-Jan-2026 05:00:38 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:00:38 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:00:38 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:00:38 | Setting target compatibility to 11 |
| 05-Jan-2026 05:00:51 | Note: Some input files use or override a deprecated API. |
| 05-Jan-2026 05:00:51 | Note: Recompile with -Xlint:deprecation for details. |
| 05-Jan-2026 05:00:51 | Note: Some input files use unchecked or unsafe operations. |
| 05-Jan-2026 05:00:51 | Note: Recompile with -Xlint:unchecked for details. |
| 05-Jan-2026 05:00:57 | |
| 05-Jan-2026 05:00:57 | > Task :processCloverResources NO-SOURCE |
| 05-Jan-2026 05:00:57 | > Task :cloverClasses |
| 05-Jan-2026 05:00:57 | > Task :copyHelp |
| 05-Jan-2026 05:00:58 | > Task :buildIndices |
| 05-Jan-2026 05:00:58 | > Task :copyResources |
| 05-Jan-2026 05:00:58 | > Task :copyChannelResources |
| 05-Jan-2026 05:00:58 | |
| 05-Jan-2026 05:00:58 | > Task :createBuildProperties |
| 05-Jan-2026 05:00:58 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 05-Jan-2026 05:00:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:00:58 | |
| 05-Jan-2026 05:00:58 | > Task :buildResources |
| 05-Jan-2026 05:00:58 | > Task :copyDocs |
| 05-Jan-2026 05:00:58 | |
| 05-Jan-2026 05:00:58 | > Task :convertMdFiles |
| 05-Jan-2026 05:00:58 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 05-Jan-2026 05:00:58 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 05-Jan-2026 05:00:58 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 05-Jan-2026 05:00:58 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-API.html |
| 05-Jan-2026 05:00:58 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/building.html |
| 05-Jan-2026 05:00:58 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/addingWebClient.html |
| 05-Jan-2026 05:00:58 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 05-Jan-2026 05:00:58 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html |
| 05-Jan-2026 05:00:59 | |
| 05-Jan-2026 05:00:59 | > Task :releasesTemplates |
| 05-Jan-2026 05:00:59 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 05-Jan-2026 05:00:59 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:00:59 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:00:59 | Stripping rc/test/etc for TEST |
| 05-Jan-2026 05:00:59 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/help/markdown/whatsnew/whatsnew-TEST.md |
| 05-Jan-2026 05:00:59 | |
| 05-Jan-2026 05:00:59 | > Task :prepare |
| 05-Jan-2026 05:01:01 | |
| 05-Jan-2026 05:01:01 | > Task :compileJava |
| 05-Jan-2026 05:01:01 | Setting target compatibility to 11 |
| 05-Jan-2026 05:01:05 | Note: Some input files use or override a deprecated API. |
| 05-Jan-2026 05:01:05 | Note: Recompile with -Xlint:deprecation for details. |
| 05-Jan-2026 05:01:05 | Note: Some input files use unchecked or unsafe operations. |
| 05-Jan-2026 05:01:05 | Note: Recompile with -Xlint:unchecked for details. |
| 05-Jan-2026 05:01:08 | |
| 05-Jan-2026 05:01:08 | > Task :compileTestJava |
| 05-Jan-2026 05:01:08 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
| 05-Jan-2026 05:01:08 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:01:08 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:01:08 | Setting target compatibility to 11 |
| 05-Jan-2026 05:01:13 | Note: Some input files use or override a deprecated API. |
| 05-Jan-2026 05:01:13 | Note: Recompile with -Xlint:deprecation for details. |
| 05-Jan-2026 05:01:13 | Note: Some input files use unchecked or unsafe operations. |
| 05-Jan-2026 05:01:13 | Note: Recompile with -Xlint:unchecked for details. |
| 05-Jan-2026 05:01:14 | |
| 05-Jan-2026 05:01:14 | > Task :processTestResources |
| 05-Jan-2026 05:01:14 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
| 05-Jan-2026 05:01:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:01:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:01:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:01:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:01:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:01:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:01:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:01:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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. |
| 05-Jan-2026 05:01:14 | |
| 05-Jan-2026 05:01:14 | > Task :testClasses |
| 05-Jan-2026 05:01:16 | |
| 05-Jan-2026 05:01:16 | > Task :testTask0 |
| 05-Jan-2026 05:01:16 | Running tests WITH clover |
| 05-Jan-2026 05:01:17 | WARNING: An illegal reflective access operation has occurred |
| 05-Jan-2026 05:01:17 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 05-Jan-2026 05:01:17 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 05-Jan-2026 05:01:17 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 05-Jan-2026 05:01:17 | WARNING: All illegal access operations will be denied in a future release |
| 05-Jan-2026 05:02:06 | |
| 05-Jan-2026 05:02:06 | Gradle suite > Gradle test > jalview.bin.CommandLineOperations > testHeadlessModeOutputOperations[7](headless -open examples/uniref50.fa, -html, test/jalview/bin/test_uniref50_out.html, true, 4096, 15000, null) FAILED |
| 05-Jan-2026 05:02:06 | java.lang.AssertionError: Didn't create an output -html file.[headless -open examples/uniref50.fa] expected [true] but found [false] |
| 05-Jan-2026 05:02:06 | at org.testng.Assert.fail(Assert.java:110) |
| 05-Jan-2026 05:02:06 | at org.testng.Assert.failNotEquals(Assert.java:1413) |
| 05-Jan-2026 05:02:06 | at org.testng.Assert.assertTrue(Assert.java:56) |
| 05-Jan-2026 05:02:06 | at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:343) |
| 05-Jan-2026 05:03:46 | |
| 05-Jan-2026 05:03:46 | Gradle suite > Gradle test > jalview.project.Jalview2xmlTests > noDuplicatePdbMappingsMade FAILED |
| 05-Jan-2026 05:03:46 | java.lang.AssertionError: Expected only two mappings for 1A70 expected [2] but found [0] |
| 05-Jan-2026 05:03:46 | at org.testng.Assert.fail(Assert.java:110) |
| 05-Jan-2026 05:03:46 | at org.testng.Assert.failNotEquals(Assert.java:1413) |
| 05-Jan-2026 05:03:46 | at org.testng.Assert.assertEqualsImpl(Assert.java:149) |
| 05-Jan-2026 05:03:46 | at org.testng.Assert.assertEquals(Assert.java:131) |
| 05-Jan-2026 05:03:46 | at org.testng.Assert.assertEquals(Assert.java:1240) |
| 05-Jan-2026 05:03:46 | at jalview.project.Jalview2xmlTests.__CLR4_4_11umpz94jwy(Jalview2xmlTests.java:355) |
| 05-Jan-2026 05:03:46 | at jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade(Jalview2xmlTests.java:331) |
| 05-Jan-2026 05:05:39 | |
| 05-Jan-2026 05:05:39 | 2102 tests completed, 2 failed |
| 05-Jan-2026 05:05:39 | There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask0/index.html |
| 05-Jan-2026 05:05:41 | |
| 05-Jan-2026 05:05:41 | > Task :testTask1 |
| 05-Jan-2026 05:05:41 | Running tests WITH clover |
| 05-Jan-2026 05:05:42 | WARNING: An illegal reflective access operation has occurred |
| 05-Jan-2026 05:05:42 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 05-Jan-2026 05:05:42 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 05-Jan-2026 05:05:42 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 05-Jan-2026 05:05:42 | WARNING: All illegal access operations will be denied in a future release |
| 05-Jan-2026 05:05:45 | Request to stop 'JB-GDB734-JOB1-6' received from jprocter |
| 05-Jan-2026 05:05:45 | Exception executing command "/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test Interrupted while waiting for process to finishcom.atlassian.utils.process.ProcessException: Interrupted while waiting for process to finish |
| 05-Jan-2026 05:05:45 | 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 143 while expected 0 |
| 05-Jan-2026 05:05:45 | Finished task 'Run tests with openclover under gradle' with result: Failed |
| 05-Jan-2026 05:05:45 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 05-Jan-2026 05:05:45 | Bamboo Artifactory Plugin version: 2.6.2 |
| 05-Jan-2026 05:05:45 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #6 (JB-GDB734-JOB1-6)' ... 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-GDB734-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_planRepository_1_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_repository_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 bamboo_CLOVER_CLASSES=1607 bamboo_buildKey=JB-GDB734-JOB1 bamboo_CLOVER_COVERED_CONDITIONALS=16926 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-GDB734-JOB1-6 bamboo_CLOVER_STATEMENTS=121136 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_agentId=196609 bamboo_CLOVER_NCLOC=290874 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 bamboo_planRepository_previousRevision=5857fe763e55a89397fc3bb157f282726c22b1a7 bamboo_CLOVER_CONDITIONALS=45046 bamboo_repository_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ bamboo_repository_46498616_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_CLOVER_PACKAGES=135 bamboo_planRepository_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch _=/usr/bin/java bamboo_CLOVER_COVERAGE_DELTA=-0.1 bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr 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 bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_ManualBuildTriggerReason_userName=jprocter 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_planKey=JB-GDB734 bamboo_planRepository_username= bamboo_repository_46498616_git_username= bamboo_repository_46498616_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7 bamboo_planRepository_1_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_CLOVER_ELEMENTS=184000 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-JOB1-6 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_CLOVER_BUILD_COVERAGE=40.8 bamboo_CLOVER_METHODS=17818 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_CLOVER_COVERED_STATEMENTS=50445 bamboo_repository_46498616_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_repository_46498616_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 bamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=6 SHELL=/bin/bash bamboo_ManualBuildTriggerReason_stageName=Default Stage bamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_shortPlanKey=GDB734 bamboo_shortJobKey=JOB1 bamboo_buildTimeStamp=2026-01-05T05:00:18.274Z bamboo_repository_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7 bamboo_CLOVER_COVERED_METHODS=7764 bamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_buildResultKey=JB-GDB734-JOB1-6 bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests bamboo_planRepository_1_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_4=/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport 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 LANG=en_GB.UTF-8 bamboo_buildFailed=true bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_jobFailed=true bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=5857fe763e55a89397fc3bb157f282726c22b1a7 bamboo_planRepository_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch bamboo_plan_storageTag=plan-46302801 bamboo_CLOVER_LOC=460432 bamboo_CLOVER_FILES=1270 USER=bamboo bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_CLOVER_COVERED_ELEMENTS=75135 bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1 bamboo_RerunBuildTriggerReason_noOfRetries=1 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_repository_46498616_name=Jalview Gitlab HOME=/home/bamboo bamboo_repository_46498616_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 05-Jan-2026 05:05:45 | 2414 |
| 05-Jan-2026 05:05:52 | |
| 05-Jan-2026 05:05:52 | > Configure project : |
| 05-Jan-2026 05:05:52 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 05-Jan-2026 05:05:52 | JALVIEW_VERSION is set to '2.12.0' |
| 05-Jan-2026 05:05:52 | HEADLESS BUILD |
| 05-Jan-2026 05:05:52 | J2S ENABLED |
| 05-Jan-2026 05:05:52 | Using a LOCAL profile. |
| 05-Jan-2026 05:05:53 | eclipseDir exists |
| 05-Jan-2026 05:05:55 | |
| 05-Jan-2026 05:05:55 | > Task :cloverHtmlReport |
| 05-Jan-2026 05:05:55 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 05-Jan-2026 05:06:00 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover' |
| 05-Jan-2026 05:06:07 | ERROR: Invalid Java source found or Clover failed to parse it: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/src/jalview/gui/AlignFrame.java |
| 05-Jan-2026 05:06:46 | Build JB-GDB734-JOB1-6 had to be cancelled: agent had been requested to stop the build but sent no response |
| 05-Jan-2026 05:06:56 | Done. Processed 137 packages in 56180ms (410ms per package). |
| 05-Jan-2026 05:07:06 | |
| 05-Jan-2026 05:07:06 | > Task :cloverXmlReport |
| 05-Jan-2026 05:07:06 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 05-Jan-2026 05:07:13 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover/clover.xml' |
| 05-Jan-2026 05:07:14 | |
| 05-Jan-2026 05:07:14 | > Task :cloverReport |
| 05-Jan-2026 05:07:14 | |
| 05-Jan-2026 05:07:14 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 05-Jan-2026 05:07:14 | |
| 05-Jan-2026 05:07:14 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 05-Jan-2026 05:07:14 | |
| 05-Jan-2026 05:07:14 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 05-Jan-2026 05:07:14 | |
| 05-Jan-2026 05:07:14 | BUILD SUCCESSFUL in 1m 28s |
| 05-Jan-2026 05:07:14 | 2 actionable tasks: 2 executed |
| 05-Jan-2026 05:07:14 | Finished task 'Clover Report' with result: Success |
| 05-Jan-2026 05:07:14 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 05-Jan-2026 05:07:14 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1... |
| 05-Jan-2026 05:07:14 | Failing task since 2 failing test cases were found. |
| 05-Jan-2026 05:07:14 | Finished task 'TestNG Parser' with result: Failed |
| 05-Jan-2026 05:07:14 | Running post build plugin 'NCover Results Collector' |
| 05-Jan-2026 05:07:14 | Running post build plugin 'Artifact Copier' |
| 05-Jan-2026 05:07:16 | Running post build plugin 'Artifactory Release Management Staging' |
| 05-Jan-2026 05:07:16 | Running post build plugin 'Artifactory Build Info Copier' |
| 05-Jan-2026 05:07:16 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 05-Jan-2026 05:07:16 | Running post build plugin 'npm Cache Cleanup' |
| 05-Jan-2026 05:07:16 | Running post build plugin 'Clover Results Collector' |
| 05-Jan-2026 05:07:16 | Running post build plugin 'Docker Container Cleanup' |
| 05-Jan-2026 05:07:16 | Finalising the build... |
| 05-Jan-2026 05:07:16 | Stopping timer. |
| 05-Jan-2026 05:07:16 | Build JB-GDB734-JOB1-6 completed. |
| 05-Jan-2026 05:07:14 | Publishing an artifact: Clover Report (System) |
| 05-Jan-2026 05:07:16 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.102 s |
| 05-Jan-2026 05:07:16 | Publishing an artifact: TestNG report |
| 05-Jan-2026 05:07:16 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/test does not exist. |
| 05-Jan-2026 05:07:16 | The artifact hasn't been successfully published after 88.60 μs |