Build: #2 failed
Job: Clover and Tests failed
Build log
The build generated 259 lines of output. Download or view full build log
| 18-Nov-2024 09:37:50 | Build Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests #2 (JB-GDB647-JOB1-2) started building on agent Default Agent |
| 18-Nov-2024 09:37:50 | |
| 18-Nov-2024 09:37:50 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1 |
| 18-Nov-2024 09:37:50 | Executing build Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests #2 (JB-GDB647-JOB1-2) |
| 18-Nov-2024 09:37:50 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 18-Nov-2024 09:37:50 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1 |
| 18-Nov-2024 09:37:50 | Updating source code to revision: 5e8bd075739b756cac8f741a47a7de952c45f879 |
| 18-Nov-2024 09:37:50 | Fetching 'refs/heads/spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure' from 'http://source.jalview.org/git/jalview.git'. |
| 18-Nov-2024 09:37:50 | Checking out revision 5e8bd075739b756cac8f741a47a7de952c45f879. |
| 18-Nov-2024 09:37:51 | Already on 'spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure' |
| 18-Nov-2024 09:37:51 | Updated source code to revision: 5e8bd075739b756cac8f741a47a7de952c45f879 |
| 18-Nov-2024 09:37:51 | Finished task 'Checkout Default Repository' with result: Success |
| 18-Nov-2024 09:37:51 | Running pre-build action: VCS Version Collector |
| 18-Nov-2024 09:37:51 | Running pre-build action: Artifactory Release Staging |
| 18-Nov-2024 09:37:52 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 18-Nov-2024 09:37:52 | Bamboo Artifactory Plugin version: 2.6.2 |
| 18-Nov-2024 09:37:52 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests #2 (JB-GDB647-JOB1-2)' ... running command line: /home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_repository_46498215_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_repository_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB647-JOB1-2 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDB647-JOB1 bamboo_shortPlanName=spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_repository_46498215_name=Jalview Git bamboo_planRepository_name=Jalview Git LOGNAME=bamboo bamboo_buildNumber=2 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB647-JOB1-2 bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_repository_46498215_git_username= bamboo_planName=Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_shortPlanKey=GDB647 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_buildTimeStamp=2024-11-18T09:37:49.999Z bamboo_repository_previous_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_planRepository_previousRevision=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_repository_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_buildResultKey=JB-GDB647-JOB1-2 bamboo_repository_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_repository_46498215_previous_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_repository_46498215_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_planRepository_1_revision=5e8bd075739b756cac8f741a47a7de952c45f879 SHLVL=1 bamboo_repository_46498215_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Git JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ bamboo_dependenciesDisabled=false LANG=en_GB.UTF-8 bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure 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=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_repository_46498215_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure _=/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-46302029 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_ManualBuildTriggerReason_userName=jprocter bamboo_repository_git_repositoryUrl=http://source.jalview.org/git/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-GDB647-JOB1 bamboo_planKey=JB-GDB647 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 18-Nov-2024 09:37:52 | 444 |
| 18-Nov-2024 09:37:52 | Starting a Gradle Daemon (subsequent builds will be faster) |
| 18-Nov-2024 09:38:04 | |
| 18-Nov-2024 09:38:04 | > Configure project : |
| 18-Nov-2024 09:38:04 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 18-Nov-2024 09:38:04 | JALVIEW_VERSION is set to '2.11.4.2' |
| 18-Nov-2024 09:38:04 | HEADLESS BUILD |
| 18-Nov-2024 09:38:04 | J2S ENABLED |
| 18-Nov-2024 09:38:04 | Using a LOCAL profile. |
| 18-Nov-2024 09:38:06 | eclipseDir exists |
| 18-Nov-2024 09:38:07 | |
| 18-Nov-2024 09:38:07 | > Task :clean |
| 18-Nov-2024 09:38:07 | > Task :cleanClover |
| 18-Nov-2024 09:38:07 | > Task :cleanTest UP-TO-DATE |
| 18-Nov-2024 09:38:09 | |
| 18-Nov-2024 09:38:09 | > Task :cloverInstrJava |
| 18-Nov-2024 09:38:09 | Clover: About to instrument 1105 files |
| 18-Nov-2024 09:38:09 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 18-Nov-2024 09:38:09 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/clover/clover.db'. |
| 18-Nov-2024 09:38:09 | Processing files at 1.9 source level. |
| 18-Nov-2024 09:38:12 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 18-Nov-2024 09:38:12 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 18-Nov-2024 09:38:12 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 18-Nov-2024 09:38:12 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 18-Nov-2024 09:38:12 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 18-Nov-2024 09:38:12 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 18-Nov-2024 09:38:12 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 18-Nov-2024 09:38:19 | Clover all over. Instrumented 1105 files (112 packages). |
| 18-Nov-2024 09:38:22 | |
| 18-Nov-2024 09:38:22 | > Task :cloverInstrTests |
| 18-Nov-2024 09:38:22 | Clover: About to instrument test files |
| 18-Nov-2024 09:38:22 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 18-Nov-2024 09:38:22 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/clover/clover.db'. |
| 18-Nov-2024 09:38:22 | Processing files at 1.9 source level. |
| 18-Nov-2024 09:38:25 | Clover all over. Instrumented 292 files (52 packages). |
| 18-Nov-2024 09:38:25 | 1600 test methods detected. |
| 18-Nov-2024 09:38:25 | |
| 18-Nov-2024 09:38:25 | > Task :cloverInstr |
| 18-Nov-2024 09:38:27 | |
| 18-Nov-2024 09:38:27 | > Task :compileCloverJava |
| 18-Nov-2024 09:38:27 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 18-Nov-2024 09:38:27 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:38:27 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:38:27 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:38:27 | Setting target compatibility to 11 |
| 18-Nov-2024 09:38:49 | Note: Some input files use or override a deprecated API. |
| 18-Nov-2024 09:38:49 | Note: Recompile with -Xlint:deprecation for details. |
| 18-Nov-2024 09:38:49 | Note: Some input files use unchecked or unsafe operations. |
| 18-Nov-2024 09:38:49 | Note: Recompile with -Xlint:unchecked for details. |
| 18-Nov-2024 09:38:54 | |
| 18-Nov-2024 09:38:54 | > Task :processCloverResources NO-SOURCE |
| 18-Nov-2024 09:38:54 | > Task :cloverClasses |
| 18-Nov-2024 09:38:55 | > Task :copyHelp |
| 18-Nov-2024 09:38:56 | > Task :buildIndices |
| 18-Nov-2024 09:38:56 | > Task :copyResources |
| 18-Nov-2024 09:38:56 | > Task :copyChannelResources |
| 18-Nov-2024 09:38:56 | |
| 18-Nov-2024 09:38:56 | > Task :createBuildProperties |
| 18-Nov-2024 09:38:56 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 18-Nov-2024 09:38:56 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:38:56 | |
| 18-Nov-2024 09:38:56 | > Task :buildResources |
| 18-Nov-2024 09:38:56 | > Task :copyDocs |
| 18-Nov-2024 09:38:57 | |
| 18-Nov-2024 09:38:57 | > Task :convertMdFiles |
| 18-Nov-2024 09:38:57 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 18-Nov-2024 09:38:57 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 18-Nov-2024 09:38:57 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 18-Nov-2024 09:38:57 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/building.html |
| 18-Nov-2024 09:38:57 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 18-Nov-2024 09:38:57 | |
| 18-Nov-2024 09:38:57 | > Task :releasesTemplates |
| 18-Nov-2024 09:38:57 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 18-Nov-2024 09:38:57 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:38:57 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:38:57 | Stripping rc/test/etc for TEST |
| 18-Nov-2024 09:38:57 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/help/markdown/whatsnew/whatsnew-TEST.md |
| 18-Nov-2024 09:38:57 | |
| 18-Nov-2024 09:38:57 | > Task :prepare |
| 18-Nov-2024 09:38:59 | |
| 18-Nov-2024 09:38:59 | > Task :compileJava |
| 18-Nov-2024 09:38:59 | Setting target compatibility to 11 |
| 18-Nov-2024 09:39:05 | Note: Some input files use or override a deprecated API. |
| 18-Nov-2024 09:39:05 | Note: Recompile with -Xlint:deprecation for details. |
| 18-Nov-2024 09:39:05 | Note: Some input files use unchecked or unsafe operations. |
| 18-Nov-2024 09:39:05 | Note: Recompile with -Xlint:unchecked for details. |
| 18-Nov-2024 09:39:08 | |
| 18-Nov-2024 09:39:08 | > Task :compileTestJava |
| 18-Nov-2024 09:39:08 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
| 18-Nov-2024 09:39:08 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:39:08 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:39:08 | Setting target compatibility to 11 |
| 18-Nov-2024 09:39:14 | Note: Some input files use or override a deprecated API. |
| 18-Nov-2024 09:39:14 | Note: Recompile with -Xlint:deprecation for details. |
| 18-Nov-2024 09:39:14 | Note: Some input files use unchecked or unsafe operations. |
| 18-Nov-2024 09:39:14 | Note: Recompile with -Xlint:unchecked for details. |
| 18-Nov-2024 09:39:15 | |
| 18-Nov-2024 09:39:15 | > Task :processTestResources |
| 18-Nov-2024 09:39:15 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
| 18-Nov-2024 09:39:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:39:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:39:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:39:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:39:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:39:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:39:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:39:15 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-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. |
| 18-Nov-2024 09:39:15 | |
| 18-Nov-2024 09:39:15 | > Task :testClasses |
| 18-Nov-2024 09:39:17 | |
| 18-Nov-2024 09:39:17 | > Task :testTask0 |
| 18-Nov-2024 09:39:17 | Running tests WITH clover |
| 18-Nov-2024 09:39:20 | WARNING: An illegal reflective access operation has occurred |
| 18-Nov-2024 09:39:20 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 18-Nov-2024 09:39:20 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 18-Nov-2024 09:39:20 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 18-Nov-2024 09:39:20 | WARNING: All illegal access operations will be denied in a future release |
| 18-Nov-2024 09:40:25 | |
| 18-Nov-2024 09:40:25 | Gradle suite > Gradle test > jalview.io.cache.JvCacheableInputBoxTest.updateCacheTest FAILED |
| 18-Nov-2024 09:40:25 | java.lang.AssertionError: Giving up after 1.4s waiting for cache to be updated. |
| 18-Nov-2024 09:40:25 | at org.junit.Assert.fail(Assert.java:88) |
| 18-Nov-2024 09:40:25 | at jalview.io.cache.JvCacheableInputBoxTest.__CLR4_4_1shislu47c8(JvCacheableInputBoxTest.java:107) |
| 18-Nov-2024 09:40:25 | at jalview.io.cache.JvCacheableInputBoxTest.updateCacheTest(JvCacheableInputBoxTest.java:82) |
| 18-Nov-2024 09:54:15 | Requesting stop of task ':testTask0' as it has exceeded its configured timeout of 15m. |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | 1157 tests completed, 1 failed, 1 skipped |
| 18-Nov-2024 09:54:15 | > Task :testTask0 FAILED |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | FAILURE: Build completed with 2 failures. |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | 1: Task failed with an exception. |
| 18-Nov-2024 09:54:15 | ----------- |
| 18-Nov-2024 09:54:15 | * What went wrong: |
| 18-Nov-2024 09:54:15 | Execution failed for task ':testTask0'. |
| 18-Nov-2024 09:54:15 | > Timeout has been exceeded |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | * Try: |
| 18-Nov-2024 09:54:15 | > Run with --stacktrace option to get the stack trace. |
| 18-Nov-2024 09:54:15 | > Run with --info or --debug option to get more log output. |
| 18-Nov-2024 09:54:15 | > Run with --scan to get full insights. |
| 18-Nov-2024 09:54:15 | ============================================================================== |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | 2: Task failed with an exception. |
| 18-Nov-2024 09:54:15 | ----------- |
| 18-Nov-2024 09:54:15 | * Where: |
| 18-Nov-2024 09:54:15 | Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build.gradle' line: 1967 |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | * What went wrong: |
| 18-Nov-2024 09:54:15 | Failed tests! |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | * Try: |
| 18-Nov-2024 09:54:15 | ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ |
| 18-Nov-2024 09:54:15 | │jalview:testTask0 results: FAILURE (1157 tests, 1155 successes, 1 failures, 1 skipped) in 14 minutes, 59.934 seconds │ |
| 18-Nov-2024 09:54:15 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/tests/testTask0/index.html│ |
| 18-Nov-2024 09:54:15 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 18-Nov-2024 09:54:15 | │OVERALL: results: FAILURE (1157 tests, 1155 successes, 1 failures, 1 skipped) in 14 minutes, 59.934 seconds │ |
| 18-Nov-2024 09:54:15 | └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 18-Nov-2024 09:54:15 | Please consult deprecation warnings for more details. |
| 18-Nov-2024 09:54:15 | 18 actionable tasks: 17 executed, 1 up-to-date |
| 18-Nov-2024 09:54:15 | > Run with --stacktrace option to get the stack trace. |
| 18-Nov-2024 09:54:15 | > Run with --info or --debug option to get more log output. |
| 18-Nov-2024 09:54:15 | > Run with --scan to get full insights. |
| 18-Nov-2024 09:54:15 | ============================================================================== |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | * Get more help at https://help.gradle.org |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | BUILD FAILED in 16m 23s |
| 18-Nov-2024 09:54:15 | |
| 18-Nov-2024 09:54:15 | 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 |
| 18-Nov-2024 09:54:15 | Finished task 'Run tests with openclover under gradle' with result: Failed |
| 18-Nov-2024 09:54:15 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 18-Nov-2024 09:54:15 | Bamboo Artifactory Plugin version: 2.6.2 |
| 18-Nov-2024 09:54:15 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests #2 (JB-GDB647-JOB1-2)' ... running command line: /home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_repository_46498215_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_repository_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB647-JOB1-2 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDB647-JOB1 bamboo_shortPlanName=spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_repository_46498215_name=Jalview Git bamboo_planRepository_name=Jalview Git LOGNAME=bamboo bamboo_buildNumber=2 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB647-JOB1-2 bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_repository_46498215_git_username= bamboo_planName=Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_shortPlanKey=GDB647 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_buildTimeStamp=2024-11-18T09:37:49.999Z bamboo_repository_previous_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_planRepository_previousRevision=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_repository_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_buildResultKey=JB-GDB647-JOB1-2 bamboo_repository_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_repository_46498215_previous_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_repository_46498215_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_planRepository_1_revision=5e8bd075739b756cac8f741a47a7de952c45f879 SHLVL=1 bamboo_repository_46498215_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Git 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_dependenciesDisabled=false 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=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure 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=5e8bd075739b756cac8f741a47a7de952c45f879 bamboo_repository_46498215_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure _=/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-46302029 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_ManualBuildTriggerReason_userName=jprocter bamboo_repository_git_repositoryUrl=http://source.jalview.org/git/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-GDB647-JOB1 bamboo_planKey=JB-GDB647 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 18-Nov-2024 09:54:15 | 444 |
| 18-Nov-2024 09:54:22 | |
| 18-Nov-2024 09:54:22 | > Configure project : |
| 18-Nov-2024 09:54:22 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 18-Nov-2024 09:54:22 | JALVIEW_VERSION is set to '2.11.4.2' |
| 18-Nov-2024 09:54:22 | HEADLESS BUILD |
| 18-Nov-2024 09:54:22 | J2S ENABLED |
| 18-Nov-2024 09:54:22 | Using a LOCAL profile. |
| 18-Nov-2024 09:54:23 | eclipseDir exists |
| 18-Nov-2024 09:54:25 | |
| 18-Nov-2024 09:54:25 | > Task :cloverHtmlReport |
| 18-Nov-2024 09:54:25 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 18-Nov-2024 09:54:26 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/clover' |
| 18-Nov-2024 09:54:53 | Done. Processed 116 packages in 26769ms (230ms per package). |
| 18-Nov-2024 09:54:57 | |
| 18-Nov-2024 09:54:57 | > Task :cloverXmlReport |
| 18-Nov-2024 09:54:57 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 18-Nov-2024 09:54:58 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/clover/clover.xml' |
| 18-Nov-2024 09:54:58 | |
| 18-Nov-2024 09:54:58 | > Task :cloverReport |
| 18-Nov-2024 09:54:58 | |
| 18-Nov-2024 09:54:58 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 18-Nov-2024 09:54:58 | |
| 18-Nov-2024 09:54:58 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 18-Nov-2024 09:54:58 | |
| 18-Nov-2024 09:54:58 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 18-Nov-2024 09:54:58 | |
| 18-Nov-2024 09:54:58 | BUILD SUCCESSFUL in 42s |
| 18-Nov-2024 09:54:58 | 2 actionable tasks: 2 executed |
| 18-Nov-2024 09:55:00 | Finished task 'Clover Report' with result: Success |
| 18-Nov-2024 09:55:00 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 18-Nov-2024 09:55:00 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1... |
| 18-Nov-2024 09:55:00 | Failing task since test cases were expected but none were found. |
| 18-Nov-2024 09:55:00 | Finished task 'TestNG Parser' with result: Failed |
| 18-Nov-2024 09:55:00 | Running post build plugin 'NCover Results Collector' |
| 18-Nov-2024 09:55:00 | Running post build plugin 'Artifact Copier' |
| 18-Nov-2024 09:55:00 | Publishing an artifact: Clover Report (System) |
| 18-Nov-2024 09:55:01 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.322 s |
| 18-Nov-2024 09:55:01 | Publishing an artifact: TestNG report |
| 18-Nov-2024 09:55:01 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB647-JOB1/build/reports/tests/test does not exist. |
| 18-Nov-2024 09:55:01 | The artifact hasn't been successfully published after 1.434 ms |
| 18-Nov-2024 09:55:01 | Running post build plugin 'Artifactory Release Management Staging' |
| 18-Nov-2024 09:55:01 | Running post build plugin 'Artifactory Build Info Copier' |
| 18-Nov-2024 09:55:01 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 18-Nov-2024 09:55:01 | Running post build plugin 'npm Cache Cleanup' |
| 18-Nov-2024 09:55:01 | Running post build plugin 'Clover Results Collector' |
| 18-Nov-2024 09:55:01 | Running post build plugin 'Docker Container Cleanup' |
| 18-Nov-2024 09:55:01 | Finalising the build... |
| 18-Nov-2024 09:55:01 | Stopping timer. |
| 18-Nov-2024 09:55:01 | Build JB-GDB647-JOB1-2 completed. |
| 18-Nov-2024 09:55:01 | Running on server: post build plugin 'NCover Results Collector' |
| 18-Nov-2024 09:55:01 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 18-Nov-2024 09:55:01 | Running on server: post build plugin 'Clover Delta Calculator' |
| 18-Nov-2024 09:55:01 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 18-Nov-2024 09:55:01 | All post build plugins have finished |
| 18-Nov-2024 09:55:01 | Generating build results summary... |
| 18-Nov-2024 09:55:01 | Saving build results to disk... |
| 18-Nov-2024 09:55:01 | Logging substituted variables... |
| 18-Nov-2024 09:55:01 | Indexing build results... |
| 18-Nov-2024 09:55:01 | Finished building JB-GDB647-JOB1-2. |