Build: #5 failed
Job: Clover and Tests failed
Build log
The build generated 515 lines of output. Download or view full build log
| 25-Apr-2024 13:59:14 | Build Jalview Builds - Gradle Develop Build - feature-JAL-4392_consensus_secondary_structure - Clover and Tests #5 (JB-GDB581-JOB1-5) started building on agent Default Agent |
| 25-Apr-2024 13:59:14 | |
| 25-Apr-2024 13:59:14 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1 |
| 25-Apr-2024 13:59:14 | Executing build Jalview Builds - Gradle Develop Build - feature-JAL-4392_consensus_secondary_structure - Clover and Tests #5 (JB-GDB581-JOB1-5) |
| 25-Apr-2024 13:59:14 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 25-Apr-2024 13:59:14 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1 |
| 25-Apr-2024 13:59:14 | Updating source code to revision: 7af2c16e2466ea2665c29b5feba6341c1e255291 |
| 25-Apr-2024 13:59:15 | Fetching 'refs/heads/feature/JAL-4392_consensus_secondary_structure' from 'http://source.jalview.org/git/jalview.git'. |
| 25-Apr-2024 13:59:17 | Checking out revision 7af2c16e2466ea2665c29b5feba6341c1e255291. |
| 25-Apr-2024 13:59:19 | Already on 'feature/JAL-4392_consensus_secondary_structure' |
| 25-Apr-2024 13:59:19 | Updated source code to revision: 7af2c16e2466ea2665c29b5feba6341c1e255291 |
| 25-Apr-2024 13:59:19 | Finished task 'Checkout Default Repository' with result: Success |
| 25-Apr-2024 13:59:19 | Running pre-build action: VCS Version Collector |
| 25-Apr-2024 13:59:19 | Running pre-build action: Artifactory Release Staging |
| 25-Apr-2024 13:59:19 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 25-Apr-2024 13:59:19 | Bamboo Artifactory Plugin version: 2.6.2 |
| 25-Apr-2024 13:59:19 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4392_consensus_secondary_structure - Clover and Tests #5 (JB-GDB581-JOB1-5)' ... 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-GDB581-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=feature/JAL-4392_consensus_secondary_structure bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_repository_46497836_revision_number=7af2c16e2466ea2665c29b5feba6341c1e255291 CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=feature/JAL-4392_consensus_secondary_structure bamboo_repository_revision_number=7af2c16e2466ea2665c29b5feba6341c1e255291 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB581-JOB1-5 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-GDB581-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDB581-JOB1 bamboo_shortPlanName=feature-JAL-4392_consensus_secondary_structure bamboo_planRepository_name=Jalview Git LOGNAME=bamboo bamboo_buildNumber=5 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-GDB581-JOB1-5 bamboo_repository_46497836_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - feature-JAL-4392_consensus_secondary_structure bamboo_shortPlanKey=GDB581 bamboo_shortJobKey=JOB1 bamboo_repository_46497836_previous_revision_number=7af2c16e2466ea2665c29b5feba6341c1e255291 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=7af2c16e2466ea2665c29b5feba6341c1e255291 bamboo_buildTimeStamp=2024-04-25T13:59:14.875+01:00 bamboo_repository_previous_revision_number=7af2c16e2466ea2665c29b5feba6341c1e255291 bamboo_planRepository_previousRevision=7af2c16e2466ea2665c29b5feba6341c1e255291 bamboo_repository_git_branch=feature/JAL-4392_consensus_secondary_structure bamboo_buildResultKey=JB-GDB581-JOB1-5 bamboo_repository_branch_name=feature/JAL-4392_consensus_secondary_structure bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - feature-JAL-4392_consensus_secondary_structure - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=7af2c16e2466ea2665c29b5feba6341c1e255291 SHLVL=1 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_repository_46497836_branch_name=feature/JAL-4392_consensus_secondary_structure 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_repository_46497836_git_branch=feature/JAL-4392_consensus_secondary_structure bamboo_planRepository_branch=feature/JAL-4392_consensus_secondary_structure 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=7af2c16e2466ea2665c29b5feba6341c1e255291 bamboo_planRepository_branchDisplayName=feature/JAL-4392_consensus_secondary_structure bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=feature/JAL-4392_consensus_secondary_structure _=/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_repository_46497836_git_username= bamboo_repository_46497836_name=Jalview Git bamboo_plan_storageTag=plan-46301271 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=reniacorreya 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-GDB581-JOB1 bamboo_planKey=JB-GDB581 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=feature/JAL-4392_consensus_secondary_structure PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 25-Apr-2024 13:59:19 | 444 |
| 25-Apr-2024 13:59:25 | Starting a Gradle Daemon, 3 busy Daemons could not be reused, use --status for details |
| 25-Apr-2024 13:59:42 | |
| 25-Apr-2024 13:59:42 | > Configure project : |
| 25-Apr-2024 13:59:42 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 25-Apr-2024 13:59:42 | JALVIEW_VERSION is set to '2.11.3.3' |
| 25-Apr-2024 13:59:42 | HEADLESS BUILD |
| 25-Apr-2024 13:59:42 | J2S ENABLED |
| 25-Apr-2024 13:59:43 | Using a LOCAL profile. |
| 25-Apr-2024 13:59:45 | eclipseDir exists |
| 25-Apr-2024 13:59:46 | |
| 25-Apr-2024 13:59:46 | > Task :clean |
| 25-Apr-2024 13:59:46 | > Task :cleanClover |
| 25-Apr-2024 13:59:46 | > Task :cleanTest UP-TO-DATE |
| 25-Apr-2024 13:59:48 | |
| 25-Apr-2024 13:59:48 | > Task :cloverInstrJava |
| 25-Apr-2024 13:59:48 | Clover: About to instrument 1086 files |
| 25-Apr-2024 13:59:48 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 25-Apr-2024 13:59:48 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/clover/clover.db'. |
| 25-Apr-2024 13:59:48 | Processing files at 1.9 source level. |
| 25-Apr-2024 13:59:51 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 25-Apr-2024 13:59:51 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 25-Apr-2024 13:59:51 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 25-Apr-2024 13:59:51 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 25-Apr-2024 13:59:51 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 25-Apr-2024 13:59:51 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 25-Apr-2024 13:59:51 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 25-Apr-2024 13:59:58 | Clover all over. Instrumented 1086 files (111 packages). |
| 25-Apr-2024 14:00:01 | |
| 25-Apr-2024 14:00:01 | > Task :cloverInstrTests |
| 25-Apr-2024 14:00:01 | Clover: About to instrument test files |
| 25-Apr-2024 14:00:01 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 25-Apr-2024 14:00:01 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/clover/clover.db'. |
| 25-Apr-2024 14:00:01 | Processing files at 1.9 source level. |
| 25-Apr-2024 14:00:04 | Clover all over. Instrumented 286 files (52 packages). |
| 25-Apr-2024 14:00:04 | 1571 test methods detected. |
| 25-Apr-2024 14:00:04 | |
| 25-Apr-2024 14:00:04 | > Task :cloverInstr |
| 25-Apr-2024 14:00:06 | |
| 25-Apr-2024 14:00:06 | > Task :compileCloverJava |
| 25-Apr-2024 14:00:06 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 25-Apr-2024 14:00:06 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:06 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:06 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:06 | Setting target compatibility to 11 |
| 25-Apr-2024 14:00:27 | /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/clover/clover-instr/jalview/analysis/Finder.java:609: warning: non-varargs call of varargs method with inexact argument type for last parameter; |
| 25-Apr-2024 14:00:27 | __CLR4_4_130xm30xmlvf942dy.R.inc(141393);allFeatures = sf.getAllFeatures(null); |
| 25-Apr-2024 14:00:27 | ^ |
| 25-Apr-2024 14:00:27 | cast to String for a varargs call |
| 25-Apr-2024 14:00:27 | cast to String[] for a non-varargs call and to suppress this warning |
| 25-Apr-2024 14:00:28 | Note: Some input files use or override a deprecated API. |
| 25-Apr-2024 14:00:28 | Note: Recompile with -Xlint:deprecation for details. |
| 25-Apr-2024 14:00:28 | Note: Some input files use unchecked or unsafe operations. |
| 25-Apr-2024 14:00:28 | Note: Recompile with -Xlint:unchecked for details. |
| 25-Apr-2024 14:00:28 | 1 warning |
| 25-Apr-2024 14:00:36 | |
| 25-Apr-2024 14:00:36 | > Task :processCloverResources NO-SOURCE |
| 25-Apr-2024 14:00:36 | > Task :cloverClasses |
| 25-Apr-2024 14:00:36 | > Task :copyHelp |
| 25-Apr-2024 14:00:37 | > Task :buildIndices |
| 25-Apr-2024 14:00:37 | > Task :copyResources |
| 25-Apr-2024 14:00:38 | > Task :copyChannelResources |
| 25-Apr-2024 14:00:38 | |
| 25-Apr-2024 14:00:38 | > Task :createBuildProperties |
| 25-Apr-2024 14:00:38 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 25-Apr-2024 14:00:38 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:38 | |
| 25-Apr-2024 14:00:38 | > Task :buildResources |
| 25-Apr-2024 14:00:38 | > Task :copyDocs |
| 25-Apr-2024 14:00:38 | |
| 25-Apr-2024 14:00:38 | > Task :convertMdFiles |
| 25-Apr-2024 14:00:38 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 25-Apr-2024 14:00:38 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 25-Apr-2024 14:00:38 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 25-Apr-2024 14:00:38 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/resources/doc_build/doc/building.html |
| 25-Apr-2024 14:00:39 | |
| 25-Apr-2024 14:00:39 | > Task :releasesTemplates |
| 25-Apr-2024 14:00:39 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 25-Apr-2024 14:00:39 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:39 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:39 | |
| 25-Apr-2024 14:00:39 | > Task :prepare |
| 25-Apr-2024 14:00:41 | |
| 25-Apr-2024 14:00:41 | > Task :compileJava |
| 25-Apr-2024 14:00:41 | Setting target compatibility to 11 |
| 25-Apr-2024 14:00:47 | /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/src/jalview/analysis/Finder.java:609: warning: non-varargs call of varargs method with inexact argument type for last parameter; |
| 25-Apr-2024 14:00:47 | allFeatures = sf.getAllFeatures(null); |
| 25-Apr-2024 14:00:47 | ^ |
| 25-Apr-2024 14:00:47 | cast to String for a varargs call |
| 25-Apr-2024 14:00:47 | cast to String[] for a non-varargs call and to suppress this warning |
| 25-Apr-2024 14:00:47 | Note: Some input files use or override a deprecated API. |
| 25-Apr-2024 14:00:47 | Note: Recompile with -Xlint:deprecation for details. |
| 25-Apr-2024 14:00:47 | Note: Some input files use unchecked or unsafe operations. |
| 25-Apr-2024 14:00:47 | Note: Recompile with -Xlint:unchecked for details. |
| 25-Apr-2024 14:00:47 | 1 warning |
| 25-Apr-2024 14:00:52 | |
| 25-Apr-2024 14:00:52 | > Task :compileTestJava |
| 25-Apr-2024 14:00:52 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
| 25-Apr-2024 14:00:52 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:52 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:52 | Setting target compatibility to 11 |
| 25-Apr-2024 14:00:57 | Note: Some input files use or override a deprecated API. |
| 25-Apr-2024 14:00:57 | Note: Recompile with -Xlint:deprecation for details. |
| 25-Apr-2024 14:00:57 | Note: Some input files use unchecked or unsafe operations. |
| 25-Apr-2024 14:00:57 | Note: Recompile with -Xlint:unchecked for details. |
| 25-Apr-2024 14:00:58 | |
| 25-Apr-2024 14:00:58 | > Task :processTestResources |
| 25-Apr-2024 14:00:58 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
| 25-Apr-2024 14:00:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-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. |
| 25-Apr-2024 14:00:58 | |
| 25-Apr-2024 14:00:58 | > Task :testClasses |
| 25-Apr-2024 14:01:00 | |
| 25-Apr-2024 14:01:00 | > Task :testTask0 |
| 25-Apr-2024 14:01:00 | Running tests WITH clover |
| 25-Apr-2024 14:01:05 | WARNING: An illegal reflective access operation has occurred |
| 25-Apr-2024 14:01:05 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 25-Apr-2024 14:01:05 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 25-Apr-2024 14:01:05 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 25-Apr-2024 14:01:05 | WARNING: All illegal access operations will be denied in a future release |
| 25-Apr-2024 14:01:18 | |
| 25-Apr-2024 14:01:18 | Gradle suite > Gradle test > jalview.gui.AnnotationRowFilterTest.testGetAnnotationItems FAILED |
| 25-Apr-2024 14:01:18 | java.lang.AssertionError: expected [[Conservation, Quality, Consensus, Occupancy, ann1Label, Significance, Significance_1, Jronn_FER_CAPAA, Jronn_FER_BRANA, Jnet_FER_BRANA, Jnet_FER_BRANA_2]] but found [[Conservation, Quality, Consensus, SecondaryStructureConsensus, Occupancy, ann1Label, Significance, Significance_1, Jronn_FER_CAPAA, Jronn_FER_BRANA, Jnet_FER_BRANA, Jnet_FER_BRANA_2]] |
| 25-Apr-2024 14:01:18 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:01:18 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:01:18 | at org.testng.Assert.assertEquals(Assert.java:125) |
| 25-Apr-2024 14:01:18 | at org.testng.Assert.assertEquals(Assert.java:178) |
| 25-Apr-2024 14:01:18 | at org.testng.Assert.assertEquals(Assert.java:188) |
| 25-Apr-2024 14:01:18 | at jalview.gui.AnnotationRowFilterTest.__CLR4_4_1eed103npt(AnnotationRowFilterTest.java:123) |
| 25-Apr-2024 14:01:18 | at jalview.gui.AnnotationRowFilterTest.testGetAnnotationItems(AnnotationRowFilterTest.java:81) |
| 25-Apr-2024 14:01:58 | |
| 25-Apr-2024 14:01:58 | Gradle suite > Gradle test > jalview.gui.AnnotationChooserTest.testDeselectType_showForAll FAILED |
| 25-Apr-2024 14:01:58 | java.lang.AssertionError: |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.fail(AssertJUnit.java:59) |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:24) |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.assertFalse(AssertJUnit.java:41) |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.assertFalse(AssertJUnit.java:49) |
| 25-Apr-2024 14:01:58 | at jalview.gui.AnnotationChooserTest.__CLR4_4_1w9icr63odr(AnnotationChooserTest.java:621) |
| 25-Apr-2024 14:01:58 | at jalview.gui.AnnotationChooserTest.testDeselectType_showForAll(AnnotationChooserTest.java:592) |
| 25-Apr-2024 14:01:58 | |
| 25-Apr-2024 14:01:58 | Gradle suite > Gradle test > jalview.gui.AnnotationChooserTest.testDeselectType_showForSelected FAILED |
| 25-Apr-2024 14:01:58 | java.lang.AssertionError: |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.fail(AssertJUnit.java:59) |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:24) |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.assertFalse(AssertJUnit.java:41) |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.assertFalse(AssertJUnit.java:49) |
| 25-Apr-2024 14:01:58 | at jalview.gui.AnnotationChooserTest.__CLR4_4_1ff5qpk3oee(AnnotationChooserTest.java:666) |
| 25-Apr-2024 14:01:58 | at jalview.gui.AnnotationChooserTest.testDeselectType_showForSelected(AnnotationChooserTest.java:635) |
| 25-Apr-2024 14:01:58 | |
| 25-Apr-2024 14:01:58 | Gradle suite > Gradle test > jalview.gui.AnnotationChooserTest.testGetAnnotationTypes FAILED |
| 25-Apr-2024 14:01:58 | java.lang.AssertionError: Not six annotation types expected:<7> but was:<8> |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.fail(AssertJUnit.java:59) |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.failNotEquals(AssertJUnit.java:364) |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:80) |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:245) |
| 25-Apr-2024 14:01:58 | at jalview.gui.AnnotationChooserTest.__CLR4_4_12j8hyr3oa8(AnnotationChooserTest.java:328) |
| 25-Apr-2024 14:01:58 | at jalview.gui.AnnotationChooserTest.testGetAnnotationTypes(AnnotationChooserTest.java:314) |
| 25-Apr-2024 14:01:58 | |
| 25-Apr-2024 14:01:58 | Gradle suite > Gradle test > jalview.gui.AnnotationChooserTest.testResetOriginalState FAILED |
| 25-Apr-2024 14:01:58 | java.lang.AssertionError: |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.fail(AssertJUnit.java:59) |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:24) |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.assertFalse(AssertJUnit.java:41) |
| 25-Apr-2024 14:01:58 | at org.testng.AssertJUnit.assertFalse(AssertJUnit.java:49) |
| 25-Apr-2024 14:01:58 | at jalview.gui.AnnotationChooserTest.__CLR4_4_1osjsty3og5(AnnotationChooserTest.java:809) |
| 25-Apr-2024 14:01:58 | at jalview.gui.AnnotationChooserTest.testResetOriginalState(AnnotationChooserTest.java:781) |
| 25-Apr-2024 14:01:59 | |
| 25-Apr-2024 14:01:59 | Gradle suite > Gradle test > jalview.gui.AnnotationChooserTest.testSelectType_hideForAll FAILED |
| 25-Apr-2024 14:01:59 | java.lang.AssertionError: |
| 25-Apr-2024 14:01:59 | at org.testng.AssertJUnit.fail(AssertJUnit.java:59) |
| 25-Apr-2024 14:01:59 | at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:24) |
| 25-Apr-2024 14:01:59 | at org.testng.AssertJUnit.assertFalse(AssertJUnit.java:41) |
| 25-Apr-2024 14:01:59 | at org.testng.AssertJUnit.assertFalse(AssertJUnit.java:49) |
| 25-Apr-2024 14:01:59 | at jalview.gui.AnnotationChooserTest.__CLR4_4_16h992w3oao(AnnotationChooserTest.java:371) |
| 25-Apr-2024 14:01:59 | at jalview.gui.AnnotationChooserTest.testSelectType_hideForAll(AnnotationChooserTest.java:347) |
| 25-Apr-2024 14:01:59 | |
| 25-Apr-2024 14:01:59 | Gradle suite > Gradle test > jalview.gui.AnnotationChooserTest.testSelectType_hideForSelected FAILED |
| 25-Apr-2024 14:01:59 | java.lang.AssertionError: |
| 25-Apr-2024 14:01:59 | at org.testng.AssertJUnit.fail(AssertJUnit.java:59) |
| 25-Apr-2024 14:01:59 | at org.testng.AssertJUnit.assertTrue(AssertJUnit.java:24) |
| 25-Apr-2024 14:01:59 | at org.testng.AssertJUnit.assertFalse(AssertJUnit.java:41) |
| 25-Apr-2024 14:01:59 | at org.testng.AssertJUnit.assertFalse(AssertJUnit.java:49) |
| 25-Apr-2024 14:01:59 | at jalview.gui.AnnotationChooserTest.__CLR4_4_19i1ypa3ob9(AnnotationChooserTest.java:412) |
| 25-Apr-2024 14:01:59 | at jalview.gui.AnnotationChooserTest.testSelectType_hideForSelected(AnnotationChooserTest.java:385) |
| 25-Apr-2024 14:02:02 | |
| 25-Apr-2024 14:02:02 | Gradle suite > Gradle test > jalview.gui.StructureChooserTest.openStructureFileForSequenceTest[0](examples/uniref50.fa, FER1_SPIOL, examples/AlphaFold/AF-P00221-F1-model_v4.cif, Default, examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json, true, false, null, 15, 7, 0, null) FAILED |
| 25-Apr-2024 14:02:02 | java.lang.AssertionError: Wrong number of viewed annotations expected:<7> but was:<8> |
| 25-Apr-2024 14:02:02 | at org.junit.Assert.fail(Assert.java:88) |
| 25-Apr-2024 14:02:02 | at org.junit.Assert.failNotEquals(Assert.java:834) |
| 25-Apr-2024 14:02:02 | at org.junit.Assert.assertEquals(Assert.java:645) |
| 25-Apr-2024 14:02:02 | at jalview.gui.StructureChooserTest.__CLR4_4_1nqeoac3n52(StructureChooserTest.java:340) |
| 25-Apr-2024 14:02:02 | at jalview.gui.StructureChooserTest.openStructureFileForSequenceTest(StructureChooserTest.java:284) |
| 25-Apr-2024 14:02:02 | |
| 25-Apr-2024 14:02:02 | Gradle suite > Gradle test > jalview.gui.StructureChooserTest.openStructureFileForSequenceTest[1](examples/uniref50.fa, FER1_SPIOL, examples/AlphaFold/AF-P00221-F1-model_v4.cif, pLDDT, examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json, true, false, null, 15, 7, 0, null) FAILED |
| 25-Apr-2024 14:02:02 | java.lang.AssertionError: Wrong number of viewed annotations expected:<7> but was:<8> |
| 25-Apr-2024 14:02:02 | at org.junit.Assert.fail(Assert.java:88) |
| 25-Apr-2024 14:02:02 | at org.junit.Assert.failNotEquals(Assert.java:834) |
| 25-Apr-2024 14:02:02 | at org.junit.Assert.assertEquals(Assert.java:645) |
| 25-Apr-2024 14:02:02 | at jalview.gui.StructureChooserTest.__CLR4_4_1nqeoac3n52(StructureChooserTest.java:340) |
| 25-Apr-2024 14:02:02 | at jalview.gui.StructureChooserTest.openStructureFileForSequenceTest(StructureChooserTest.java:284) |
| 25-Apr-2024 14:02:03 | |
| 25-Apr-2024 14:02:03 | Gradle suite > Gradle test > jalview.gui.StructureChooserTest.openStructureFileForSequenceTest[2](examples/uniref50.fa, FER1_SPIOL, examples/AlphaFold/AF-P00221-F1-model_v4.cif, pLDDT, examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json, false, false, null, 15, 4, 0, null) FAILED |
| 25-Apr-2024 14:02:03 | java.lang.AssertionError: Wrong number of viewed annotations expected:<4> but was:<5> |
| 25-Apr-2024 14:02:03 | at org.junit.Assert.fail(Assert.java:88) |
| 25-Apr-2024 14:02:03 | at org.junit.Assert.failNotEquals(Assert.java:834) |
| 25-Apr-2024 14:02:03 | at org.junit.Assert.assertEquals(Assert.java:645) |
| 25-Apr-2024 14:02:03 | at jalview.gui.StructureChooserTest.__CLR4_4_1nqeoac3n52(StructureChooserTest.java:340) |
| 25-Apr-2024 14:02:03 | at jalview.gui.StructureChooserTest.openStructureFileForSequenceTest(StructureChooserTest.java:284) |
| 25-Apr-2024 14:02:04 | |
| 25-Apr-2024 14:02:04 | Gradle suite > Gradle test > jalview.gui.StructureChooserTest.openStructureFileForSequenceTest[3](examples/uniref50.fa, FER1_SPIOL, examples/AlphaFold/AF-P00221-F1-model_v4.cif, Default, examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json, true, false, JMOL, 15, 7, 1, null) FAILED |
| 25-Apr-2024 14:02:04 | java.lang.AssertionError: Wrong number of viewed annotations expected:<7> but was:<8> |
| 25-Apr-2024 14:02:04 | at org.junit.Assert.fail(Assert.java:88) |
| 25-Apr-2024 14:02:04 | at org.junit.Assert.failNotEquals(Assert.java:834) |
| 25-Apr-2024 14:02:04 | at org.junit.Assert.assertEquals(Assert.java:645) |
| 25-Apr-2024 14:02:04 | at jalview.gui.StructureChooserTest.__CLR4_4_1nqeoac3n52(StructureChooserTest.java:340) |
| 25-Apr-2024 14:02:04 | at jalview.gui.StructureChooserTest.openStructureFileForSequenceTest(StructureChooserTest.java:284) |
| 25-Apr-2024 14:02:05 | |
| 25-Apr-2024 14:02:05 | Gradle suite > Gradle test > jalview.gui.StructureChooserTest.openStructureFileForSequenceTest[4](examples/uniref50.fa, FER1_SPIOL, examples/AlphaFold/AF-P00221-F1-model_v4.cif, pLDDT, examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json, true, false, JMOL, 15, 7, 1, null) FAILED |
| 25-Apr-2024 14:02:05 | java.lang.AssertionError: Wrong number of viewed annotations expected:<7> but was:<8> |
| 25-Apr-2024 14:02:05 | at org.junit.Assert.fail(Assert.java:88) |
| 25-Apr-2024 14:02:05 | at org.junit.Assert.failNotEquals(Assert.java:834) |
| 25-Apr-2024 14:02:05 | at org.junit.Assert.assertEquals(Assert.java:645) |
| 25-Apr-2024 14:02:05 | at jalview.gui.StructureChooserTest.__CLR4_4_1nqeoac3n52(StructureChooserTest.java:340) |
| 25-Apr-2024 14:02:05 | at jalview.gui.StructureChooserTest.openStructureFileForSequenceTest(StructureChooserTest.java:284) |
| 25-Apr-2024 14:02:06 | |
| 25-Apr-2024 14:02:06 | Gradle suite > Gradle test > jalview.gui.StructureChooserTest.openStructureFileForSequenceTest[5](examples/uniref50.fa, FER1_SPIOL, examples/AlphaFold/AF-P00221-F1-model_v4.cif, pLDDT, examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json, false, false, JMOL, 15, 4, 1, null) FAILED |
| 25-Apr-2024 14:02:06 | java.lang.AssertionError: Wrong number of viewed annotations expected:<4> but was:<5> |
| 25-Apr-2024 14:02:06 | at org.junit.Assert.fail(Assert.java:88) |
| 25-Apr-2024 14:02:06 | at org.junit.Assert.failNotEquals(Assert.java:834) |
| 25-Apr-2024 14:02:06 | at org.junit.Assert.assertEquals(Assert.java:645) |
| 25-Apr-2024 14:02:06 | at jalview.gui.StructureChooserTest.__CLR4_4_1nqeoac3n52(StructureChooserTest.java:340) |
| 25-Apr-2024 14:02:06 | at jalview.gui.StructureChooserTest.openStructureFileForSequenceTest(StructureChooserTest.java:284) |
| 25-Apr-2024 14:04:56 | |
| 25-Apr-2024 14:04:56 | 1628 tests completed, 13 failed |
| 25-Apr-2024 14:04:56 | There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/reports/tests/testTask0/index.html |
| 25-Apr-2024 14:04:59 | |
| 25-Apr-2024 14:04:59 | > Task :testTask1 |
| 25-Apr-2024 14:04:59 | Running tests WITH clover |
| 25-Apr-2024 14:05:02 | WARNING: An illegal reflective access operation has occurred |
| 25-Apr-2024 14:05:02 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 25-Apr-2024 14:05:02 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 25-Apr-2024 14:05:02 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 25-Apr-2024 14:05:02 | WARNING: All illegal access operations will be denied in a future release |
| 25-Apr-2024 14:05:07 | |
| 25-Apr-2024 14:05:07 | Gradle suite > Gradle test > jalview.gui.AnnotationLabelsTest2.testIdWidthChanges[0](./test/files/annotation_label_width/sample.a2m, false, 50, 70, 100, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json, true, pLDDT, null, 115, 130) FAILED |
| 25-Apr-2024 14:05:07 | java.lang.AssertionError: idWidth (154) is not narrower than70 expected [true] but found [false] |
| 25-Apr-2024 14:05:07 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:05:07 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:05:07 | at org.testng.Assert.assertTrue(Assert.java:42) |
| 25-Apr-2024 14:05:07 | at jalview.gui.AnnotationLabelsTest2.__CLR4_4_140rce13nnz(AnnotationLabelsTest2.java:113) |
| 25-Apr-2024 14:05:07 | at jalview.gui.AnnotationLabelsTest2.testIdWidthChanges(AnnotationLabelsTest2.java:95) |
| 25-Apr-2024 14:05:07 | |
| 25-Apr-2024 14:05:07 | Gradle suite > Gradle test > jalview.gui.AnnotationLabelsTest2.testIdWidthChanges[1](./test/files/annotation_label_width/sample.a2m, true, 50, 70, 100, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json, true, pLDDT, null, 115, 130) FAILED |
| 25-Apr-2024 14:05:07 | java.lang.AssertionError: idWidth (154) is not narrower than70 expected [true] but found [false] |
| 25-Apr-2024 14:05:07 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:05:07 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:05:07 | at org.testng.Assert.assertTrue(Assert.java:42) |
| 25-Apr-2024 14:05:07 | at jalview.gui.AnnotationLabelsTest2.__CLR4_4_140rce13nnz(AnnotationLabelsTest2.java:113) |
| 25-Apr-2024 14:05:07 | at jalview.gui.AnnotationLabelsTest2.testIdWidthChanges(AnnotationLabelsTest2.java:95) |
| 25-Apr-2024 14:05:08 | |
| 25-Apr-2024 14:05:08 | Gradle suite > Gradle test > jalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges[0](./test/files/annotation_label_width/sample.a2m, false, 50, 70, 100, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json, true, pLDDT, null, 115, 130) FAILED |
| 25-Apr-2024 14:05:08 | java.lang.AssertionError: idWidth (154) is not narrower than70 expected [true] but found [false] |
| 25-Apr-2024 14:05:08 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:05:08 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:05:08 | at org.testng.Assert.assertTrue(Assert.java:42) |
| 25-Apr-2024 14:05:08 | at jalview.gui.AnnotationLabelsTest2.__CLR4_4_1roan143nos(AnnotationLabelsTest2.java:183) |
| 25-Apr-2024 14:05:08 | at jalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges(AnnotationLabelsTest2.java:165) |
| 25-Apr-2024 14:05:08 | |
| 25-Apr-2024 14:05:08 | Gradle suite > Gradle test > jalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges[1](./test/files/annotation_label_width/sample.a2m, true, 50, 70, 100, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json, true, pLDDT, null, 115, 130) FAILED |
| 25-Apr-2024 14:05:08 | java.lang.AssertionError: idWidth (154) is not narrower than70 expected [true] but found [false] |
| 25-Apr-2024 14:05:08 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:05:08 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:05:08 | at org.testng.Assert.assertTrue(Assert.java:42) |
| 25-Apr-2024 14:05:08 | at jalview.gui.AnnotationLabelsTest2.__CLR4_4_1roan143nos(AnnotationLabelsTest2.java:183) |
| 25-Apr-2024 14:05:08 | at jalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges(AnnotationLabelsTest2.java:165) |
| 25-Apr-2024 14:06:21 | |
| 25-Apr-2024 14:06:21 | Gradle suite > Gradle test > jalview.bin.CommandsTest2.structureOpeningArgsTest[0](--gui --nonews --nosplash --debug --append=examples/uniref50.fa --colour=gecos-flower --structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif --paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --props=test/jalview/bin/commandsTest2.jvprops1 , 15, 7, 1) FAILED |
| 25-Apr-2024 14:06:21 | java.lang.AssertionError: Wrong number of visible annotations expected [7] but found [8] |
| 25-Apr-2024 14:06:21 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:06:21 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:06:21 | at org.testng.Assert.assertEquals(Assert.java:125) |
| 25-Apr-2024 14:06:21 | at org.testng.Assert.assertEquals(Assert.java:372) |
| 25-Apr-2024 14:06:21 | at jalview.bin.CommandsTest2.__CLR4_4_1bvgd5r448e(CommandsTest2.java:132) |
| 25-Apr-2024 14:06:21 | at jalview.bin.CommandsTest2.structureOpeningArgsTest(CommandsTest2.java:84) |
| 25-Apr-2024 14:06:22 | |
| 25-Apr-2024 14:06:22 | Gradle suite > Gradle test > jalview.bin.CommandsTest2.structureOpeningArgsTest[1](--gui --nonews --nosplash --debug --append=examples/uniref50.fa --colour=gecos-flower --structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif --paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --props=test/jalview/bin/commandsTest2.jvprops2 , 15, 4, 1) FAILED |
| 25-Apr-2024 14:06:22 | java.lang.AssertionError: Wrong number of visible annotations expected [4] but found [5] |
| 25-Apr-2024 14:06:22 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:06:22 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:06:22 | at org.testng.Assert.assertEquals(Assert.java:125) |
| 25-Apr-2024 14:06:22 | at org.testng.Assert.assertEquals(Assert.java:372) |
| 25-Apr-2024 14:06:22 | at jalview.bin.CommandsTest2.__CLR4_4_1bvgd5r448e(CommandsTest2.java:132) |
| 25-Apr-2024 14:06:22 | at jalview.bin.CommandsTest2.structureOpeningArgsTest(CommandsTest2.java:84) |
| 25-Apr-2024 14:06:24 | |
| 25-Apr-2024 14:06:24 | Gradle suite > Gradle test > jalview.bin.CommandsTest2.structureOpeningArgsTest[2](--gui --nonews --nosplash --debug --append=examples/uniref50.fa --colour=gecos-flower --structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif --paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --noshowssannotations --props=test/jalview/bin/commandsTest2.jvprops1 , 15, 4, 1) FAILED |
| 25-Apr-2024 14:06:24 | java.lang.AssertionError: Wrong number of visible annotations expected [4] but found [5] |
| 25-Apr-2024 14:06:24 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:06:24 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:06:24 | at org.testng.Assert.assertEquals(Assert.java:125) |
| 25-Apr-2024 14:06:24 | at org.testng.Assert.assertEquals(Assert.java:372) |
| 25-Apr-2024 14:06:24 | at jalview.bin.CommandsTest2.__CLR4_4_1bvgd5r448e(CommandsTest2.java:132) |
| 25-Apr-2024 14:06:24 | at jalview.bin.CommandsTest2.structureOpeningArgsTest(CommandsTest2.java:84) |
| 25-Apr-2024 14:06:31 | |
| 25-Apr-2024 14:06:31 | Gradle suite > Gradle test > jalview.bin.CommandsTest2.structureOpeningArgsTest[6](--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 , 16, 19, 3) FAILED |
| 25-Apr-2024 14:06:31 | java.lang.AssertionError: Wrong number of visible annotations expected [19] but found [20] |
| 25-Apr-2024 14:06:31 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:06:31 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:06:31 | at org.testng.Assert.assertEquals(Assert.java:125) |
| 25-Apr-2024 14:06:31 | at org.testng.Assert.assertEquals(Assert.java:372) |
| 25-Apr-2024 14:06:31 | at jalview.bin.CommandsTest2.__CLR4_4_1bvgd5r448e(CommandsTest2.java:132) |
| 25-Apr-2024 14:06:31 | at jalview.bin.CommandsTest2.structureOpeningArgsTest(CommandsTest2.java:84) |
| 25-Apr-2024 14:06:35 | |
| 25-Apr-2024 14:06:35 | Gradle suite > Gradle test > jalview.bin.CommandsTest2.structureOpeningArgsTest[8](--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m --allstructures --structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb --structureviewer=none --structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb --structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb, 16, 10, 0) FAILED |
| 25-Apr-2024 14:06:35 | java.lang.AssertionError: Wrong number of visible annotations expected [10] but found [11] |
| 25-Apr-2024 14:06:35 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:06:35 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:06:35 | at org.testng.Assert.assertEquals(Assert.java:125) |
| 25-Apr-2024 14:06:35 | at org.testng.Assert.assertEquals(Assert.java:372) |
| 25-Apr-2024 14:06:35 | at jalview.bin.CommandsTest2.__CLR4_4_1bvgd5r448e(CommandsTest2.java:132) |
| 25-Apr-2024 14:06:35 | at jalview.bin.CommandsTest2.structureOpeningArgsTest(CommandsTest2.java:84) |
| 25-Apr-2024 14:06:37 | |
| 25-Apr-2024 14:06:37 | Gradle suite > Gradle test > jalview.bin.CommandsTest2.structureOpeningArgsTest[9](--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m --allstructures --structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb --noallstructures --structureviewer=none --structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb --structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb, 16, 10, 2) FAILED |
| 25-Apr-2024 14:06:37 | java.lang.AssertionError: Wrong number of visible annotations expected [10] but found [11] |
| 25-Apr-2024 14:06:37 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:06:37 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:06:37 | at org.testng.Assert.assertEquals(Assert.java:125) |
| 25-Apr-2024 14:06:37 | at org.testng.Assert.assertEquals(Assert.java:372) |
| 25-Apr-2024 14:06:37 | at jalview.bin.CommandsTest2.__CLR4_4_1bvgd5r448e(CommandsTest2.java:132) |
| 25-Apr-2024 14:06:37 | at jalview.bin.CommandsTest2.structureOpeningArgsTest(CommandsTest2.java:84) |
| 25-Apr-2024 14:06:37 | |
| 25-Apr-2024 14:06:37 | 49 tests completed, 10 failed |
| 25-Apr-2024 14:06:37 | There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/reports/tests/testTask1/index.html |
| 25-Apr-2024 14:06:39 | |
| 25-Apr-2024 14:06:39 | > Task :testTask2 |
| 25-Apr-2024 14:06:39 | Running tests WITH clover |
| 25-Apr-2024 14:06:43 | |
| 25-Apr-2024 14:06:43 | > Task :testTask3 |
| 25-Apr-2024 14:06:43 | Running tests WITH clover |
| 25-Apr-2024 14:06:44 | WARNING: An illegal reflective access operation has occurred |
| 25-Apr-2024 14:06:44 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 25-Apr-2024 14:06:44 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 25-Apr-2024 14:06:44 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 25-Apr-2024 14:06:44 | WARNING: All illegal access operations will be denied in a future release |
| 25-Apr-2024 14:07:03 | |
| 25-Apr-2024 14:07:03 | Gradle suite > Gradle test > jalview.bin.CommandsTest.structureImageAnnotationsOutputTest[2](--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa --structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb --seqid=FER1_SPIOL --structureviewer=jmol --paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image=test/jalview/bin/argparser/testfiles/test_annotations.png --tempfac=plddt --overwrite --noshowssannotations --showannotations, test/jalview/bin/argparser/testfiles/test_annotations.png, 524) FAILED |
| 25-Apr-2024 14:07:03 | java.lang.AssertionError: Output image 'test/jalview/bin/argparser/testfiles/test_annotations.png' is not in the expected height range, possibly because of the wrong number of annotations expected [597] but found [524] |
| 25-Apr-2024 14:07:03 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:07:03 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:07:03 | at org.testng.Assert.assertEquals(Assert.java:125) |
| 25-Apr-2024 14:07:03 | at org.testng.Assert.assertEquals(Assert.java:372) |
| 25-Apr-2024 14:07:03 | at jalview.bin.CommandsTest.__CLR4_4_1seuffr44mc(CommandsTest.java:876) |
| 25-Apr-2024 14:07:03 | at jalview.bin.CommandsTest.structureImageAnnotationsOutputTest(CommandsTest.java:870) |
| 25-Apr-2024 14:07:04 | |
| 25-Apr-2024 14:07:04 | Gradle suite > Gradle test > jalview.bin.CommandsTest.structureImageAnnotationsOutputTest[3](--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa --structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb --seqid=FER1_SPIOL --structureviewer=jmol --paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image=test/jalview/bin/argparser/testfiles/test_annotations.png --tempfac=plddt --overwrite --showssannotations --showannotations, test/jalview/bin/argparser/testfiles/test_annotations.png, 660) FAILED |
| 25-Apr-2024 14:07:04 | java.lang.AssertionError: Output image 'test/jalview/bin/argparser/testfiles/test_annotations.png' is not in the expected height range, possibly because of the wrong number of annotations expected [733] but found [660] |
| 25-Apr-2024 14:07:04 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:07:04 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:07:04 | at org.testng.Assert.assertEquals(Assert.java:125) |
| 25-Apr-2024 14:07:04 | at org.testng.Assert.assertEquals(Assert.java:372) |
| 25-Apr-2024 14:07:04 | at jalview.bin.CommandsTest.__CLR4_4_1seuffr44mc(CommandsTest.java:876) |
| 25-Apr-2024 14:07:04 | at jalview.bin.CommandsTest.structureImageAnnotationsOutputTest(CommandsTest.java:870) |
| 25-Apr-2024 14:07:07 | |
| 25-Apr-2024 14:07:07 | Gradle suite > Gradle test > jalview.bin.CommandsTest.structureImageAnnotationsOutputTest[6](--gui --nonews --nosplash --open=./examples/uniref50.fa --structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb --seqid=FER1_SPIOL --structureviewer=jmol --paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image=test/jalview/bin/argparser/testfiles/test_annotations.png --tempfac=plddt --overwrite --noshowssannotations --showannotations, test/jalview/bin/argparser/testfiles/test_annotations.png, 524) FAILED |
| 25-Apr-2024 14:07:07 | java.lang.AssertionError: Output image 'test/jalview/bin/argparser/testfiles/test_annotations.png' is not in the expected height range, possibly because of the wrong number of annotations expected [597] but found [524] |
| 25-Apr-2024 14:07:07 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:07:07 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:07:07 | at org.testng.Assert.assertEquals(Assert.java:125) |
| 25-Apr-2024 14:07:07 | at org.testng.Assert.assertEquals(Assert.java:372) |
| 25-Apr-2024 14:07:07 | at jalview.bin.CommandsTest.__CLR4_4_1seuffr44mc(CommandsTest.java:876) |
| 25-Apr-2024 14:07:07 | at jalview.bin.CommandsTest.structureImageAnnotationsOutputTest(CommandsTest.java:870) |
| 25-Apr-2024 14:07:08 | |
| 25-Apr-2024 14:07:08 | Gradle suite > Gradle test > jalview.bin.CommandsTest.structureImageAnnotationsOutputTest[7](--gui --nonews --nosplash --open=./examples/uniref50.fa --structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb --seqid=FER1_SPIOL --structureviewer=jmol --paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image=test/jalview/bin/argparser/testfiles/test_annotations.png --tempfac=plddt --overwrite --showssannotations --showannotations, test/jalview/bin/argparser/testfiles/test_annotations.png, 660) FAILED |
| 25-Apr-2024 14:07:08 | java.lang.AssertionError: Output image 'test/jalview/bin/argparser/testfiles/test_annotations.png' is not in the expected height range, possibly because of the wrong number of annotations expected [733] but found [660] |
| 25-Apr-2024 14:07:08 | at org.testng.Assert.fail(Assert.java:94) |
| 25-Apr-2024 14:07:08 | at org.testng.Assert.failNotEquals(Assert.java:496) |
| 25-Apr-2024 14:07:08 | at org.testng.Assert.assertEquals(Assert.java:125) |
| 25-Apr-2024 14:07:08 | at org.testng.Assert.assertEquals(Assert.java:372) |
| 25-Apr-2024 14:07:08 | at jalview.bin.CommandsTest.__CLR4_4_1seuffr44mc(CommandsTest.java:876) |
| 25-Apr-2024 14:07:08 | at jalview.bin.CommandsTest.structureImageAnnotationsOutputTest(CommandsTest.java:870) |
| 25-Apr-2024 14:07:30 | There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/reports/tests/testTask3/index.html |
| 25-Apr-2024 14:07:30 | |
| 25-Apr-2024 14:07:30 | > Task :test NO-SOURCE |
| 25-Apr-2024 14:07:30 | |
| 25-Apr-2024 14:07:30 | 25 tests completed, 4 failed |
| 25-Apr-2024 14:07:31 | ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ |
| 25-Apr-2024 14:07:31 | │jalview:testTask0 results: FAILURE (1628 tests, 1615 successes, 13 failures, 0 skipped) in 3 minutes, 57.776 seconds │ |
| 25-Apr-2024 14:07:31 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/reports/tests/testTask0/index.html│ |
| 25-Apr-2024 14:07:31 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 25-Apr-2024 14:07:31 | │jalview:testTask1 results: FAILURE (49 tests, 39 successes, 10 failures, 0 skipped) in 1 minutes, 40.417 seconds │ |
| 25-Apr-2024 14:07:31 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/reports/tests/testTask1/index.html│ |
| 25-Apr-2024 14:07:31 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 25-Apr-2024 14:07:31 | │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.541 seconds │ |
| 25-Apr-2024 14:07:31 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/reports/tests/testTask2/index.html│ |
| 25-Apr-2024 14:07:31 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 25-Apr-2024 14:07:31 | │jalview:testTask3 results: FAILURE (25 tests, 21 successes, 4 failures, 0 skipped) in 49.548 seconds │ |
| 25-Apr-2024 14:07:31 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/reports/tests/testTask3/index.html│ |
| 25-Apr-2024 14:07:31 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 25-Apr-2024 14:07:31 | │OVERALL: results: FAILURE (1703 tests, 1676 successes, 27 failures, 0 skipped) in 4 minutes, 151.282 seconds │ |
| 25-Apr-2024 14:07:31 | └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ |
| 25-Apr-2024 14:07:31 | |
| 25-Apr-2024 14:07:31 | |
| 25-Apr-2024 14:07:31 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 25-Apr-2024 14:07:31 | |
| 25-Apr-2024 14:07:31 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 25-Apr-2024 14:07:31 | |
| 25-Apr-2024 14:07:31 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 25-Apr-2024 14:07:31 | |
| 25-Apr-2024 14:07:31 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 25-Apr-2024 14:07:31 | Please consult deprecation warnings for more details. |
| 25-Apr-2024 14:07:31 | 21 actionable tasks: 20 executed, 1 up-to-date |
| 25-Apr-2024 14:07:31 | FAILURE: Build failed with an exception. |
| 25-Apr-2024 14:07:31 | |
| 25-Apr-2024 14:07:31 | * Where: |
| 25-Apr-2024 14:07:31 | Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build.gradle' line: 1924 |
| 25-Apr-2024 14:07:31 | |
| 25-Apr-2024 14:07:31 | * What went wrong: |
| 25-Apr-2024 14:07:31 | Failed tests! |
| 25-Apr-2024 14:07:31 | |
| 25-Apr-2024 14:07:31 | * Try: |
| 25-Apr-2024 14:07:31 | > Run with --stacktrace option to get the stack trace. |
| 25-Apr-2024 14:07:31 | > Run with --info or --debug option to get more log output. |
| 25-Apr-2024 14:07:31 | > Run with --scan to get full insights. |
| 25-Apr-2024 14:07:31 | |
| 25-Apr-2024 14:07:31 | * Get more help at https://help.gradle.org |
| 25-Apr-2024 14:07:31 | |
| 25-Apr-2024 14:07:31 | BUILD FAILED in 8m 11s |
| 25-Apr-2024 14:07:31 | |
| 25-Apr-2024 14:07:31 | 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 |
| 25-Apr-2024 14:07:31 | Finished task 'Run tests with openclover under gradle' with result: Failed |
| 25-Apr-2024 14:07:31 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 25-Apr-2024 14:07:31 | Bamboo Artifactory Plugin version: 2.6.2 |
| 25-Apr-2024 14:07:31 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4392_consensus_secondary_structure - Clover and Tests #5 (JB-GDB581-JOB1-5)' ... 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-GDB581-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=feature/JAL-4392_consensus_secondary_structure bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_repository_46497836_revision_number=7af2c16e2466ea2665c29b5feba6341c1e255291 CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=feature/JAL-4392_consensus_secondary_structure bamboo_repository_revision_number=7af2c16e2466ea2665c29b5feba6341c1e255291 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB581-JOB1-5 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-GDB581-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDB581-JOB1 bamboo_shortPlanName=feature-JAL-4392_consensus_secondary_structure bamboo_planRepository_name=Jalview Git LOGNAME=bamboo bamboo_buildNumber=5 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-GDB581-JOB1-5 bamboo_repository_46497836_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - feature-JAL-4392_consensus_secondary_structure bamboo_shortPlanKey=GDB581 bamboo_shortJobKey=JOB1 bamboo_repository_46497836_previous_revision_number=7af2c16e2466ea2665c29b5feba6341c1e255291 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=7af2c16e2466ea2665c29b5feba6341c1e255291 bamboo_buildTimeStamp=2024-04-25T13:59:14.875+01:00 bamboo_repository_previous_revision_number=7af2c16e2466ea2665c29b5feba6341c1e255291 bamboo_planRepository_previousRevision=7af2c16e2466ea2665c29b5feba6341c1e255291 bamboo_repository_git_branch=feature/JAL-4392_consensus_secondary_structure bamboo_buildResultKey=JB-GDB581-JOB1-5 bamboo_repository_branch_name=feature/JAL-4392_consensus_secondary_structure bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - feature-JAL-4392_consensus_secondary_structure - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=7af2c16e2466ea2665c29b5feba6341c1e255291 SHLVL=1 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_repository_46497836_branch_name=feature/JAL-4392_consensus_secondary_structure 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_repository_46497836_git_branch=feature/JAL-4392_consensus_secondary_structure bamboo_planRepository_branch=feature/JAL-4392_consensus_secondary_structure 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=7af2c16e2466ea2665c29b5feba6341c1e255291 bamboo_planRepository_branchDisplayName=feature/JAL-4392_consensus_secondary_structure bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=feature/JAL-4392_consensus_secondary_structure _=/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_repository_46497836_git_username= bamboo_repository_46497836_name=Jalview Git bamboo_plan_storageTag=plan-46301271 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=reniacorreya 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-GDB581-JOB1 bamboo_planKey=JB-GDB581 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=feature/JAL-4392_consensus_secondary_structure PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 25-Apr-2024 14:07:32 | 444 |
| 25-Apr-2024 14:07:49 | |
| 25-Apr-2024 14:07:49 | > Configure project : |
| 25-Apr-2024 14:07:49 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 25-Apr-2024 14:07:49 | JALVIEW_VERSION is set to '2.11.3.3' |
| 25-Apr-2024 14:07:49 | HEADLESS BUILD |
| 25-Apr-2024 14:07:49 | J2S ENABLED |
| 25-Apr-2024 14:07:50 | Using a LOCAL profile. |
| 25-Apr-2024 14:07:51 | eclipseDir exists |
| 25-Apr-2024 14:07:54 | |
| 25-Apr-2024 14:07:54 | > Task :cloverHtmlReport |
| 25-Apr-2024 14:07:54 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 25-Apr-2024 14:07:56 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/reports/clover' |
| 25-Apr-2024 14:08:36 | Done. Processed 115 packages in 39364ms (342ms per package). |
| 25-Apr-2024 14:08:48 | |
| 25-Apr-2024 14:08:48 | > Task :cloverXmlReport |
| 25-Apr-2024 14:08:48 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 25-Apr-2024 14:08:51 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/reports/clover/clover.xml' |
| 25-Apr-2024 14:08:51 | |
| 25-Apr-2024 14:08:51 | > Task :cloverReport |
| 25-Apr-2024 14:08:51 | |
| 25-Apr-2024 14:08:51 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 25-Apr-2024 14:08:51 | |
| 25-Apr-2024 14:08:51 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 25-Apr-2024 14:08:51 | |
| 25-Apr-2024 14:08:51 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 25-Apr-2024 14:08:51 | |
| 25-Apr-2024 14:08:51 | BUILD SUCCESSFUL in 1m 19s |
| 25-Apr-2024 14:08:51 | 2 actionable tasks: 2 executed |
| 25-Apr-2024 14:08:51 | Finished task 'Clover Report' with result: Success |
| 25-Apr-2024 14:08:51 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 25-Apr-2024 14:08:51 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1... |
| 25-Apr-2024 14:08:51 | Failing task since 27 failing test cases were found. |
| 25-Apr-2024 14:08:51 | Finished task 'TestNG Parser' with result: Failed |
| 25-Apr-2024 14:08:51 | Running post build plugin 'NCover Results Collector' |
| 25-Apr-2024 14:08:51 | Running post build plugin 'Artifact Copier' |
| 25-Apr-2024 14:08:51 | Publishing an artifact: Clover Report (System) |
| 25-Apr-2024 14:08:53 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.647 s |
| 25-Apr-2024 14:08:53 | Publishing an artifact: TestNG report |
| 25-Apr-2024 14:08:53 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB581-JOB1/build/reports/tests/test does not exist. |
| 25-Apr-2024 14:08:53 | The artifact hasn't been successfully published after 1.140 ms |
| 25-Apr-2024 14:08:53 | Running post build plugin 'Artifactory Release Management Staging' |
| 25-Apr-2024 14:08:53 | Running post build plugin 'Artifactory Build Info Copier' |
| 25-Apr-2024 14:08:53 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 25-Apr-2024 14:08:53 | Running post build plugin 'npm Cache Cleanup' |
| 25-Apr-2024 14:08:53 | Running post build plugin 'Clover Results Collector' |
| 25-Apr-2024 14:08:53 | Running post build plugin 'Docker Container Cleanup' |
| 25-Apr-2024 14:08:53 | Finalising the build... |
| 25-Apr-2024 14:08:53 | Stopping timer. |
| 25-Apr-2024 14:08:53 | Build JB-GDB581-JOB1-5 completed. |
| 25-Apr-2024 14:08:53 | Running on server: post build plugin 'NCover Results Collector' |
| 25-Apr-2024 14:08:53 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 25-Apr-2024 14:08:53 | Running on server: post build plugin 'Clover Delta Calculator' |
| 25-Apr-2024 14:08:53 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 25-Apr-2024 14:08:53 | All post build plugins have finished |
| 25-Apr-2024 14:08:53 | Generating build results summary... |
| 25-Apr-2024 14:08:54 | Saving build results to disk... |
| 25-Apr-2024 14:08:54 | Logging substituted variables... |
| 25-Apr-2024 14:08:54 | Indexing build results... |
| 25-Apr-2024 14:08:54 | Finished building JB-GDB581-JOB1-5. |