Build: #2 failed
Job: Clover and Tests failed
Build log
The build generated 280 lines of output. Download or view full build log
11-Nov-2024 15:05:16 | Build Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests #2 (JB-GDB642-JOB1-2) started building on agent Default Agent |
11-Nov-2024 15:05:16 | |
11-Nov-2024 15:05:16 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1 |
11-Nov-2024 15:05:16 | Executing build Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests #2 (JB-GDB642-JOB1-2) |
11-Nov-2024 15:05:16 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
11-Nov-2024 15:05:16 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1 |
11-Nov-2024 15:05:16 | Updating source code to revision: f6be36d7152321642e41db9d8bdbd2580431541e |
11-Nov-2024 15:05:16 | Fetching 'refs/heads/features/JAL-4489_cluster_pca_and_pasimap' from 'http://source.jalview.org/git/jalview.git'. |
11-Nov-2024 15:05:16 | Checking out revision f6be36d7152321642e41db9d8bdbd2580431541e. |
11-Nov-2024 15:05:16 | From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 |
11-Nov-2024 15:05:16 | 3e7d1be..f6be36d features/JAL-4489_cluster_pca_and_pasimap -> origin/features/JAL-4489_cluster_pca_and_pasimap |
11-Nov-2024 15:05:18 | Already on 'features/JAL-4489_cluster_pca_and_pasimap' |
11-Nov-2024 15:05:18 | Your branch is behind 'origin/features/JAL-4489_cluster_pca_and_pasimap' by 1 commit, and can be fast-forwarded. |
11-Nov-2024 15:05:18 | (use "git pull" to update your local branch) |
11-Nov-2024 15:05:18 | HEAD is now at f6be36d JAL-4489 organise imports |
11-Nov-2024 15:05:18 | Updated source code to revision: f6be36d7152321642e41db9d8bdbd2580431541e |
11-Nov-2024 15:05:18 | Finished task 'Checkout Default Repository' with result: Success |
11-Nov-2024 15:05:18 | Running pre-build action: VCS Version Collector |
11-Nov-2024 15:05:18 | Running pre-build action: Artifactory Release Staging |
11-Nov-2024 15:05:18 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
11-Nov-2024 15:05:18 | Bamboo Artifactory Plugin version: 2.6.2 |
11-Nov-2024 15:05:18 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests #2 (JB-GDB642-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-GDB642-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=features/JAL-4489_cluster_pca_and_pasimap bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap bamboo_repository_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB642-JOB1-2 bamboo_repository_46498184_git_branch=features/JAL-4489_cluster_pca_and_pasimap 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-GDB642-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDB642-JOB1 bamboo_shortPlanName=features-JAL-4489_cluster_pca_and_pasimap 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-GDB642-JOB1-2 bamboo_repository_46498184_name=Jalview Git bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_repository_46498184_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap bamboo_shortPlanKey=GDB642 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=f6be36d7152321642e41db9d8bdbd2580431541e bamboo_repository_46498184_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e bamboo_buildTimeStamp=2024-11-11T15:05:16.749Z bamboo_repository_previous_revision_number=3e7d1be29f1857c4d5cf237b1cf6420218752458 bamboo_planRepository_previousRevision=3e7d1be29f1857c4d5cf237b1cf6420218752458 bamboo_repository_git_branch=features/JAL-4489_cluster_pca_and_pasimap bamboo_buildResultKey=JB-GDB642-JOB1-2 bamboo_repository_branch_name=features/JAL-4489_cluster_pca_and_pasimap bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=f6be36d7152321642e41db9d8bdbd2580431541e 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/ 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=features/JAL-4489_cluster_pca_and_pasimap 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=3e7d1be29f1857c4d5cf237b1cf6420218752458 bamboo_repository_46498184_git_username= bamboo_planRepository_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=features/JAL-4489_cluster_pca_and_pasimap _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_repository_46498184_previous_revision_number=3e7d1be29f1857c4d5cf237b1cf6420218752458 bamboo_capability_system_builderivy_Ivy=/usr bamboo_plan_storageTag=plan-46301967 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_git_repositoryUrl=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-GDB642-JOB1 bamboo_planKey=JB-GDB642 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= bamboo_repository_46498184_branch_name=features/JAL-4489_cluster_pca_and_pasimap HOME=/home/bamboo bamboo_planRepository_1_branchName=features/JAL-4489_cluster_pca_and_pasimap PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
11-Nov-2024 15:05:18 | 444 |
11-Nov-2024 15:05:19 | |
11-Nov-2024 15:05:19 | > Configure project : |
11-Nov-2024 15:05:19 | Using properties from file './utils/channels/default/channel_gradle.properties' |
11-Nov-2024 15:05:19 | JALVIEW_VERSION is set to '2.11.4.1' |
11-Nov-2024 15:05:19 | HEADLESS BUILD |
11-Nov-2024 15:05:19 | J2S ENABLED |
11-Nov-2024 15:05:19 | Using a LOCAL profile. |
11-Nov-2024 15:05:19 | eclipseDir exists |
11-Nov-2024 15:05:19 | |
11-Nov-2024 15:05:19 | > Task :clean |
11-Nov-2024 15:05:19 | > Task :cleanClover |
11-Nov-2024 15:05:19 | > Task :cleanTest UP-TO-DATE |
11-Nov-2024 15:05:21 | |
11-Nov-2024 15:05:21 | > Task :cloverInstrJava |
11-Nov-2024 15:05:21 | Clover: About to instrument 1106 files |
11-Nov-2024 15:05:21 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
11-Nov-2024 15:05:21 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover.db'. |
11-Nov-2024 15:05:21 | Processing files at 1.9 source level. |
11-Nov-2024 15:05:24 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
11-Nov-2024 15:05:24 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
11-Nov-2024 15:05:24 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
11-Nov-2024 15:05:24 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
11-Nov-2024 15:05:24 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
11-Nov-2024 15:05:24 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
11-Nov-2024 15:05:24 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
11-Nov-2024 15:05:31 | Clover all over. Instrumented 1106 files (112 packages). |
11-Nov-2024 15:05:33 | |
11-Nov-2024 15:05:33 | > Task :cloverInstrTests |
11-Nov-2024 15:05:33 | Clover: About to instrument test files |
11-Nov-2024 15:05:33 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
11-Nov-2024 15:05:33 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover.db'. |
11-Nov-2024 15:05:33 | Processing files at 1.9 source level. |
11-Nov-2024 15:05:36 | Clover all over. Instrumented 291 files (52 packages). |
11-Nov-2024 15:05:36 | 1594 test methods detected. |
11-Nov-2024 15:05:36 | |
11-Nov-2024 15:05:36 | > Task :cloverInstr |
11-Nov-2024 15:05:38 | |
11-Nov-2024 15:05:38 | > Task :compileCloverJava |
11-Nov-2024 15:05:38 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
11-Nov-2024 15:05:38 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:05:38 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:05:38 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:05:38 | Setting target compatibility to 11 |
11-Nov-2024 15:05:52 | Note: Some input files use or override a deprecated API. |
11-Nov-2024 15:05:52 | Note: Recompile with -Xlint:deprecation for details. |
11-Nov-2024 15:05:52 | Note: Some input files use unchecked or unsafe operations. |
11-Nov-2024 15:05:52 | Note: Recompile with -Xlint:unchecked for details. |
11-Nov-2024 15:05:56 | |
11-Nov-2024 15:05:56 | > Task :processCloverResources NO-SOURCE |
11-Nov-2024 15:05:56 | > Task :cloverClasses |
11-Nov-2024 15:05:57 | > Task :copyHelp |
11-Nov-2024 15:05:58 | > Task :buildIndices |
11-Nov-2024 15:05:58 | > Task :copyResources |
11-Nov-2024 15:05:58 | > Task :copyChannelResources |
11-Nov-2024 15:05:58 | |
11-Nov-2024 15:05:58 | > Task :createBuildProperties |
11-Nov-2024 15:05:58 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
11-Nov-2024 15:05:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:05:58 | |
11-Nov-2024 15:05:58 | > Task :buildResources |
11-Nov-2024 15:05:58 | > Task :copyDocs |
11-Nov-2024 15:05:58 | |
11-Nov-2024 15:05:58 | > Task :convertMdFiles |
11-Nov-2024 15:05:58 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
11-Nov-2024 15:05:58 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/releaseprocess.html |
11-Nov-2024 15:05:58 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
11-Nov-2024 15:05:58 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/building.html |
11-Nov-2024 15:05:58 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/resources/doc_build/doc/jalview-projects.html |
11-Nov-2024 15:05:58 | |
11-Nov-2024 15:05:58 | > Task :releasesTemplates |
11-Nov-2024 15:05:58 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
11-Nov-2024 15:05:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:05:58 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:05:58 | Stripping rc/test/etc for TEST |
11-Nov-2024 15:05:58 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/help/markdown/whatsnew/whatsnew-TEST.md |
11-Nov-2024 15:05:58 | |
11-Nov-2024 15:05:58 | > Task :prepare |
11-Nov-2024 15:06:00 | |
11-Nov-2024 15:06:00 | > Task :compileJava |
11-Nov-2024 15:06:00 | Setting target compatibility to 11 |
11-Nov-2024 15:06:06 | Note: Some input files use or override a deprecated API. |
11-Nov-2024 15:06:06 | Note: Recompile with -Xlint:deprecation for details. |
11-Nov-2024 15:06:06 | Note: Some input files use unchecked or unsafe operations. |
11-Nov-2024 15:06:06 | Note: Recompile with -Xlint:unchecked for details. |
11-Nov-2024 15:06:10 | |
11-Nov-2024 15:06:10 | > Task :compileTestJava |
11-Nov-2024 15:06:10 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
11-Nov-2024 15:06:10 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:06:10 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:06:10 | Setting target compatibility to 11 |
11-Nov-2024 15:06:15 | Note: Some input files use or override a deprecated API. |
11-Nov-2024 15:06:15 | Note: Recompile with -Xlint:deprecation for details. |
11-Nov-2024 15:06:15 | Note: Some input files use unchecked or unsafe operations. |
11-Nov-2024 15:06:15 | Note: Recompile with -Xlint:unchecked for details. |
11-Nov-2024 15:06:16 | |
11-Nov-2024 15:06:16 | > Task :processTestResources |
11-Nov-2024 15:06:16 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
11-Nov-2024 15:06:16 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:06:16 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:06:16 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:06:16 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:06:16 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:06:16 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:06:16 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:06:16 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-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. |
11-Nov-2024 15:06:16 | |
11-Nov-2024 15:06:16 | > Task :testClasses |
11-Nov-2024 15:06:18 | |
11-Nov-2024 15:06:18 | > Task :testTask0 |
11-Nov-2024 15:06:18 | Running tests WITH clover |
11-Nov-2024 15:06:21 | WARNING: An illegal reflective access operation has occurred |
11-Nov-2024 15:06:21 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
11-Nov-2024 15:06:21 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
11-Nov-2024 15:06:21 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
11-Nov-2024 15:06:21 | WARNING: All illegal access operations will be denied in a future release |
11-Nov-2024 15:09:59 | |
11-Nov-2024 15:09:59 | > Task :testTask1 |
11-Nov-2024 15:09:59 | Running tests WITH clover |
11-Nov-2024 15:10:00 | WARNING: An illegal reflective access operation has occurred |
11-Nov-2024 15:10:00 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
11-Nov-2024 15:10:00 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
11-Nov-2024 15:10:00 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
11-Nov-2024 15:10:00 | WARNING: All illegal access operations will be denied in a future release |
11-Nov-2024 15:11:35 | |
11-Nov-2024 15:11:35 | > Task :testTask2 |
11-Nov-2024 15:11:35 | Running tests WITH clover |
11-Nov-2024 15:11:39 | |
11-Nov-2024 15:11:39 | > Task :testTask3 |
11-Nov-2024 15:11:39 | Running tests WITH clover |
11-Nov-2024 15:11:40 | WARNING: An illegal reflective access operation has occurred |
11-Nov-2024 15:11:40 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
11-Nov-2024 15:11:40 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
11-Nov-2024 15:11:40 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
11-Nov-2024 15:11:40 | WARNING: All illegal access operations will be denied in a future release |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | Gradle suite > Gradle test > jalview.bin.CommandsTest.structureImageOutputTest[3](--headless --noquit --open ./examples/1gaq.txt --append ./examples/3W5V.pdb --structure examples/1gaq.txt --seqid "1GAQ|A" --structureimage test/jalview/bin/argparser/testfiles/structureimage3-1gaq.png --structure examples/3W5V.pdb --seqid "3W5V|A" --structureimage test/jalview/bin/argparser/testfiles/structureimage3-3w5v.png --overwrite, [Ljava.lang.String;@402d6012) FAILED |
11-Nov-2024 15:12:26 | java.lang.AssertionError: Expected test/jalview/bin/argparser/testfiles/structureimage3-1gaq.png to be larger than test/jalview/bin/argparser/testfiles/structureimage3-3w5v.png expected [true] but found [false] |
11-Nov-2024 15:12:26 | at org.testng.Assert.fail(Assert.java:94) |
11-Nov-2024 15:12:26 | at org.testng.Assert.failNotEquals(Assert.java:496) |
11-Nov-2024 15:12:26 | at org.testng.Assert.assertTrue(Assert.java:42) |
11-Nov-2024 15:12:26 | at jalview.bin.CommandsTest.verifyOrderedFileSet(CommandsTest.java:297) |
11-Nov-2024 15:12:26 | at jalview.bin.CommandsTest.verifyIncreasingSize(CommandsTest.java:274) |
11-Nov-2024 15:12:26 | at jalview.bin.CommandsTest.__CLR4_4_1shrjyq47q9(CommandsTest.java:194) |
11-Nov-2024 15:12:26 | at jalview.bin.CommandsTest.structureImageOutputTest(CommandsTest.java:186) |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | 25 tests completed, 1 failed |
11-Nov-2024 15:12:26 | There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask3/index.html |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | FAILURE: Build failed with an exception. |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | * Where: |
11-Nov-2024 15:12:26 | Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build.gradle' line: 1966 |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | * What went wrong: |
11-Nov-2024 15:12:26 | Failed tests! |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | * Try: |
11-Nov-2024 15:12:26 | > Run with --stacktrace option to get the stack trace. |
11-Nov-2024 15:12:26 | > Run with --info or --debug option to get more log output. |
11-Nov-2024 15:12:26 | > Run with --scan to get full insights. |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | * Get more help at https://help.gradle.org |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | BUILD FAILED in 7m 8s |
11-Nov-2024 15:12:26 | > Task :test NO-SOURCE |
11-Nov-2024 15:12:26 | ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ |
11-Nov-2024 15:12:26 | │jalview:testTask0 results: SUCCESS (1728 tests, 1728 successes, 0 failures, 0 skipped) in 3 minutes, 40.394 seconds │ |
11-Nov-2024 15:12:26 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask0/index.html│ |
11-Nov-2024 15:12:26 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
11-Nov-2024 15:12:26 | │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 36.185 seconds │ |
11-Nov-2024 15:12:26 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask1/index.html│ |
11-Nov-2024 15:12:26 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
11-Nov-2024 15:12:26 | │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.640 seconds │ |
11-Nov-2024 15:12:26 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask2/index.html│ |
11-Nov-2024 15:12:26 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
11-Nov-2024 15:12:26 | │jalview:testTask3 results: FAILURE (25 tests, 24 successes, 1 failures, 0 skipped) in 48.923 seconds │ |
11-Nov-2024 15:12:26 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/testTask3/index.html│ |
11-Nov-2024 15:12:26 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
11-Nov-2024 15:12:26 | │OVERALL: results: FAILURE (1803 tests, 1802 successes, 1 failures, 0 skipped) in 4 minutes, 129.142 seconds │ |
11-Nov-2024 15:12:26 | └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
11-Nov-2024 15:12:26 | Please consult deprecation warnings for more details. |
11-Nov-2024 15:12:26 | 21 actionable tasks: 20 executed, 1 up-to-date |
11-Nov-2024 15:12:26 | |
11-Nov-2024 15:12:26 | 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 |
11-Nov-2024 15:12:26 | Finished task 'Run tests with openclover under gradle' with result: Failed |
11-Nov-2024 15:12:26 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
11-Nov-2024 15:12:26 | Bamboo Artifactory Plugin version: 2.6.2 |
11-Nov-2024 15:12:26 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests #2 (JB-GDB642-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-GDB642-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=features/JAL-4489_cluster_pca_and_pasimap bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap bamboo_repository_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB642-JOB1-2 bamboo_repository_46498184_git_branch=features/JAL-4489_cluster_pca_and_pasimap 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-GDB642-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDB642-JOB1 bamboo_shortPlanName=features-JAL-4489_cluster_pca_and_pasimap 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-GDB642-JOB1-2 bamboo_repository_46498184_name=Jalview Git bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_repository_46498184_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap bamboo_shortPlanKey=GDB642 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=f6be36d7152321642e41db9d8bdbd2580431541e bamboo_repository_46498184_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e bamboo_buildTimeStamp=2024-11-11T15:05:16.749Z bamboo_repository_previous_revision_number=3e7d1be29f1857c4d5cf237b1cf6420218752458 bamboo_planRepository_previousRevision=3e7d1be29f1857c4d5cf237b1cf6420218752458 bamboo_repository_git_branch=features/JAL-4489_cluster_pca_and_pasimap bamboo_buildResultKey=JB-GDB642-JOB1-2 bamboo_repository_branch_name=features/JAL-4489_cluster_pca_and_pasimap bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=f6be36d7152321642e41db9d8bdbd2580431541e 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/ 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=features/JAL-4489_cluster_pca_and_pasimap 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=3e7d1be29f1857c4d5cf237b1cf6420218752458 bamboo_repository_46498184_git_username= bamboo_planRepository_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=features/JAL-4489_cluster_pca_and_pasimap _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_repository_46498184_previous_revision_number=3e7d1be29f1857c4d5cf237b1cf6420218752458 bamboo_capability_system_builderivy_Ivy=/usr bamboo_plan_storageTag=plan-46301967 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_git_repositoryUrl=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-GDB642-JOB1 bamboo_planKey=JB-GDB642 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= bamboo_repository_46498184_branch_name=features/JAL-4489_cluster_pca_and_pasimap HOME=/home/bamboo bamboo_planRepository_1_branchName=features/JAL-4489_cluster_pca_and_pasimap PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
11-Nov-2024 15:12:26 | 444 |
11-Nov-2024 15:12:32 | |
11-Nov-2024 15:12:32 | > Configure project : |
11-Nov-2024 15:12:32 | Using properties from file './utils/channels/default/channel_gradle.properties' |
11-Nov-2024 15:12:32 | JALVIEW_VERSION is set to '2.11.4.1' |
11-Nov-2024 15:12:32 | HEADLESS BUILD |
11-Nov-2024 15:12:32 | J2S ENABLED |
11-Nov-2024 15:12:32 | Using a LOCAL profile. |
11-Nov-2024 15:12:33 | eclipseDir exists |
11-Nov-2024 15:12:35 | |
11-Nov-2024 15:12:35 | > Task :cloverHtmlReport |
11-Nov-2024 15:12:35 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
11-Nov-2024 15:12:36 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/clover' |
11-Nov-2024 15:13:14 | Done. Processed 116 packages in 37819ms (326ms per package). |
11-Nov-2024 15:13:19 | |
11-Nov-2024 15:13:19 | > Task :cloverXmlReport |
11-Nov-2024 15:13:19 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
11-Nov-2024 15:13:20 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/clover/clover.xml' |
11-Nov-2024 15:13:21 | |
11-Nov-2024 15:13:21 | > Task :cloverReport |
11-Nov-2024 15:13:21 | |
11-Nov-2024 15:13:21 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
11-Nov-2024 15:13:21 | |
11-Nov-2024 15:13:21 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
11-Nov-2024 15:13:21 | |
11-Nov-2024 15:13:21 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
11-Nov-2024 15:13:21 | |
11-Nov-2024 15:13:21 | BUILD SUCCESSFUL in 54s |
11-Nov-2024 15:13:21 | 2 actionable tasks: 2 executed |
11-Nov-2024 15:13:21 | Finished task 'Clover Report' with result: Success |
11-Nov-2024 15:13:21 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
11-Nov-2024 15:13:21 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1... |
11-Nov-2024 15:13:21 | Failing task since 1 failing test cases were found. |
11-Nov-2024 15:13:21 | Finished task 'TestNG Parser' with result: Failed |
11-Nov-2024 15:13:21 | Running post build plugin 'NCover Results Collector' |
11-Nov-2024 15:13:21 | Running post build plugin 'Artifact Copier' |
11-Nov-2024 15:13:21 | Publishing an artifact: Clover Report (System) |
11-Nov-2024 15:13:22 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.460 s |
11-Nov-2024 15:13:22 | Publishing an artifact: TestNG report |
11-Nov-2024 15:13:22 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build/reports/tests/test does not exist. |
11-Nov-2024 15:13:22 | The artifact hasn't been successfully published after 2.206 ms |
11-Nov-2024 15:13:22 | Running post build plugin 'Artifactory Release Management Staging' |
11-Nov-2024 15:13:22 | Running post build plugin 'Artifactory Build Info Copier' |
11-Nov-2024 15:13:22 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
11-Nov-2024 15:13:22 | Running post build plugin 'npm Cache Cleanup' |
11-Nov-2024 15:13:22 | Running post build plugin 'Clover Results Collector' |
11-Nov-2024 15:13:22 | Running post build plugin 'Docker Container Cleanup' |
11-Nov-2024 15:13:22 | Finalising the build... |
11-Nov-2024 15:13:22 | Stopping timer. |
11-Nov-2024 15:13:22 | Build JB-GDB642-JOB1-2 completed. |
11-Nov-2024 15:13:22 | Running on server: post build plugin 'NCover Results Collector' |
11-Nov-2024 15:13:22 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
11-Nov-2024 15:13:22 | Running on server: post build plugin 'Clover Delta Calculator' |
11-Nov-2024 15:13:22 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
11-Nov-2024 15:13:22 | All post build plugins have finished |
11-Nov-2024 15:13:22 | Generating build results summary... |
11-Nov-2024 15:13:23 | Saving build results to disk... |
11-Nov-2024 15:13:23 | Logging substituted variables... |
11-Nov-2024 15:13:23 | Indexing build results... |
11-Nov-2024 15:13:23 | Finished building JB-GDB642-JOB1-2. |