simple 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 simple 11-Nov-2024 15:05:16 simple 11-Nov-2024 15:05:16 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1 simple 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) simple 11-Nov-2024 15:05:16 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 11-Nov-2024 15:05:16 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1 simple 11-Nov-2024 15:05:16 Updating source code to revision: f6be36d7152321642e41db9d8bdbd2580431541e simple 11-Nov-2024 15:05:16 Fetching 'refs/heads/features/JAL-4489_cluster_pca_and_pasimap' from 'http://source.jalview.org/git/jalview.git'. simple 11-Nov-2024 15:05:16 Checking out revision f6be36d7152321642e41db9d8bdbd2580431541e. simple 11-Nov-2024 15:05:16 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 11-Nov-2024 15:05:16 3e7d1be..f6be36d features/JAL-4489_cluster_pca_and_pasimap -> origin/features/JAL-4489_cluster_pca_and_pasimap simple 11-Nov-2024 15:05:18 Already on 'features/JAL-4489_cluster_pca_and_pasimap' simple 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. simple 11-Nov-2024 15:05:18 (use "git pull" to update your local branch) simple 11-Nov-2024 15:05:18 HEAD is now at f6be36d JAL-4489 organise imports simple 11-Nov-2024 15:05:18 Updated source code to revision: f6be36d7152321642e41db9d8bdbd2580431541e simple 11-Nov-2024 15:05:18 Finished task 'Checkout Default Repository' with result: Success simple 11-Nov-2024 15:05:18 Running pre-build action: VCS Version Collector simple 11-Nov-2024 15:05:18 Running pre-build action: Artifactory Release Staging simple 11-Nov-2024 15:05:18 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 11-Nov-2024 15:05:18 Bamboo Artifactory Plugin version: 2.6.2 command 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)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_repository_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB642-JOB1-2\nbamboo_repository_46498184_git_branch=features/JAL-4489_cluster_pca_and_pasimap\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB642-JOB1\nbamboo_shortPlanName=features-JAL-4489_cluster_pca_and_pasimap\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB642-JOB1-2\nbamboo_repository_46498184_name=Jalview Git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498184_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap\nbamboo_shortPlanKey=GDB642\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_repository_46498184_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_buildTimeStamp=2024-11-11T15:05:16.749Z\nbamboo_repository_previous_revision_number=3e7d1be29f1857c4d5cf237b1cf6420218752458\nbamboo_planRepository_previousRevision=3e7d1be29f1857c4d5cf237b1cf6420218752458\nbamboo_repository_git_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_buildResultKey=JB-GDB642-JOB1-2\nbamboo_repository_branch_name=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=f6be36d7152321642e41db9d8bdbd2580431541e\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=3e7d1be29f1857c4d5cf237b1cf6420218752458\nbamboo_repository_46498184_git_username=\nbamboo_planRepository_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=features/JAL-4489_cluster_pca_and_pasimap\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498184_previous_revision_number=3e7d1be29f1857c4d5cf237b1cf6420218752458\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301967\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1\nbamboo_planKey=JB-GDB642\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498184_branch_name=features/JAL-4489_cluster_pca_and_pasimap\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=features/JAL-4489_cluster_pca_and_pasimap\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 11-Nov-2024 15:05:18 444 build 11-Nov-2024 15:05:19 build 11-Nov-2024 15:05:19 > Configure project : build 11-Nov-2024 15:05:19 Using properties from file './utils/channels/default/channel_gradle.properties' build 11-Nov-2024 15:05:19 JALVIEW_VERSION is set to '2.11.4.1' build 11-Nov-2024 15:05:19 HEADLESS BUILD build 11-Nov-2024 15:05:19 J2S ENABLED build 11-Nov-2024 15:05:19 Using a LOCAL profile. build 11-Nov-2024 15:05:19 eclipseDir exists build 11-Nov-2024 15:05:19 build 11-Nov-2024 15:05:19 > Task :clean build 11-Nov-2024 15:05:19 > Task :cleanClover build 11-Nov-2024 15:05:19 > Task :cleanTest UP-TO-DATE build 11-Nov-2024 15:05:21 build 11-Nov-2024 15:05:21 > Task :cloverInstrJava build 11-Nov-2024 15:05:21 Clover: About to instrument 1106 files build 11-Nov-2024 15:05:21 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 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'. build 11-Nov-2024 15:05:21 Processing files at 1.9 source level. error 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? error 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? error 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? error 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? error 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? error 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? error 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? build 11-Nov-2024 15:05:31 Clover all over. Instrumented 1106 files (112 packages). build 11-Nov-2024 15:05:33 build 11-Nov-2024 15:05:33 > Task :cloverInstrTests build 11-Nov-2024 15:05:33 Clover: About to instrument test files build 11-Nov-2024 15:05:33 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 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'. build 11-Nov-2024 15:05:33 Processing files at 1.9 source level. build 11-Nov-2024 15:05:36 Clover all over. Instrumented 291 files (52 packages). build 11-Nov-2024 15:05:36 1594 test methods detected. build 11-Nov-2024 15:05:36 build 11-Nov-2024 15:05:36 > Task :cloverInstr build 11-Nov-2024 15:05:38 build 11-Nov-2024 15:05:38 > Task :compileCloverJava build 11-Nov-2024 15:05:38 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 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. build 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. build 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. build 11-Nov-2024 15:05:38 Setting target compatibility to 11 error 11-Nov-2024 15:05:52 Note: Some input files use or override a deprecated API. error 11-Nov-2024 15:05:52 Note: Recompile with -Xlint:deprecation for details. error 11-Nov-2024 15:05:52 Note: Some input files use unchecked or unsafe operations. error 11-Nov-2024 15:05:52 Note: Recompile with -Xlint:unchecked for details. build 11-Nov-2024 15:05:56 build 11-Nov-2024 15:05:56 > Task :processCloverResources NO-SOURCE build 11-Nov-2024 15:05:56 > Task :cloverClasses build 11-Nov-2024 15:05:57 > Task :copyHelp build 11-Nov-2024 15:05:58 > Task :buildIndices build 11-Nov-2024 15:05:58 > Task :copyResources build 11-Nov-2024 15:05:58 > Task :copyChannelResources build 11-Nov-2024 15:05:58 build 11-Nov-2024 15:05:58 > Task :createBuildProperties build 11-Nov-2024 15:05:58 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 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. build 11-Nov-2024 15:05:58 build 11-Nov-2024 15:05:58 > Task :buildResources build 11-Nov-2024 15:05:58 > Task :copyDocs build 11-Nov-2024 15:05:58 build 11-Nov-2024 15:05:58 > Task :convertMdFiles build 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 build 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 build 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 build 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 build 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 build 11-Nov-2024 15:05:58 build 11-Nov-2024 15:05:58 > Task :releasesTemplates build 11-Nov-2024 15:05:58 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 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. build 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. build 11-Nov-2024 15:05:58 Stripping rc/test/etc for TEST build 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 build 11-Nov-2024 15:05:58 build 11-Nov-2024 15:05:58 > Task :prepare build 11-Nov-2024 15:06:00 build 11-Nov-2024 15:06:00 > Task :compileJava build 11-Nov-2024 15:06:00 Setting target compatibility to 11 error 11-Nov-2024 15:06:06 Note: Some input files use or override a deprecated API. error 11-Nov-2024 15:06:06 Note: Recompile with -Xlint:deprecation for details. error 11-Nov-2024 15:06:06 Note: Some input files use unchecked or unsafe operations. error 11-Nov-2024 15:06:06 Note: Recompile with -Xlint:unchecked for details. build 11-Nov-2024 15:06:10 build 11-Nov-2024 15:06:10 > Task :compileTestJava build 11-Nov-2024 15:06:10 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 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. build 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. build 11-Nov-2024 15:06:10 Setting target compatibility to 11 error 11-Nov-2024 15:06:15 Note: Some input files use or override a deprecated API. error 11-Nov-2024 15:06:15 Note: Recompile with -Xlint:deprecation for details. error 11-Nov-2024 15:06:15 Note: Some input files use unchecked or unsafe operations. error 11-Nov-2024 15:06:15 Note: Recompile with -Xlint:unchecked for details. build 11-Nov-2024 15:06:16 build 11-Nov-2024 15:06:16 > Task :processTestResources build 11-Nov-2024 15:06:16 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 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. build 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. build 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. build 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. build 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. build 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. build 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. build 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. build 11-Nov-2024 15:06:16 build 11-Nov-2024 15:06:16 > Task :testClasses build 11-Nov-2024 15:06:18 build 11-Nov-2024 15:06:18 > Task :testTask0 build 11-Nov-2024 15:06:18 Running tests WITH clover error 11-Nov-2024 15:06:21 WARNING: An illegal reflective access operation has occurred error 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 error 11-Nov-2024 15:06:21 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 11-Nov-2024 15:06:21 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 11-Nov-2024 15:06:21 WARNING: All illegal access operations will be denied in a future release build 11-Nov-2024 15:09:59 build 11-Nov-2024 15:09:59 > Task :testTask1 build 11-Nov-2024 15:09:59 Running tests WITH clover error 11-Nov-2024 15:10:00 WARNING: An illegal reflective access operation has occurred error 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 error 11-Nov-2024 15:10:00 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 11-Nov-2024 15:10:00 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 11-Nov-2024 15:10:00 WARNING: All illegal access operations will be denied in a future release build 11-Nov-2024 15:11:35 build 11-Nov-2024 15:11:35 > Task :testTask2 build 11-Nov-2024 15:11:35 Running tests WITH clover build 11-Nov-2024 15:11:39 build 11-Nov-2024 15:11:39 > Task :testTask3 build 11-Nov-2024 15:11:39 Running tests WITH clover error 11-Nov-2024 15:11:40 WARNING: An illegal reflective access operation has occurred error 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 error 11-Nov-2024 15:11:40 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 11-Nov-2024 15:11:40 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 11-Nov-2024 15:11:40 WARNING: All illegal access operations will be denied in a future release build 11-Nov-2024 15:12:26 build 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 build 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] build 11-Nov-2024 15:12:26 at org.testng.Assert.fail(Assert.java:94) build 11-Nov-2024 15:12:26 at org.testng.Assert.failNotEquals(Assert.java:496) build 11-Nov-2024 15:12:26 at org.testng.Assert.assertTrue(Assert.java:42) build 11-Nov-2024 15:12:26 at jalview.bin.CommandsTest.verifyOrderedFileSet(CommandsTest.java:297) build 11-Nov-2024 15:12:26 at jalview.bin.CommandsTest.verifyIncreasingSize(CommandsTest.java:274) build 11-Nov-2024 15:12:26 at jalview.bin.CommandsTest.__CLR4_4_1shrjyq47q9(CommandsTest.java:194) build 11-Nov-2024 15:12:26 at jalview.bin.CommandsTest.structureImageOutputTest(CommandsTest.java:186) error 11-Nov-2024 15:12:26 error 11-Nov-2024 15:12:26 25 tests completed, 1 failed build 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 error 11-Nov-2024 15:12:26 error 11-Nov-2024 15:12:26 FAILURE: Build failed with an exception. error 11-Nov-2024 15:12:26 error 11-Nov-2024 15:12:26 * Where: error 11-Nov-2024 15:12:26 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1/build.gradle' line: 1966 error 11-Nov-2024 15:12:26 error 11-Nov-2024 15:12:26 * What went wrong: error 11-Nov-2024 15:12:26 Failed tests! error 11-Nov-2024 15:12:26 error 11-Nov-2024 15:12:26 * Try: error 11-Nov-2024 15:12:26 > Run with --stacktrace option to get the stack trace. error 11-Nov-2024 15:12:26 > Run with --info or --debug option to get more log output. error 11-Nov-2024 15:12:26 > Run with --scan to get full insights. error 11-Nov-2024 15:12:26 error 11-Nov-2024 15:12:26 * Get more help at https://help.gradle.org error 11-Nov-2024 15:12:26 build 11-Nov-2024 15:12:26 error 11-Nov-2024 15:12:26 BUILD FAILED in 7m 8s build 11-Nov-2024 15:12:26 > Task :test NO-SOURCE build 11-Nov-2024 15:12:26 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 11-Nov-2024 15:12:26 │jalview:testTask0 results: SUCCESS (1728 tests, 1728 successes, 0 failures, 0 skipped) in 3 minutes, 40.394 seconds │ build 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│ build 11-Nov-2024 15:12:26 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Nov-2024 15:12:26 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 36.185 seconds │ build 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│ build 11-Nov-2024 15:12:26 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Nov-2024 15:12:26 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.640 seconds │ build 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│ build 11-Nov-2024 15:12:26 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Nov-2024 15:12:26 │jalview:testTask3 results: FAILURE (25 tests, 24 successes, 1 failures, 0 skipped) in 48.923 seconds │ build 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│ build 11-Nov-2024 15:12:26 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Nov-2024 15:12:26 │OVERALL: results: FAILURE (1803 tests, 1802 successes, 1 failures, 0 skipped) in 4 minutes, 129.142 seconds │ build 11-Nov-2024 15:12:26 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 11-Nov-2024 15:12:26 build 11-Nov-2024 15:12:26 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 11-Nov-2024 15:12:26 build 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. build 11-Nov-2024 15:12:26 build 11-Nov-2024 15:12:26 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 11-Nov-2024 15:12:26 build 11-Nov-2024 15:12:26 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 11-Nov-2024 15:12:26 Please consult deprecation warnings for more details. build 11-Nov-2024 15:12:26 21 actionable tasks: 20 executed, 1 up-to-date simple 11-Nov-2024 15:12:26 simple 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 simple 11-Nov-2024 15:12:26 Finished task 'Run tests with openclover under gradle' with result: Failed simple 11-Nov-2024 15:12:26 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 11-Nov-2024 15:12:26 Bamboo Artifactory Plugin version: 2.6.2 command 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)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_repository_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB642-JOB1-2\nbamboo_repository_46498184_git_branch=features/JAL-4489_cluster_pca_and_pasimap\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB642-JOB1\nbamboo_shortPlanName=features-JAL-4489_cluster_pca_and_pasimap\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB642-JOB1-2\nbamboo_repository_46498184_name=Jalview Git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498184_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap\nbamboo_shortPlanKey=GDB642\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_repository_46498184_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_buildTimeStamp=2024-11-11T15:05:16.749Z\nbamboo_repository_previous_revision_number=3e7d1be29f1857c4d5cf237b1cf6420218752458\nbamboo_planRepository_previousRevision=3e7d1be29f1857c4d5cf237b1cf6420218752458\nbamboo_repository_git_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_buildResultKey=JB-GDB642-JOB1-2\nbamboo_repository_branch_name=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - features-JAL-4489_cluster_pca_and_pasimap - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=f6be36d7152321642e41db9d8bdbd2580431541e\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_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\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=true\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=3e7d1be29f1857c4d5cf237b1cf6420218752458\nbamboo_repository_46498184_git_username=\nbamboo_planRepository_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=features/JAL-4489_cluster_pca_and_pasimap\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498184_previous_revision_number=3e7d1be29f1857c4d5cf237b1cf6420218752458\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301967\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1\nbamboo_planKey=JB-GDB642\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498184_branch_name=features/JAL-4489_cluster_pca_and_pasimap\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=features/JAL-4489_cluster_pca_and_pasimap\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 11-Nov-2024 15:12:26 444 build 11-Nov-2024 15:12:32 build 11-Nov-2024 15:12:32 > Configure project : build 11-Nov-2024 15:12:32 Using properties from file './utils/channels/default/channel_gradle.properties' build 11-Nov-2024 15:12:32 JALVIEW_VERSION is set to '2.11.4.1' build 11-Nov-2024 15:12:32 HEADLESS BUILD build 11-Nov-2024 15:12:32 J2S ENABLED build 11-Nov-2024 15:12:32 Using a LOCAL profile. build 11-Nov-2024 15:12:33 eclipseDir exists build 11-Nov-2024 15:12:35 build 11-Nov-2024 15:12:35 > Task :cloverHtmlReport build 11-Nov-2024 15:12:35 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 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' build 11-Nov-2024 15:13:14 Done. Processed 116 packages in 37819ms (326ms per package). build 11-Nov-2024 15:13:19 build 11-Nov-2024 15:13:19 > Task :cloverXmlReport build 11-Nov-2024 15:13:19 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 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' build 11-Nov-2024 15:13:21 build 11-Nov-2024 15:13:21 > Task :cloverReport build 11-Nov-2024 15:13:21 build 11-Nov-2024 15:13:21 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 11-Nov-2024 15:13:21 build 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. build 11-Nov-2024 15:13:21 build 11-Nov-2024 15:13:21 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 11-Nov-2024 15:13:21 build 11-Nov-2024 15:13:21 BUILD SUCCESSFUL in 54s build 11-Nov-2024 15:13:21 2 actionable tasks: 2 executed simple 11-Nov-2024 15:13:21 Finished task 'Clover Report' with result: Success simple 11-Nov-2024 15:13:21 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 11-Nov-2024 15:13:21 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB642-JOB1... simple 11-Nov-2024 15:13:21 Failing task since 1 failing test cases were found. simple 11-Nov-2024 15:13:21 Finished task 'TestNG Parser' with result: Failed simple 11-Nov-2024 15:13:21 Running post build plugin 'NCover Results Collector' simple 11-Nov-2024 15:13:21 Running post build plugin 'Artifact Copier' simple 11-Nov-2024 15:13:21 Publishing an artifact: Clover Report (System) simple 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 simple 11-Nov-2024 15:13:22 Publishing an artifact: TestNG report error 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. simple 11-Nov-2024 15:13:22 The artifact hasn't been successfully published after 2.206 ms simple 11-Nov-2024 15:13:22 Running post build plugin 'Artifactory Release Management Staging' simple 11-Nov-2024 15:13:22 Running post build plugin 'Artifactory Build Info Copier' simple 11-Nov-2024 15:13:22 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 11-Nov-2024 15:13:22 Running post build plugin 'npm Cache Cleanup' simple 11-Nov-2024 15:13:22 Running post build plugin 'Clover Results Collector' simple 11-Nov-2024 15:13:22 Running post build plugin 'Docker Container Cleanup' simple 11-Nov-2024 15:13:22 Finalising the build... simple 11-Nov-2024 15:13:22 Stopping timer. simple 11-Nov-2024 15:13:22 Build JB-GDB642-JOB1-2 completed. simple 11-Nov-2024 15:13:22 Running on server: post build plugin 'NCover Results Collector' simple 11-Nov-2024 15:13:22 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 11-Nov-2024 15:13:22 Running on server: post build plugin 'Clover Delta Calculator' simple 11-Nov-2024 15:13:22 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 11-Nov-2024 15:13:22 All post build plugins have finished simple 11-Nov-2024 15:13:22 Generating build results summary... simple 11-Nov-2024 15:13:23 Saving build results to disk... simple 11-Nov-2024 15:13:23 Logging substituted variables... simple 11-Nov-2024 15:13:23 Indexing build results... simple 11-Nov-2024 15:13:23 Finished building JB-GDB642-JOB1-2.