simple 30-Jun-2023 17:28:19 Build Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests #63 (JB-GDB329-JOB1-63) started building on agent Default Agent simple 30-Jun-2023 17:28:19 simple 30-Jun-2023 17:28:19 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1 simple 30-Jun-2023 17:28:19 Executing build Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests #63 (JB-GDB329-JOB1-63) simple 30-Jun-2023 17:28:19 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 30-Jun-2023 17:28:19 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1 simple 30-Jun-2023 17:28:19 Updating source code to revision: bd990168d0b3c7772c961b56144c3dee94a09054 simple 30-Jun-2023 17:28:19 Fetching 'refs/heads/releases/Release_2_11_2_Branch' from 'http://source.jalview.org/git/jalview.git'. simple 30-Jun-2023 17:28:19 Checking out revision bd990168d0b3c7772c961b56144c3dee94a09054. simple 30-Jun-2023 17:28:19 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 30-Jun-2023 17:28:19 28bae9d..bd99016 releases/Release_2_11_2_Branch -> origin/releases/Release_2_11_2_Branch simple 30-Jun-2023 17:28:19 Already on 'releases/Release_2_11_2_Branch' simple 30-Jun-2023 17:28:19 Your branch is behind 'origin/releases/Release_2_11_2_Branch' by 1 commit, and can be fast-forwarded. simple 30-Jun-2023 17:28:19 (use "git pull" to update your local branch) simple 30-Jun-2023 17:28:19 HEAD is now at bd99016 JAL-4117 JAL-1551 source licensing simple 30-Jun-2023 17:28:19 Updated source code to revision: bd990168d0b3c7772c961b56144c3dee94a09054 simple 30-Jun-2023 17:28:19 Finished task 'Checkout Default Repository' with result: Success simple 30-Jun-2023 17:28:19 Running pre-build action: VCS Version Collector simple 30-Jun-2023 17:28:19 Running pre-build action: Artifactory Release Staging simple 30-Jun-2023 17:28:19 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 30-Jun-2023 17:28:19 Bamboo Artifactory Plugin version: 2.6.2 command 30-Jun-2023 17:28:19 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests #63 (JB-GDB329-JOB1-63)'\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-GDB329-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=releases/Release_2_11_2_Branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=releases/Release_2_11_2_Branch\nbamboo_repository_revision_number=bd990168d0b3c7772c961b56144c3dee94a09054\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB329-JOB1-63\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-GDB329-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB329-JOB1\nbamboo_shortPlanName=releases-Release_2_11_2_Branch\nbamboo_repository_27918600_previous_revision_number=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_27918600_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=63\nPWD=/\nbamboo_repository_27918600_git_username=\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-GDB329-JOB1-63\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch\nbamboo_shortPlanKey=GDB329\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=bd990168d0b3c7772c961b56144c3dee94a09054\nbamboo_buildTimeStamp=2023-06-30T17:28:19.294+01:00\nbamboo_repository_previous_revision_number=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f\nbamboo_repository_27918600_revision_number=bd990168d0b3c7772c961b56144c3dee94a09054\nbamboo_planRepository_previousRevision=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f\nbamboo_repository_git_branch=releases/Release_2_11_2_Branch\nbamboo_buildResultKey=JB-GDB329-JOB1-63\nbamboo_repository_branch_name=releases/Release_2_11_2_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_27918600_git_branch=releases/Release_2_11_2_Branch\nbamboo_planRepository_1_revision=bd990168d0b3c7772c961b56144c3dee94a09054\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_repository_27918600_git_repositoryUrl=http://source.jalview.org/git/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=releases/Release_2_11_2_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_repository_27918600_branch_name=releases/Release_2_11_2_Branch\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f\nbamboo_planRepository_branchDisplayName=releases/Release_2_11_2_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=releases/Release_2_11_2_Branch\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-27623951\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-GDB329-JOB1\nbamboo_planKey=JB-GDB329\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=releases/Release_2_11_2_Branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 30-Jun-2023 17:28:19 4894 build 30-Jun-2023 17:28:20 build 30-Jun-2023 17:28:20 > Configure project : build 30-Jun-2023 17:28:20 Using properties from file './utils/channels/default/channel_gradle.properties' build 30-Jun-2023 17:28:20 JALVIEW_VERSION is set to '2.11.2.7' build 30-Jun-2023 17:28:20 HEADLESS BUILD build 30-Jun-2023 17:28:20 J2S ENABLED build 30-Jun-2023 17:28:20 Using a LOCAL profile. build 30-Jun-2023 17:28:20 eclipseDir exists build 30-Jun-2023 17:28:21 build 30-Jun-2023 17:28:21 > Task :clean build 30-Jun-2023 17:28:21 > Task :cleanClover build 30-Jun-2023 17:28:21 > Task :cleanTest UP-TO-DATE build 30-Jun-2023 17:28:23 build 30-Jun-2023 17:28:23 > Task :cloverInstrJava build 30-Jun-2023 17:28:23 Clover: About to instrument 1041 files build 30-Jun-2023 17:28:23 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 30-Jun-2023 17:28:23 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/clover/clover.db'. build 30-Jun-2023 17:28:23 Processing files at 1.9 source level. build 30-Jun-2023 17:28:32 Clover all over. Instrumented 1041 files (103 packages). build 30-Jun-2023 17:28:34 build 30-Jun-2023 17:28:34 > Task :cloverInstrTests build 30-Jun-2023 17:28:34 Clover: About to instrument test files build 30-Jun-2023 17:28:34 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 30-Jun-2023 17:28:34 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/clover/clover.db'. build 30-Jun-2023 17:28:34 Processing files at 1.9 source level. build 30-Jun-2023 17:28:36 Clover all over. Instrumented 269 files (50 packages). build 30-Jun-2023 17:28:36 1495 test methods detected. build 30-Jun-2023 17:28:36 build 30-Jun-2023 17:28:36 > Task :cloverInstr build 30-Jun-2023 17:28:38 build 30-Jun-2023 17:28:38 > Task :compileCloverJava build 30-Jun-2023 17:28:38 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 30-Jun-2023 17:28:38 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:28:38 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:28:38 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:28:38 Setting target compatibility to 11 error 30-Jun-2023 17:28:51 Note: Some input files use or override a deprecated API. error 30-Jun-2023 17:28:51 Note: Recompile with -Xlint:deprecation for details. error 30-Jun-2023 17:28:51 Note: Some input files use unchecked or unsafe operations. error 30-Jun-2023 17:28:51 Note: Recompile with -Xlint:unchecked for details. build 30-Jun-2023 17:28:54 build 30-Jun-2023 17:28:54 > Task :processCloverResources NO-SOURCE build 30-Jun-2023 17:28:54 > Task :cloverClasses build 30-Jun-2023 17:28:55 > Task :copyHelp build 30-Jun-2023 17:28:56 > Task :buildIndices build 30-Jun-2023 17:28:56 > Task :copyResources build 30-Jun-2023 17:28:56 > Task :copyChannelResources build 30-Jun-2023 17:28:56 build 30-Jun-2023 17:28:56 > Task :createBuildProperties build 30-Jun-2023 17:28:56 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 30-Jun-2023 17:28:56 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:28:56 build 30-Jun-2023 17:28:56 > Task :buildResources build 30-Jun-2023 17:28:56 > Task :copyDocs build 30-Jun-2023 17:28:56 build 30-Jun-2023 17:28:56 > Task :convertMdFiles build 30-Jun-2023 17:28:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 30-Jun-2023 17:28:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build/doc/releaseprocess.html build 30-Jun-2023 17:28:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 30-Jun-2023 17:28:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/resources/doc_build/doc/building.html build 30-Jun-2023 17:28:57 build 30-Jun-2023 17:28:57 > Task :releasesTemplates build 30-Jun-2023 17:28:57 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 30-Jun-2023 17:28:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:28:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:28:57 build 30-Jun-2023 17:28:57 > Task :prepare build 30-Jun-2023 17:28:59 build 30-Jun-2023 17:28:59 > Task :compileTestJava build 30-Jun-2023 17:28:59 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 30-Jun-2023 17:28:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:28:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:28:59 Setting target compatibility to 11 error 30-Jun-2023 17:29:03 Note: Some input files use or override a deprecated API. error 30-Jun-2023 17:29:03 Note: Recompile with -Xlint:deprecation for details. error 30-Jun-2023 17:29:03 Note: Some input files use unchecked or unsafe operations. error 30-Jun-2023 17:29:03 Note: Recompile with -Xlint:unchecked for details. build 30-Jun-2023 17:29:04 build 30-Jun-2023 17:29:04 > Task :processTestResources build 30-Jun-2023 17:29:04 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 30-Jun-2023 17:29:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:29:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:29:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:29:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:29:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:29:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:29:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:29:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-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 30-Jun-2023 17:29:04 build 30-Jun-2023 17:29:04 > Task :testClasses build 30-Jun-2023 17:29:06 build 30-Jun-2023 17:29:06 > Task :test build 30-Jun-2023 17:29:06 Running tests WITH clover error 30-Jun-2023 17:29:29 WARNING: An illegal reflective access operation has occurred error 30-Jun-2023 17:29:29 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 30-Jun-2023 17:29:29 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 30-Jun-2023 17:29:29 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 30-Jun-2023 17:29:29 WARNING: All illegal access operations will be denied in a future release build 30-Jun-2023 17:31:42 build 30-Jun-2023 17:31:42 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 30-Jun-2023 17:31:42 build 30-Jun-2023 17:31:42 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 30-Jun-2023 17:31:42 build 30-Jun-2023 17:31:42 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 30-Jun-2023 17:31:42 build 30-Jun-2023 17:31:42 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 30-Jun-2023 17:31:42 Please consult deprecation warnings for more details. build 30-Jun-2023 17:31:42 build 30-Jun-2023 17:31:42 BUILD SUCCESSFUL in 3m 23s build 30-Jun-2023 17:31:42 17 actionable tasks: 16 executed, 1 up-to-date simple 30-Jun-2023 17:31:43 Finished task 'Run tests with openclover under gradle' with result: Success simple 30-Jun-2023 17:31:43 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 30-Jun-2023 17:31:43 Bamboo Artifactory Plugin version: 2.6.2 command 30-Jun-2023 17:31:43 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests #63 (JB-GDB329-JOB1-63)'\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-GDB329-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=releases/Release_2_11_2_Branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=releases/Release_2_11_2_Branch\nbamboo_repository_revision_number=bd990168d0b3c7772c961b56144c3dee94a09054\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB329-JOB1-63\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-GDB329-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB329-JOB1\nbamboo_shortPlanName=releases-Release_2_11_2_Branch\nbamboo_repository_27918600_previous_revision_number=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_27918600_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=63\nPWD=/\nbamboo_repository_27918600_git_username=\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-GDB329-JOB1-63\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch\nbamboo_shortPlanKey=GDB329\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=bd990168d0b3c7772c961b56144c3dee94a09054\nbamboo_buildTimeStamp=2023-06-30T17:28:19.294+01:00\nbamboo_repository_previous_revision_number=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f\nbamboo_repository_27918600_revision_number=bd990168d0b3c7772c961b56144c3dee94a09054\nbamboo_planRepository_previousRevision=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f\nbamboo_repository_git_branch=releases/Release_2_11_2_Branch\nbamboo_buildResultKey=JB-GDB329-JOB1-63\nbamboo_repository_branch_name=releases/Release_2_11_2_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - releases-Release_2_11_2_Branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_27918600_git_branch=releases/Release_2_11_2_Branch\nbamboo_planRepository_1_revision=bd990168d0b3c7772c961b56144c3dee94a09054\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_repository_27918600_git_repositoryUrl=http://source.jalview.org/git/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=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=releases/Release_2_11_2_Branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_repository_27918600_branch_name=releases/Release_2_11_2_Branch\nbamboo_jobFailed=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=28bae9d81ae10f2b9be9d729cfa4f6eb75d2025f\nbamboo_planRepository_branchDisplayName=releases/Release_2_11_2_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=releases/Release_2_11_2_Branch\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-27623951\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-GDB329-JOB1\nbamboo_planKey=JB-GDB329\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=releases/Release_2_11_2_Branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 30-Jun-2023 17:31:43 4894 build 30-Jun-2023 17:31:49 build 30-Jun-2023 17:31:49 > Configure project : build 30-Jun-2023 17:31:49 Using properties from file './utils/channels/default/channel_gradle.properties' build 30-Jun-2023 17:31:49 JALVIEW_VERSION is set to '2.11.2.7' build 30-Jun-2023 17:31:49 HEADLESS BUILD build 30-Jun-2023 17:31:49 J2S ENABLED build 30-Jun-2023 17:31:49 Using a LOCAL profile. build 30-Jun-2023 17:31:50 eclipseDir exists build 30-Jun-2023 17:31:52 build 30-Jun-2023 17:31:52 > Task :cloverHtmlReport build 30-Jun-2023 17:31:52 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 30-Jun-2023 17:31:53 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/reports/clover' build 30-Jun-2023 17:32:22 Done. Processed 107 packages in 28864ms (269ms per package). build 30-Jun-2023 17:32:26 build 30-Jun-2023 17:32:26 > Task :cloverXmlReport build 30-Jun-2023 17:32:26 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 30-Jun-2023 17:32:27 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1/build/reports/clover/clover.xml' build 30-Jun-2023 17:32:27 build 30-Jun-2023 17:32:27 > Task :cloverReport build 30-Jun-2023 17:32:27 build 30-Jun-2023 17:32:27 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 30-Jun-2023 17:32:27 build 30-Jun-2023 17:32:27 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 30-Jun-2023 17:32:27 build 30-Jun-2023 17:32:27 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 30-Jun-2023 17:32:27 build 30-Jun-2023 17:32:27 BUILD SUCCESSFUL in 44s build 30-Jun-2023 17:32:27 2 actionable tasks: 2 executed simple 30-Jun-2023 17:32:27 Finished task 'Clover Report' with result: Success simple 30-Jun-2023 17:32:27 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 30-Jun-2023 17:32:27 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB329-JOB1... simple 30-Jun-2023 17:32:27 Finished task 'TestNG Parser' with result: Success simple 30-Jun-2023 17:32:27 Running post build plugin 'NCover Results Collector' simple 30-Jun-2023 17:32:27 Running post build plugin 'Artifact Copier' simple 30-Jun-2023 17:32:27 Publishing an artifact: Clover Report (System) simple 30-Jun-2023 17:32:29 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.680 s simple 30-Jun-2023 17:32:29 Publishing an artifact: TestNG report simple 30-Jun-2023 17:32:29 Finished publishing of artifact Job artifact: [TestNG report], pattern: [**/*] anchored at: [build/reports/tests/test] in 92.97 ms simple 30-Jun-2023 17:32:29 Running post build plugin 'Artifactory Release Management Staging' simple 30-Jun-2023 17:32:29 Running post build plugin 'Artifactory Build Info Copier' simple 30-Jun-2023 17:32:29 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 30-Jun-2023 17:32:29 Running post build plugin 'npm Cache Cleanup' simple 30-Jun-2023 17:32:29 Running post build plugin 'Clover Results Collector' simple 30-Jun-2023 17:32:29 Running post build plugin 'Docker Container Cleanup' simple 30-Jun-2023 17:32:29 Finalising the build... simple 30-Jun-2023 17:32:29 Stopping timer. simple 30-Jun-2023 17:32:29 Build JB-GDB329-JOB1-63 completed. simple 30-Jun-2023 17:32:29 Running on server: post build plugin 'NCover Results Collector' simple 30-Jun-2023 17:32:29 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 30-Jun-2023 17:32:29 Running on server: post build plugin 'Clover Delta Calculator' simple 30-Jun-2023 17:32:29 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 30-Jun-2023 17:32:29 All post build plugins have finished simple 30-Jun-2023 17:32:29 Generating build results summary... simple 30-Jun-2023 17:32:29 Saving build results to disk... simple 30-Jun-2023 17:32:29 Logging substituted variables... simple 30-Jun-2023 17:32:29 Indexing build results... simple 30-Jun-2023 17:32:29 Finished building JB-GDB329-JOB1-63.