simple 26-Aug-2024 17:36:00 Build Jalview Builds - Gradle Develop Build - jims-JAL-4420_review_redo - Clover and Tests #1 (JB-GDB613-JOB1-1) started building on agent Default Agent simple 26-Aug-2024 17:36:00 simple 26-Aug-2024 17:36:00 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1 simple 26-Aug-2024 17:36:00 Executing build Jalview Builds - Gradle Develop Build - jims-JAL-4420_review_redo - Clover and Tests #1 (JB-GDB613-JOB1-1) simple 26-Aug-2024 17:36:00 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 26-Aug-2024 17:36:00 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1 simple 26-Aug-2024 17:36:00 Updating source code to revision: 85e30a861f26369f9be8cffa4a1345c79092a895 simple 26-Aug-2024 17:36:00 Fetching 'refs/heads/jims/JAL-4420_review_redo' from 'http://source.jalview.org/git/jalview.git'. simple 26-Aug-2024 17:36:00 Checking out revision 85e30a861f26369f9be8cffa4a1345c79092a895. simple 26-Aug-2024 17:36:00 Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/.git'. simple 26-Aug-2024 17:36:00 Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1'... simple 26-Aug-2024 17:36:00 done. simple 26-Aug-2024 17:36:05 Switched to a new branch 'jims/JAL-4420_review_redo' simple 26-Aug-2024 17:36:05 Branch jims/JAL-4420_review_redo set up to track remote branch jims/JAL-4420_review_redo from origin. simple 26-Aug-2024 17:36:05 Updated source code to revision: 85e30a861f26369f9be8cffa4a1345c79092a895 simple 26-Aug-2024 17:36:05 Finished task 'Checkout Default Repository' with result: Success simple 26-Aug-2024 17:36:05 Running pre-build action: VCS Version Collector simple 26-Aug-2024 17:36:05 Running pre-build action: Artifactory Release Staging simple 26-Aug-2024 17:36:05 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 26-Aug-2024 17:36:05 Bamboo Artifactory Plugin version: 2.6.2 command 26-Aug-2024 17:36:05 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - jims-JAL-4420_review_redo - Clover and Tests #1 (JB-GDB613-JOB1-1)'\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-GDB613-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=jims/JAL-4420_review_redo\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=jims/JAL-4420_review_redo\nbamboo_repository_revision_number=85e30a861f26369f9be8cffa4a1345c79092a895\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB613-JOB1-1\nbamboo_repository_46498039_revision_number=85e30a861f26369f9be8cffa4a1345c79092a895\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-GDB613-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB613-JOB1\nbamboo_shortPlanName=jims-JAL-4420_review_redo\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=1\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-GDB613-JOB1-1\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - jims-JAL-4420_review_redo\nbamboo_shortPlanKey=GDB613\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=85e30a861f26369f9be8cffa4a1345c79092a895\nbamboo_repository_46498039_git_branch=jims/JAL-4420_review_redo\nbamboo_buildTimeStamp=2024-08-26T17:36:00.463+01:00\nbamboo_repository_46498039_name=Jalview Git\nbamboo_repository_git_branch=jims/JAL-4420_review_redo\nbamboo_buildResultKey=JB-GDB613-JOB1-1\nbamboo_repository_branch_name=jims/JAL-4420_review_redo\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - jims-JAL-4420_review_redo - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=85e30a861f26369f9be8cffa4a1345c79092a895\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498039_git_repositoryUrl=http://source.jalview.org/git/jalview.git\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=jims/JAL-4420_review_redo\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=jims/JAL-4420_review_redo\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=jims/JAL-4420_review_redo\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-46301677\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_repository_46498039_git_username=\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_repository_46498039_branch_name=jims/JAL-4420_review_redo\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-GDB613-JOB1\nbamboo_planKey=JB-GDB613\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=jims/JAL-4420_review_redo\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 26-Aug-2024 17:36:05 444 build 26-Aug-2024 17:36:07 build 26-Aug-2024 17:36:07 > Configure project : build 26-Aug-2024 17:36:07 Using properties from file './utils/channels/default/channel_gradle.properties' build 26-Aug-2024 17:36:07 JALVIEW_VERSION is set to '2.11.4.0' build 26-Aug-2024 17:36:07 HEADLESS BUILD build 26-Aug-2024 17:36:07 J2S ENABLED build 26-Aug-2024 17:36:07 Using a LOCAL profile. build 26-Aug-2024 17:36:07 eclipseDir exists build 26-Aug-2024 17:36:07 build 26-Aug-2024 17:36:07 > Task :clean build 26-Aug-2024 17:36:07 > Task :cleanClover build 26-Aug-2024 17:36:07 > Task :cleanTest UP-TO-DATE build 26-Aug-2024 17:36:10 build 26-Aug-2024 17:36:10 > Task :cloverInstrJava build 26-Aug-2024 17:36:10 Clover: About to instrument 1102 files build 26-Aug-2024 17:36:10 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 26-Aug-2024 17:36:10 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/clover/clover.db'. build 26-Aug-2024 17:36:10 Processing files at 1.9 source level. error 26-Aug-2024 17:36:15 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 26-Aug-2024 17:36:15 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 26-Aug-2024 17:36:15 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 26-Aug-2024 17:36:15 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 26-Aug-2024 17:36:15 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 26-Aug-2024 17:36:15 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 26-Aug-2024 17:36:15 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 26-Aug-2024 17:36:21 Clover all over. Instrumented 1102 files (111 packages). build 26-Aug-2024 17:36:23 build 26-Aug-2024 17:36:23 > Task :cloverInstrTests build 26-Aug-2024 17:36:23 Clover: About to instrument test files build 26-Aug-2024 17:36:23 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 26-Aug-2024 17:36:23 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/clover/clover.db'. build 26-Aug-2024 17:36:23 Processing files at 1.9 source level. build 26-Aug-2024 17:36:26 Clover all over. Instrumented 290 files (52 packages). build 26-Aug-2024 17:36:26 1592 test methods detected. build 26-Aug-2024 17:36:26 build 26-Aug-2024 17:36:26 > Task :cloverInstr build 26-Aug-2024 17:36:30 build 26-Aug-2024 17:36:30 > Task :compileCloverJava build 26-Aug-2024 17:36:30 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 26-Aug-2024 17:36:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:36:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:36:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:36:30 Setting target compatibility to 11 error 26-Aug-2024 17:36:44 Note: Some input files use or override a deprecated API. error 26-Aug-2024 17:36:44 Note: Recompile with -Xlint:deprecation for details. error 26-Aug-2024 17:36:44 Note: Some input files use unchecked or unsafe operations. error 26-Aug-2024 17:36:44 Note: Recompile with -Xlint:unchecked for details. build 26-Aug-2024 17:36:48 build 26-Aug-2024 17:36:48 > Task :processCloverResources NO-SOURCE build 26-Aug-2024 17:36:48 > Task :cloverClasses build 26-Aug-2024 17:36:48 > Task :copyHelp build 26-Aug-2024 17:36:50 > Task :buildIndices build 26-Aug-2024 17:36:50 > Task :copyResources build 26-Aug-2024 17:36:50 > Task :copyChannelResources build 26-Aug-2024 17:36:50 build 26-Aug-2024 17:36:50 > Task :createBuildProperties build 26-Aug-2024 17:36:50 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 26-Aug-2024 17:36:50 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:36:50 build 26-Aug-2024 17:36:50 > Task :buildResources build 26-Aug-2024 17:36:50 > Task :copyDocs build 26-Aug-2024 17:36:50 build 26-Aug-2024 17:36:50 > Task :convertMdFiles build 26-Aug-2024 17:36:50 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 26-Aug-2024 17:36:50 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/resources/doc_build/doc/releaseprocess.html build 26-Aug-2024 17:36:50 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 26-Aug-2024 17:36:50 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/resources/doc_build/doc/building.html build 26-Aug-2024 17:36:50 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/resources/doc_build/doc/jalview-projects.html build 26-Aug-2024 17:36:50 build 26-Aug-2024 17:36:50 > Task :releasesTemplates build 26-Aug-2024 17:36:50 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 26-Aug-2024 17:36:50 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:36:50 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:36:50 build 26-Aug-2024 17:36:50 > Task :prepare build 26-Aug-2024 17:36:52 build 26-Aug-2024 17:36:52 > Task :compileJava build 26-Aug-2024 17:36:52 Setting target compatibility to 11 error 26-Aug-2024 17:36:57 Note: Some input files use or override a deprecated API. error 26-Aug-2024 17:36:57 Note: Recompile with -Xlint:deprecation for details. error 26-Aug-2024 17:36:57 Note: Some input files use unchecked or unsafe operations. error 26-Aug-2024 17:36:57 Note: Recompile with -Xlint:unchecked for details. build 26-Aug-2024 17:37:00 build 26-Aug-2024 17:37:00 > Task :compileTestJava build 26-Aug-2024 17:37:00 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 26-Aug-2024 17:37:00 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:37:00 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:37:00 Setting target compatibility to 11 error 26-Aug-2024 17:37:04 Note: Some input files use or override a deprecated API. error 26-Aug-2024 17:37:04 Note: Recompile with -Xlint:deprecation for details. error 26-Aug-2024 17:37:04 Note: Some input files use unchecked or unsafe operations. error 26-Aug-2024 17:37:04 Note: Recompile with -Xlint:unchecked for details. build 26-Aug-2024 17:37:05 build 26-Aug-2024 17:37:05 > Task :processTestResources build 26-Aug-2024 17:37:05 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 26-Aug-2024 17:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-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 26-Aug-2024 17:37:05 build 26-Aug-2024 17:37:05 > Task :testClasses build 26-Aug-2024 17:37:07 build 26-Aug-2024 17:37:07 > Task :testTask0 build 26-Aug-2024 17:37:07 Running tests WITH clover error 26-Aug-2024 17:37:10 WARNING: An illegal reflective access operation has occurred error 26-Aug-2024 17:37:10 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 26-Aug-2024 17:37:10 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 26-Aug-2024 17:37:10 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 26-Aug-2024 17:37:10 WARNING: All illegal access operations will be denied in a future release build 26-Aug-2024 17:40:47 build 26-Aug-2024 17:40:47 > Task :testTask1 build 26-Aug-2024 17:40:47 Running tests WITH clover error 26-Aug-2024 17:40:49 WARNING: An illegal reflective access operation has occurred error 26-Aug-2024 17:40:49 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 26-Aug-2024 17:40:49 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 26-Aug-2024 17:40:49 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 26-Aug-2024 17:40:49 WARNING: All illegal access operations will be denied in a future release build 26-Aug-2024 17:42:22 build 26-Aug-2024 17:42:22 > Task :testTask2 build 26-Aug-2024 17:42:22 Running tests WITH clover build 26-Aug-2024 17:42:25 build 26-Aug-2024 17:42:25 > Task :testTask3 build 26-Aug-2024 17:42:25 Running tests WITH clover error 26-Aug-2024 17:42:27 WARNING: An illegal reflective access operation has occurred error 26-Aug-2024 17:42:27 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 26-Aug-2024 17:42:27 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 26-Aug-2024 17:42:27 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 26-Aug-2024 17:42:27 WARNING: All illegal access operations will be denied in a future release build 26-Aug-2024 17:43:12 build 26-Aug-2024 17:43:12 > Task :test NO-SOURCE build 26-Aug-2024 17:43:12 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 26-Aug-2024 17:43:12 │jalview:testTask0 results: SUCCESS (1693 tests, 1693 successes, 0 failures, 0 skipped) in 3 minutes, 39.764 seconds │ build 26-Aug-2024 17:43:12 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/reports/tests/testTask0/index.html│ build 26-Aug-2024 17:43:12 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 26-Aug-2024 17:43:12 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 34.572 seconds │ build 26-Aug-2024 17:43:12 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/reports/tests/testTask1/index.html│ build 26-Aug-2024 17:43:12 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 26-Aug-2024 17:43:12 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.309 seconds │ build 26-Aug-2024 17:43:12 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/reports/tests/testTask2/index.html│ build 26-Aug-2024 17:43:12 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 26-Aug-2024 17:43:12 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 48.097 seconds │ build 26-Aug-2024 17:43:12 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/reports/tests/testTask3/index.html│ build 26-Aug-2024 17:43:12 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 26-Aug-2024 17:43:12 │OVERALL: results: SUCCESS (1768 tests, 1768 successes, 0 failures, 0 skipped) in 4 minutes, 125.742 seconds │ build 26-Aug-2024 17:43:12 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 26-Aug-2024 17:43:12 build 26-Aug-2024 17:43:12 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 26-Aug-2024 17:43:12 build 26-Aug-2024 17:43:12 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 26-Aug-2024 17:43:12 build 26-Aug-2024 17:43:12 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 26-Aug-2024 17:43:12 build 26-Aug-2024 17:43:12 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 26-Aug-2024 17:43:12 Please consult deprecation warnings for more details. build 26-Aug-2024 17:43:12 build 26-Aug-2024 17:43:12 BUILD SUCCESSFUL in 7m 6s build 26-Aug-2024 17:43:12 21 actionable tasks: 20 executed, 1 up-to-date simple 26-Aug-2024 17:43:12 Finished task 'Run tests with openclover under gradle' with result: Success simple 26-Aug-2024 17:43:12 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 26-Aug-2024 17:43:12 Bamboo Artifactory Plugin version: 2.6.2 command 26-Aug-2024 17:43:12 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - jims-JAL-4420_review_redo - Clover and Tests #1 (JB-GDB613-JOB1-1)'\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-GDB613-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=jims/JAL-4420_review_redo\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=jims/JAL-4420_review_redo\nbamboo_repository_revision_number=85e30a861f26369f9be8cffa4a1345c79092a895\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB613-JOB1-1\nbamboo_repository_46498039_revision_number=85e30a861f26369f9be8cffa4a1345c79092a895\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-GDB613-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB613-JOB1\nbamboo_shortPlanName=jims-JAL-4420_review_redo\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=1\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-GDB613-JOB1-1\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - jims-JAL-4420_review_redo\nbamboo_shortPlanKey=GDB613\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=85e30a861f26369f9be8cffa4a1345c79092a895\nbamboo_repository_46498039_git_branch=jims/JAL-4420_review_redo\nbamboo_buildTimeStamp=2024-08-26T17:36:00.463+01:00\nbamboo_repository_46498039_name=Jalview Git\nbamboo_repository_git_branch=jims/JAL-4420_review_redo\nbamboo_buildResultKey=JB-GDB613-JOB1-1\nbamboo_repository_branch_name=jims/JAL-4420_review_redo\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - jims-JAL-4420_review_redo - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=85e30a861f26369f9be8cffa4a1345c79092a895\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498039_git_repositoryUrl=http://source.jalview.org/git/jalview.git\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=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=jims/JAL-4420_review_redo\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=jims/JAL-4420_review_redo\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=jims/JAL-4420_review_redo\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-46301677\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_repository_46498039_git_username=\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_repository_46498039_branch_name=jims/JAL-4420_review_redo\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-GDB613-JOB1\nbamboo_planKey=JB-GDB613\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=jims/JAL-4420_review_redo\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 26-Aug-2024 17:43:12 444 build 26-Aug-2024 17:43:19 build 26-Aug-2024 17:43:19 > Configure project : build 26-Aug-2024 17:43:19 Using properties from file './utils/channels/default/channel_gradle.properties' build 26-Aug-2024 17:43:19 JALVIEW_VERSION is set to '2.11.4.0' build 26-Aug-2024 17:43:19 HEADLESS BUILD build 26-Aug-2024 17:43:19 J2S ENABLED build 26-Aug-2024 17:43:19 Using a LOCAL profile. build 26-Aug-2024 17:43:20 eclipseDir exists build 26-Aug-2024 17:43:22 build 26-Aug-2024 17:43:22 > Task :cloverHtmlReport build 26-Aug-2024 17:43:22 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 26-Aug-2024 17:43:23 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/reports/clover' build 26-Aug-2024 17:44:00 Done. Processed 115 packages in 36443ms (316ms per package). build 26-Aug-2024 17:44:05 build 26-Aug-2024 17:44:05 > Task :cloverXmlReport build 26-Aug-2024 17:44:05 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 26-Aug-2024 17:44:06 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/reports/clover/clover.xml' build 26-Aug-2024 17:44:07 build 26-Aug-2024 17:44:07 > Task :cloverReport build 26-Aug-2024 17:44:07 build 26-Aug-2024 17:44:07 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 26-Aug-2024 17:44:07 build 26-Aug-2024 17:44:07 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 26-Aug-2024 17:44:07 build 26-Aug-2024 17:44:07 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 26-Aug-2024 17:44:07 build 26-Aug-2024 17:44:07 BUILD SUCCESSFUL in 54s build 26-Aug-2024 17:44:07 2 actionable tasks: 2 executed simple 26-Aug-2024 17:44:07 Finished task 'Clover Report' with result: Success simple 26-Aug-2024 17:44:07 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 26-Aug-2024 17:44:07 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1... simple 26-Aug-2024 17:44:07 Finished task 'TestNG Parser' with result: Success simple 26-Aug-2024 17:44:07 Running post build plugin 'NCover Results Collector' simple 26-Aug-2024 17:44:07 Running post build plugin 'Artifact Copier' simple 26-Aug-2024 17:44:07 Publishing an artifact: Clover Report (System) simple 26-Aug-2024 17:44:08 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.787 s simple 26-Aug-2024 17:44:08 Publishing an artifact: TestNG report error 26-Aug-2024 17:44:08 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB613-JOB1/build/reports/tests/test does not exist. simple 26-Aug-2024 17:44:08 The artifact hasn't been successfully published after 1.211 ms simple 26-Aug-2024 17:44:08 Running post build plugin 'Artifactory Release Management Staging' simple 26-Aug-2024 17:44:08 Running post build plugin 'Artifactory Build Info Copier' simple 26-Aug-2024 17:44:08 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 26-Aug-2024 17:44:08 Running post build plugin 'npm Cache Cleanup' simple 26-Aug-2024 17:44:08 Running post build plugin 'Clover Results Collector' simple 26-Aug-2024 17:44:08 Running post build plugin 'Docker Container Cleanup' simple 26-Aug-2024 17:44:08 Finalising the build... simple 26-Aug-2024 17:44:08 Stopping timer. simple 26-Aug-2024 17:44:08 Build JB-GDB613-JOB1-1 completed. simple 26-Aug-2024 17:44:08 Running on server: post build plugin 'NCover Results Collector' simple 26-Aug-2024 17:44:09 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 26-Aug-2024 17:44:09 Running on server: post build plugin 'Clover Delta Calculator' simple 26-Aug-2024 17:44:09 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 26-Aug-2024 17:44:09 All post build plugins have finished simple 26-Aug-2024 17:44:09 Generating build results summary... simple 26-Aug-2024 17:44:09 Saving build results to disk... simple 26-Aug-2024 17:44:09 Logging substituted variables... simple 26-Aug-2024 17:44:09 Indexing build results... simple 26-Aug-2024 17:44:09 Finished building JB-GDB613-JOB1-1.