simple	01-Nov-2024 11:46:00	Build Jalview Builds - Gradle Develop Build - JAL-4474_jalview.ps1_not_working - Clover and Tests #1 (JB-GDB638-JOB1-1) started building on agent Default Agent
simple	01-Nov-2024 11:46:00	
simple	01-Nov-2024 11:46:00	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1
simple	01-Nov-2024 11:46:00	Executing build Jalview Builds - Gradle Develop Build - JAL-4474_jalview.ps1_not_working - Clover and Tests #1 (JB-GDB638-JOB1-1)
simple	01-Nov-2024 11:46:00	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	01-Nov-2024 11:46:00	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1
simple	01-Nov-2024 11:46:00	Updating source code to revision: 1da3b80194892879ba275911738cdb4372a29ad4
simple	01-Nov-2024 11:46:00	Fetching 'refs/heads/JAL-4474_jalview.ps1_not_working' from 'http://source.jalview.org/git/jalview.git'.
simple	01-Nov-2024 11:46:01	Checking out revision 1da3b80194892879ba275911738cdb4372a29ad4.
simple	01-Nov-2024 11:46:01	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/.git'.
simple	01-Nov-2024 11:46:01	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1'...
simple	01-Nov-2024 11:46:01	done.
simple	01-Nov-2024 11:46:13	Branch JAL-4474_jalview.ps1_not_working set up to track remote branch JAL-4474_jalview.ps1_not_working from origin.
simple	01-Nov-2024 11:46:13	Switched to a new branch 'JAL-4474_jalview.ps1_not_working'
simple	01-Nov-2024 11:46:13	Updated source code to revision: 1da3b80194892879ba275911738cdb4372a29ad4
simple	01-Nov-2024 11:46:13	Finished task 'Checkout Default Repository' with result: Success
simple	01-Nov-2024 11:46:13	Running pre-build action: VCS Version Collector
simple	01-Nov-2024 11:46:13	Running pre-build action: Artifactory Release Staging
simple	01-Nov-2024 11:46:13	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	01-Nov-2024 11:46:13	Bamboo Artifactory Plugin version: 2.6.2
command	01-Nov-2024 11:46:13	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - JAL-4474_jalview.ps1_not_working - Clover and Tests #1 (JB-GDB638-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-GDB638-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=JAL-4474_jalview.ps1_not_working\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=JAL-4474_jalview.ps1_not_working\nbamboo_repository_revision_number=1da3b80194892879ba275911738cdb4372a29ad4\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB638-JOB1-1\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-GDB638-JOB1\nbamboo_repository_46498161_git_branch=JAL-4474_jalview.ps1_not_working\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB638-JOB1\nbamboo_shortPlanName=JAL-4474_jalview.ps1_not_working\nbamboo_repository_46498161_revision_number=1da3b80194892879ba275911738cdb4372a29ad4\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-GDB638-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 - JAL-4474_jalview.ps1_not_working\nbamboo_shortPlanKey=GDB638\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1da3b80194892879ba275911738cdb4372a29ad4\nbamboo_repository_previous_revision_number=1da3b80194892879ba275911738cdb4372a29ad4\nbamboo_buildTimeStamp=2024-11-01T11:46:00.703Z\nbamboo_planRepository_previousRevision=1da3b80194892879ba275911738cdb4372a29ad4\nbamboo_repository_git_branch=JAL-4474_jalview.ps1_not_working\nbamboo_buildResultKey=JB-GDB638-JOB1-1\nbamboo_repository_branch_name=JAL-4474_jalview.ps1_not_working\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - JAL-4474_jalview.ps1_not_working - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=1da3b80194892879ba275911738cdb4372a29ad4\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/\nbamboo_repository_46498161_git_username=\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=JAL-4474_jalview.ps1_not_working\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=1da3b80194892879ba275911738cdb4372a29ad4\nbamboo_repository_46498161_name=Jalview Git\nbamboo_planRepository_branchDisplayName=JAL-4474_jalview.ps1_not_working\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=JAL-4474_jalview.ps1_not_working\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_repository_46498161_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_plan_storageTag=plan-46301921\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_repository_46498161_previous_revision_number=1da3b80194892879ba275911738cdb4372a29ad4\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-GDB638-JOB1\nbamboo_planKey=JB-GDB638\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498161_branch_name=JAL-4474_jalview.ps1_not_working\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=JAL-4474_jalview.ps1_not_working\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	01-Nov-2024 11:46:13	444
build	01-Nov-2024 11:46:13	Starting a Gradle Daemon (subsequent builds will be faster)
build	01-Nov-2024 11:46:21	
build	01-Nov-2024 11:46:21	> Configure project :
build	01-Nov-2024 11:46:21	Using properties from file './utils/channels/default/channel_gradle.properties'
build	01-Nov-2024 11:46:21	JALVIEW_VERSION is set to '2.11.4.1'
build	01-Nov-2024 11:46:21	HEADLESS BUILD
build	01-Nov-2024 11:46:21	J2S ENABLED
build	01-Nov-2024 11:46:21	Using a LOCAL profile.
build	01-Nov-2024 11:46:22	eclipseDir exists
build	01-Nov-2024 11:46:22	
build	01-Nov-2024 11:46:22	> Task :clean
build	01-Nov-2024 11:46:22	> Task :cleanClover
build	01-Nov-2024 11:46:22	> Task :cleanTest UP-TO-DATE
build	01-Nov-2024 11:46:25	
build	01-Nov-2024 11:46:25	> Task :cloverInstrJava
build	01-Nov-2024 11:46:25	Clover: About to instrument 1103 files
build	01-Nov-2024 11:46:25	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	01-Nov-2024 11:46:25	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/clover/clover.db'.
build	01-Nov-2024 11:46:25	Processing files at 1.9 source level.
error	01-Nov-2024 11:46:30	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	01-Nov-2024 11:46:30	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	01-Nov-2024 11:46:30	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	01-Nov-2024 11:46:30	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	01-Nov-2024 11:46:30	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	01-Nov-2024 11:46:30	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	01-Nov-2024 11:46:30	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	01-Nov-2024 11:46:36	Clover all over. Instrumented 1103 files (112 packages).
build	01-Nov-2024 11:46:38	
build	01-Nov-2024 11:46:38	> Task :cloverInstrTests
build	01-Nov-2024 11:46:38	Clover: About to instrument test files
build	01-Nov-2024 11:46:38	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	01-Nov-2024 11:46:38	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/clover/clover.db'.
build	01-Nov-2024 11:46:38	Processing files at 1.9 source level.
build	01-Nov-2024 11:46:42	Clover all over. Instrumented 291 files (52 packages).
build	01-Nov-2024 11:46:42	1594 test methods detected.
build	01-Nov-2024 11:46:42	
build	01-Nov-2024 11:46:42	> Task :cloverInstr
build	01-Nov-2024 11:46:46	
build	01-Nov-2024 11:46:46	> Task :compileCloverJava
build	01-Nov-2024 11:46:46	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	01-Nov-2024 11:46:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:46:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:46:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:46:46	Setting target compatibility to 11
error	01-Nov-2024 11:47:09	Note: Some input files use or override a deprecated API.
error	01-Nov-2024 11:47:09	Note: Recompile with -Xlint:deprecation for details.
error	01-Nov-2024 11:47:09	Note: Some input files use unchecked or unsafe operations.
error	01-Nov-2024 11:47:09	Note: Recompile with -Xlint:unchecked for details.
build	01-Nov-2024 11:47:15	
build	01-Nov-2024 11:47:15	> Task :processCloverResources NO-SOURCE
build	01-Nov-2024 11:47:15	> Task :cloverClasses
build	01-Nov-2024 11:47:15	> Task :copyHelp
build	01-Nov-2024 11:47:17	> Task :buildIndices
build	01-Nov-2024 11:47:17	> Task :copyResources
build	01-Nov-2024 11:47:17	> Task :copyChannelResources
build	01-Nov-2024 11:47:17	
build	01-Nov-2024 11:47:17	> Task :createBuildProperties
build	01-Nov-2024 11:47:17	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	01-Nov-2024 11:47:17	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:47:17	
build	01-Nov-2024 11:47:17	> Task :buildResources
build	01-Nov-2024 11:47:17	> Task :copyDocs
build	01-Nov-2024 11:47:18	
build	01-Nov-2024 11:47:18	> Task :convertMdFiles
build	01-Nov-2024 11:47:18	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	01-Nov-2024 11:47:18	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	01-Nov-2024 11:47:18	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	01-Nov-2024 11:47:18	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/resources/doc_build/doc/building.html
build	01-Nov-2024 11:47:18	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	01-Nov-2024 11:47:18	
build	01-Nov-2024 11:47:18	> Task :releasesTemplates
build	01-Nov-2024 11:47:18	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	01-Nov-2024 11:47:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:47:18	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:47:18	Stripping rc/test/etc for TEST
build	01-Nov-2024 11:47:18	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	01-Nov-2024 11:47:18	
build	01-Nov-2024 11:47:18	> Task :prepare
build	01-Nov-2024 11:47:20	
build	01-Nov-2024 11:47:20	> Task :compileJava
build	01-Nov-2024 11:47:20	Setting target compatibility to 11
error	01-Nov-2024 11:47:26	Note: Some input files use or override a deprecated API.
error	01-Nov-2024 11:47:26	Note: Recompile with -Xlint:deprecation for details.
error	01-Nov-2024 11:47:26	Note: Some input files use unchecked or unsafe operations.
error	01-Nov-2024 11:47:26	Note: Recompile with -Xlint:unchecked for details.
build	01-Nov-2024 11:47:30	
build	01-Nov-2024 11:47:30	> Task :compileTestJava
build	01-Nov-2024 11:47:30	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	01-Nov-2024 11:47:30	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:47:30	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:47:30	Setting target compatibility to 11
error	01-Nov-2024 11:47:35	Note: Some input files use or override a deprecated API.
error	01-Nov-2024 11:47:35	Note: Recompile with -Xlint:deprecation for details.
error	01-Nov-2024 11:47:35	Note: Some input files use unchecked or unsafe operations.
error	01-Nov-2024 11:47:35	Note: Recompile with -Xlint:unchecked for details.
build	01-Nov-2024 11:47:36	
build	01-Nov-2024 11:47:36	> Task :processTestResources
build	01-Nov-2024 11:47:36	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	01-Nov-2024 11:47:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:47:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:47:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:47:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:47:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:47:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:47:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-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	01-Nov-2024 11:47:36	
build	01-Nov-2024 11:47:36	> Task :testClasses
build	01-Nov-2024 11:47:38	
build	01-Nov-2024 11:47:38	> Task :testTask0
build	01-Nov-2024 11:47:38	Running tests WITH clover
error	01-Nov-2024 11:47:42	WARNING: An illegal reflective access operation has occurred
error	01-Nov-2024 11:47:42	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	01-Nov-2024 11:47:42	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	01-Nov-2024 11:47:42	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	01-Nov-2024 11:47:42	WARNING: All illegal access operations will be denied in a future release
build	01-Nov-2024 11:51:33	
build	01-Nov-2024 11:51:33	> Task :testTask1
build	01-Nov-2024 11:51:33	Running tests WITH clover
error	01-Nov-2024 11:51:34	WARNING: An illegal reflective access operation has occurred
error	01-Nov-2024 11:51:34	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	01-Nov-2024 11:51:34	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	01-Nov-2024 11:51:34	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	01-Nov-2024 11:51:34	WARNING: All illegal access operations will be denied in a future release
build	01-Nov-2024 11:53:08	
build	01-Nov-2024 11:53:08	> Task :testTask2
build	01-Nov-2024 11:53:08	Running tests WITH clover
build	01-Nov-2024 11:53:11	
build	01-Nov-2024 11:53:11	> Task :testTask3
build	01-Nov-2024 11:53:11	Running tests WITH clover
error	01-Nov-2024 11:53:13	WARNING: An illegal reflective access operation has occurred
error	01-Nov-2024 11:53:13	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	01-Nov-2024 11:53:13	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	01-Nov-2024 11:53:13	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	01-Nov-2024 11:53:13	WARNING: All illegal access operations will be denied in a future release
build	01-Nov-2024 11:53:59	
build	01-Nov-2024 11:53:59	> Task :test NO-SOURCE
build	01-Nov-2024 11:53:59	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	01-Nov-2024 11:53:59	│jalview:testTask0 results: SUCCESS (1728 tests, 1728 successes, 0 failures, 0 skipped) in 3 minutes, 53.514 seconds   │
build	01-Nov-2024 11:53:59	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/reports/tests/testTask0/index.html│
build	01-Nov-2024 11:53:59	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	01-Nov-2024 11:53:59	│jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 34.981 seconds       │
build	01-Nov-2024 11:53:59	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/reports/tests/testTask1/index.html│
build	01-Nov-2024 11:53:59	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	01-Nov-2024 11:53:59	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.527 seconds                     │
build	01-Nov-2024 11:53:59	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/reports/tests/testTask2/index.html│
build	01-Nov-2024 11:53:59	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	01-Nov-2024 11:53:59	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 49.455 seconds                  │
build	01-Nov-2024 11:53:59	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/reports/tests/testTask3/index.html│
build	01-Nov-2024 11:53:59	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	01-Nov-2024 11:53:59	│OVERALL: results: SUCCESS (1803 tests, 1803 successes, 0 failures, 0 skipped) in 4 minutes, 141.477 seconds           │
build	01-Nov-2024 11:53:59	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	01-Nov-2024 11:53:59	
build	01-Nov-2024 11:53:59	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	01-Nov-2024 11:53:59	
build	01-Nov-2024 11:53:59	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	01-Nov-2024 11:53:59	
build	01-Nov-2024 11:53:59	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	01-Nov-2024 11:53:59	
build	01-Nov-2024 11:53:59	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	01-Nov-2024 11:53:59	Please consult deprecation warnings for more details.
build	01-Nov-2024 11:53:59	
build	01-Nov-2024 11:53:59	BUILD SUCCESSFUL in 7m 46s
build	01-Nov-2024 11:53:59	21 actionable tasks: 20 executed, 1 up-to-date
simple	01-Nov-2024 11:53:59	Finished task 'Run tests with openclover under gradle' with result: Success
simple	01-Nov-2024 11:53:59	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	01-Nov-2024 11:53:59	Bamboo Artifactory Plugin version: 2.6.2
command	01-Nov-2024 11:53:59	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - JAL-4474_jalview.ps1_not_working - Clover and Tests #1 (JB-GDB638-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-GDB638-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=JAL-4474_jalview.ps1_not_working\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=JAL-4474_jalview.ps1_not_working\nbamboo_repository_revision_number=1da3b80194892879ba275911738cdb4372a29ad4\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB638-JOB1-1\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-GDB638-JOB1\nbamboo_repository_46498161_git_branch=JAL-4474_jalview.ps1_not_working\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB638-JOB1\nbamboo_shortPlanName=JAL-4474_jalview.ps1_not_working\nbamboo_repository_46498161_revision_number=1da3b80194892879ba275911738cdb4372a29ad4\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-GDB638-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 - JAL-4474_jalview.ps1_not_working\nbamboo_shortPlanKey=GDB638\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1da3b80194892879ba275911738cdb4372a29ad4\nbamboo_repository_previous_revision_number=1da3b80194892879ba275911738cdb4372a29ad4\nbamboo_buildTimeStamp=2024-11-01T11:46:00.703Z\nbamboo_planRepository_previousRevision=1da3b80194892879ba275911738cdb4372a29ad4\nbamboo_repository_git_branch=JAL-4474_jalview.ps1_not_working\nbamboo_buildResultKey=JB-GDB638-JOB1-1\nbamboo_repository_branch_name=JAL-4474_jalview.ps1_not_working\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - JAL-4474_jalview.ps1_not_working - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=1da3b80194892879ba275911738cdb4372a29ad4\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/\nbamboo_repository_46498161_git_username=\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=JAL-4474_jalview.ps1_not_working\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_1_previousRevision=1da3b80194892879ba275911738cdb4372a29ad4\nbamboo_repository_46498161_name=Jalview Git\nbamboo_planRepository_branchDisplayName=JAL-4474_jalview.ps1_not_working\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=JAL-4474_jalview.ps1_not_working\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_repository_46498161_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_plan_storageTag=plan-46301921\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_repository_46498161_previous_revision_number=1da3b80194892879ba275911738cdb4372a29ad4\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-GDB638-JOB1\nbamboo_planKey=JB-GDB638\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498161_branch_name=JAL-4474_jalview.ps1_not_working\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=JAL-4474_jalview.ps1_not_working\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	01-Nov-2024 11:54:00	444
build	01-Nov-2024 11:54:15	
build	01-Nov-2024 11:54:15	> Configure project :
build	01-Nov-2024 11:54:15	Using properties from file './utils/channels/default/channel_gradle.properties'
build	01-Nov-2024 11:54:15	JALVIEW_VERSION is set to '2.11.4.1'
build	01-Nov-2024 11:54:15	HEADLESS BUILD
build	01-Nov-2024 11:54:15	J2S ENABLED
build	01-Nov-2024 11:54:16	Using a LOCAL profile.
build	01-Nov-2024 11:54:17	eclipseDir exists
build	01-Nov-2024 11:54:19	
build	01-Nov-2024 11:54:19	> Task :cloverHtmlReport
build	01-Nov-2024 11:54:19	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	01-Nov-2024 11:54:21	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/reports/clover'
build	01-Nov-2024 11:54:59	Done. Processed 116 packages in 38584ms (332ms per package).
build	01-Nov-2024 11:55:04	
build	01-Nov-2024 11:55:04	> Task :cloverXmlReport
build	01-Nov-2024 11:55:04	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	01-Nov-2024 11:55:05	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/reports/clover/clover.xml'
build	01-Nov-2024 11:55:05	
build	01-Nov-2024 11:55:05	> Task :cloverReport
build	01-Nov-2024 11:55:05	
build	01-Nov-2024 11:55:05	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	01-Nov-2024 11:55:05	
build	01-Nov-2024 11:55:05	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	01-Nov-2024 11:55:05	
build	01-Nov-2024 11:55:05	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	01-Nov-2024 11:55:05	
build	01-Nov-2024 11:55:05	BUILD SUCCESSFUL in 1m 5s
build	01-Nov-2024 11:55:05	2 actionable tasks: 2 executed
simple	01-Nov-2024 11:55:05	Finished task 'Clover Report' with result: Success
simple	01-Nov-2024 11:55:05	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	01-Nov-2024 11:55:05	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1...
simple	01-Nov-2024 11:55:05	Finished task 'TestNG Parser' with result: Success
simple	01-Nov-2024 11:55:05	Running post build plugin 'NCover Results Collector'
simple	01-Nov-2024 11:55:05	Running post build plugin 'Artifact Copier'
simple	01-Nov-2024 11:55:05	Publishing an artifact: Clover Report (System)
simple	01-Nov-2024 11:55:07	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.434 s
simple	01-Nov-2024 11:55:07	Publishing an artifact: TestNG report
error	01-Nov-2024 11:55:07	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB638-JOB1/build/reports/tests/test does not exist.
simple	01-Nov-2024 11:55:07	The artifact hasn't been successfully published after 1.385 ms
simple	01-Nov-2024 11:55:07	Running post build plugin 'Artifactory Release Management Staging'
simple	01-Nov-2024 11:55:07	Running post build plugin 'Artifactory Build Info Copier'
simple	01-Nov-2024 11:55:07	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	01-Nov-2024 11:55:07	Running post build plugin 'npm Cache Cleanup'
simple	01-Nov-2024 11:55:07	Running post build plugin 'Clover Results Collector'
simple	01-Nov-2024 11:55:07	Running post build plugin 'Docker Container Cleanup'
simple	01-Nov-2024 11:55:07	Finalising the build...
simple	01-Nov-2024 11:55:07	Stopping timer.
simple	01-Nov-2024 11:55:07	Build JB-GDB638-JOB1-1 completed.
simple	01-Nov-2024 11:55:07	Running on server: post build plugin 'NCover Results Collector'
simple	01-Nov-2024 11:55:07	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	01-Nov-2024 11:55:07	Running on server: post build plugin 'Clover Delta Calculator'
simple	01-Nov-2024 11:55:07	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	01-Nov-2024 11:55:07	All post build plugins have finished
simple	01-Nov-2024 11:55:07	Generating build results summary...
simple	01-Nov-2024 11:55:07	Saving build results to disk...
simple	01-Nov-2024 11:55:07	Logging substituted variables...
simple	01-Nov-2024 11:55:07	Indexing build results...
simple	01-Nov-2024 11:55:07	Finished building JB-GDB638-JOB1-1.