simple	11-Nov-2024 16:01:00	Build Jalview Builds - Gradle Develop Build - bug-JAL-4482_gradle_task_linkCheck_fails - Clover and Tests #1 (JB-GDB643-JOB1-1) started building on agent Default Agent
simple	11-Nov-2024 16:01:00	
simple	11-Nov-2024 16:01:00	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1
simple	11-Nov-2024 16:01:00	Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4482_gradle_task_linkCheck_fails - Clover and Tests #1 (JB-GDB643-JOB1-1)
simple	11-Nov-2024 16:01:00	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	11-Nov-2024 16:01:00	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1
simple	11-Nov-2024 16:01:00	Updating source code to revision: 85dead08e22e1ed61738f045b58349c18b8131b2
simple	11-Nov-2024 16:01:00	Fetching 'refs/heads/bug/JAL-4482_gradle_task_linkCheck_fails' from 'http://source.jalview.org/git/jalview.git'.
simple	11-Nov-2024 16:01:00	Checking out revision 85dead08e22e1ed61738f045b58349c18b8131b2.
simple	11-Nov-2024 16:01:00	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/.git'.
simple	11-Nov-2024 16:01:00	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1'...
simple	11-Nov-2024 16:01:00	done.
simple	11-Nov-2024 16:01:06	Branch bug/JAL-4482_gradle_task_linkCheck_fails set up to track remote branch bug/JAL-4482_gradle_task_linkCheck_fails from origin.
simple	11-Nov-2024 16:01:06	Switched to a new branch 'bug/JAL-4482_gradle_task_linkCheck_fails'
simple	11-Nov-2024 16:01:06	Updated source code to revision: 85dead08e22e1ed61738f045b58349c18b8131b2
simple	11-Nov-2024 16:01:06	Finished task 'Checkout Default Repository' with result: Success
simple	11-Nov-2024 16:01:06	Running pre-build action: VCS Version Collector
simple	11-Nov-2024 16:01:06	Running pre-build action: Artifactory Release Staging
simple	11-Nov-2024 16:01:06	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	11-Nov-2024 16:01:06	Bamboo Artifactory Plugin version: 2.6.2
command	11-Nov-2024 16:01:06	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4482_gradle_task_linkCheck_fails - Clover and Tests #1 (JB-GDB643-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-GDB643-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4482_gradle_task_linkCheck_fails\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4482_gradle_task_linkCheck_fails\nbamboo_repository_revision_number=85dead08e22e1ed61738f045b58349c18b8131b2\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB643-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-GDB643-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB643-JOB1\nbamboo_shortPlanName=bug-JAL-4482_gradle_task_linkCheck_fails\nbamboo_repository_46498192_revision_number=85dead08e22e1ed61738f045b58349c18b8131b2\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-GDB643-JOB1-1\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498192_name=Jalview Git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4482_gradle_task_linkCheck_fails\nbamboo_shortPlanKey=GDB643\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=85dead08e22e1ed61738f045b58349c18b8131b2\nbamboo_buildTimeStamp=2024-11-11T16:01:00.565Z\nbamboo_repository_git_branch=bug/JAL-4482_gradle_task_linkCheck_fails\nbamboo_buildResultKey=JB-GDB643-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4482_gradle_task_linkCheck_fails\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4482_gradle_task_linkCheck_fails - Clover and Tests\nbamboo_repository_46498192_git_username=\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=85dead08e22e1ed61738f045b58349c18b8131b2\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=bug/JAL-4482_gradle_task_linkCheck_fails\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=bug/JAL-4482_gradle_task_linkCheck_fails\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4482_gradle_task_linkCheck_fails\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-46301983\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46498192_git_branch=bug/JAL-4482_gradle_task_linkCheck_fails\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-GDB643-JOB1\nbamboo_repository_46498192_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planKey=JB-GDB643\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498192_branch_name=bug/JAL-4482_gradle_task_linkCheck_fails\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4482_gradle_task_linkCheck_fails\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	11-Nov-2024 16:01:06	444
build	11-Nov-2024 16:01:25	
build	11-Nov-2024 16:01:25	> Configure project :
build	11-Nov-2024 16:01:25	Using properties from file './utils/channels/default/channel_gradle.properties'
build	11-Nov-2024 16:01:25	JALVIEW_VERSION is set to '2.11.4.1'
build	11-Nov-2024 16:01:25	HEADLESS BUILD
build	11-Nov-2024 16:01:25	J2S ENABLED
build	11-Nov-2024 16:01:25	Using a LOCAL profile.
build	11-Nov-2024 16:01:25	eclipseDir exists
build	11-Nov-2024 16:01:25	
build	11-Nov-2024 16:01:25	> Task :clean
build	11-Nov-2024 16:01:25	> Task :cleanClover
build	11-Nov-2024 16:01:25	> Task :cleanTest UP-TO-DATE
build	11-Nov-2024 16:01:27	
build	11-Nov-2024 16:01:27	> Task :cloverInstrJava
build	11-Nov-2024 16:01:27	Clover: About to instrument 1103 files
build	11-Nov-2024 16:01:28	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	11-Nov-2024 16:01:28	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/clover/clover.db'.
build	11-Nov-2024 16:01:28	Processing files at 1.9 source level.
error	11-Nov-2024 16:01:32	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	11-Nov-2024 16:01:32	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	11-Nov-2024 16:01:32	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	11-Nov-2024 16:01:32	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	11-Nov-2024 16:01:32	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	11-Nov-2024 16:01:32	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	11-Nov-2024 16:01:32	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
build	11-Nov-2024 16:01:39	Clover all over. Instrumented 1103 files (112 packages).
build	11-Nov-2024 16:01:41	
build	11-Nov-2024 16:01:41	> Task :cloverInstrTests
build	11-Nov-2024 16:01:41	Clover: About to instrument test files
build	11-Nov-2024 16:01:41	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	11-Nov-2024 16:01:41	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/clover/clover.db'.
build	11-Nov-2024 16:01:41	Processing files at 1.9 source level.
build	11-Nov-2024 16:01:44	Clover all over. Instrumented 291 files (52 packages).
build	11-Nov-2024 16:01:44	1594 test methods detected.
build	11-Nov-2024 16:01:44	
build	11-Nov-2024 16:01:44	> Task :cloverInstr
build	11-Nov-2024 16:01:47	
build	11-Nov-2024 16:01:47	> Task :compileCloverJava
build	11-Nov-2024 16:01:47	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	11-Nov-2024 16:01:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrJava' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:01:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrTests' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:01:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/clover/clover-instr'. Reason: Task ':compileCloverJava' uses this output of task ':cloverInstrJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:01:47	Setting target compatibility to 11
error	11-Nov-2024 16:02:02	Note: Some input files use or override a deprecated API.
error	11-Nov-2024 16:02:02	Note: Recompile with -Xlint:deprecation for details.
error	11-Nov-2024 16:02:02	Note: Some input files use unchecked or unsafe operations.
error	11-Nov-2024 16:02:02	Note: Recompile with -Xlint:unchecked for details.
build	11-Nov-2024 16:02:06	
build	11-Nov-2024 16:02:06	> Task :processCloverResources NO-SOURCE
build	11-Nov-2024 16:02:06	> Task :cloverClasses
build	11-Nov-2024 16:02:06	> Task :copyHelp
build	11-Nov-2024 16:02:07	> Task :buildIndices
build	11-Nov-2024 16:02:07	> Task :copyResources
build	11-Nov-2024 16:02:07	> Task :copyChannelResources
build	11-Nov-2024 16:02:07	
build	11-Nov-2024 16:02:07	> Task :createBuildProperties
build	11-Nov-2024 16:02:07	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	11-Nov-2024 16:02:07	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:02:07	
build	11-Nov-2024 16:02:07	> Task :buildResources
build	11-Nov-2024 16:02:07	> Task :copyDocs
build	11-Nov-2024 16:02:07	
build	11-Nov-2024 16:02:07	> Task :convertMdFiles
build	11-Nov-2024 16:02:07	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	11-Nov-2024 16:02:07	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	11-Nov-2024 16:02:07	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	11-Nov-2024 16:02:07	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/doc_build/doc/building.html
build	11-Nov-2024 16:02:07	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	11-Nov-2024 16:02:07	
build	11-Nov-2024 16:02:07	> Task :releasesTemplates
build	11-Nov-2024 16:02:07	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	11-Nov-2024 16:02:07	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:02:07	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:02:07	Stripping rc/test/etc for TEST
build	11-Nov-2024 16:02:07	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	11-Nov-2024 16:02:07	
build	11-Nov-2024 16:02:07	> Task :prepare
build	11-Nov-2024 16:02:09	
build	11-Nov-2024 16:02:09	> Task :compileJava
build	11-Nov-2024 16:02:09	Setting target compatibility to 11
error	11-Nov-2024 16:02:15	Note: Some input files use or override a deprecated API.
error	11-Nov-2024 16:02:15	Note: Recompile with -Xlint:deprecation for details.
error	11-Nov-2024 16:02:15	Note: Some input files use unchecked or unsafe operations.
error	11-Nov-2024 16:02:15	Note: Recompile with -Xlint:unchecked for details.
build	11-Nov-2024 16:02:17	
build	11-Nov-2024 16:02:17	> Task :compileTestJava
build	11-Nov-2024 16:02:17	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	11-Nov-2024 16:02:17	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/clover/clover-classes'. Reason: Task ':compileTestJava' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:02:17	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/clover/clover-test-instr'. Reason: Task ':compileTestJava' uses this output of task ':cloverInstrTests' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:02:17	Setting target compatibility to 11
error	11-Nov-2024 16:02:22	Note: Some input files use or override a deprecated API.
error	11-Nov-2024 16:02:22	Note: Recompile with -Xlint:deprecation for details.
error	11-Nov-2024 16:02:22	Note: Some input files use unchecked or unsafe operations.
error	11-Nov-2024 16:02:22	Note: Recompile with -Xlint:unchecked for details.
build	11-Nov-2024 16:02:23	
build	11-Nov-2024 16:02:23	> Task :processTestResources
build	11-Nov-2024 16:02:23	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	11-Nov-2024 16:02:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:02:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:02:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:02:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:02:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:02:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:02:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	11-Nov-2024 16:02:23	
build	11-Nov-2024 16:02:23	> Task :testClasses
build	11-Nov-2024 16:02:25	
build	11-Nov-2024 16:02:25	> Task :testTask0
build	11-Nov-2024 16:02:25	Running tests WITH clover
error	11-Nov-2024 16:02:28	WARNING: An illegal reflective access operation has occurred
error	11-Nov-2024 16:02:28	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	11-Nov-2024 16:02:28	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	11-Nov-2024 16:02:28	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	11-Nov-2024 16:02:28	WARNING: All illegal access operations will be denied in a future release
build	11-Nov-2024 16:06:22	
build	11-Nov-2024 16:06:22	> Task :testTask1
build	11-Nov-2024 16:06:22	Running tests WITH clover
error	11-Nov-2024 16:06:23	WARNING: An illegal reflective access operation has occurred
error	11-Nov-2024 16:06:23	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	11-Nov-2024 16:06:23	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	11-Nov-2024 16:06:23	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	11-Nov-2024 16:06:23	WARNING: All illegal access operations will be denied in a future release
build	11-Nov-2024 16:07:58	
build	11-Nov-2024 16:07:58	> Task :testTask2
build	11-Nov-2024 16:07:58	Running tests WITH clover
build	11-Nov-2024 16:08:01	
build	11-Nov-2024 16:08:01	> Task :testTask3
build	11-Nov-2024 16:08:01	Running tests WITH clover
error	11-Nov-2024 16:08:03	WARNING: An illegal reflective access operation has occurred
error	11-Nov-2024 16:08:03	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	11-Nov-2024 16:08:03	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	11-Nov-2024 16:08:03	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	11-Nov-2024 16:08:03	WARNING: All illegal access operations will be denied in a future release
build	11-Nov-2024 16:08:49	
build	11-Nov-2024 16:08:49	> Task :test NO-SOURCE
build	11-Nov-2024 16:08:49	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	11-Nov-2024 16:08:49	│jalview:testTask0 results: SUCCESS (1728 tests, 1728 successes, 0 failures, 0 skipped) in 3 minutes, 56.120 seconds   │
build	11-Nov-2024 16:08:49	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/reports/tests/testTask0/index.html│
build	11-Nov-2024 16:08:49	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	11-Nov-2024 16:08:49	│jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 36.217 seconds       │
build	11-Nov-2024 16:08:49	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/reports/tests/testTask1/index.html│
build	11-Nov-2024 16:08:49	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	11-Nov-2024 16:08:49	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.414 seconds                     │
build	11-Nov-2024 16:08:49	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/reports/tests/testTask2/index.html│
build	11-Nov-2024 16:08:49	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	11-Nov-2024 16:08:49	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 49.374 seconds                  │
build	11-Nov-2024 16:08:49	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/reports/tests/testTask3/index.html│
build	11-Nov-2024 16:08:49	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	11-Nov-2024 16:08:49	│OVERALL: results: SUCCESS (1803 tests, 1803 successes, 0 failures, 0 skipped) in 4 minutes, 145.125 seconds           │
build	11-Nov-2024 16:08:49	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	11-Nov-2024 16:08:49	
build	11-Nov-2024 16:08:49	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	11-Nov-2024 16:08:49	
build	11-Nov-2024 16:08:49	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	11-Nov-2024 16:08:49	
build	11-Nov-2024 16:08:49	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	11-Nov-2024 16:08:49	
build	11-Nov-2024 16:08:49	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	11-Nov-2024 16:08:49	Please consult deprecation warnings for more details.
build	11-Nov-2024 16:08:49	
build	11-Nov-2024 16:08:49	BUILD SUCCESSFUL in 7m 43s
build	11-Nov-2024 16:08:49	21 actionable tasks: 20 executed, 1 up-to-date
simple	11-Nov-2024 16:08:49	Finished task 'Run tests with openclover under gradle' with result: Success
simple	11-Nov-2024 16:08:49	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	11-Nov-2024 16:08:49	Bamboo Artifactory Plugin version: 2.6.2
command	11-Nov-2024 16:08:49	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4482_gradle_task_linkCheck_fails - Clover and Tests #1 (JB-GDB643-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-GDB643-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4482_gradle_task_linkCheck_fails\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4482_gradle_task_linkCheck_fails\nbamboo_repository_revision_number=85dead08e22e1ed61738f045b58349c18b8131b2\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB643-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-GDB643-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB643-JOB1\nbamboo_shortPlanName=bug-JAL-4482_gradle_task_linkCheck_fails\nbamboo_repository_46498192_revision_number=85dead08e22e1ed61738f045b58349c18b8131b2\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-GDB643-JOB1-1\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498192_name=Jalview Git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4482_gradle_task_linkCheck_fails\nbamboo_shortPlanKey=GDB643\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=85dead08e22e1ed61738f045b58349c18b8131b2\nbamboo_buildTimeStamp=2024-11-11T16:01:00.565Z\nbamboo_repository_git_branch=bug/JAL-4482_gradle_task_linkCheck_fails\nbamboo_buildResultKey=JB-GDB643-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4482_gradle_task_linkCheck_fails\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4482_gradle_task_linkCheck_fails - Clover and Tests\nbamboo_repository_46498192_git_username=\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=85dead08e22e1ed61738f045b58349c18b8131b2\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=bug/JAL-4482_gradle_task_linkCheck_fails\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=bug/JAL-4482_gradle_task_linkCheck_fails\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4482_gradle_task_linkCheck_fails\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-46301983\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46498192_git_branch=bug/JAL-4482_gradle_task_linkCheck_fails\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-GDB643-JOB1\nbamboo_repository_46498192_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planKey=JB-GDB643\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498192_branch_name=bug/JAL-4482_gradle_task_linkCheck_fails\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4482_gradle_task_linkCheck_fails\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	11-Nov-2024 16:08:49	444
build	11-Nov-2024 16:09:02	
build	11-Nov-2024 16:09:02	> Configure project :
build	11-Nov-2024 16:09:02	Using properties from file './utils/channels/default/channel_gradle.properties'
build	11-Nov-2024 16:09:02	JALVIEW_VERSION is set to '2.11.4.1'
build	11-Nov-2024 16:09:02	HEADLESS BUILD
build	11-Nov-2024 16:09:02	J2S ENABLED
build	11-Nov-2024 16:09:03	Using a LOCAL profile.
build	11-Nov-2024 16:09:04	eclipseDir exists
build	11-Nov-2024 16:09:06	
build	11-Nov-2024 16:09:06	> Task :cloverHtmlReport
build	11-Nov-2024 16:09:06	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	11-Nov-2024 16:09:07	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/reports/clover'
build	11-Nov-2024 16:09:46	Done. Processed 116 packages in 38739ms (333ms per package).
build	11-Nov-2024 16:09:51	
build	11-Nov-2024 16:09:51	> Task :cloverXmlReport
build	11-Nov-2024 16:09:51	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	11-Nov-2024 16:09:52	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/reports/clover/clover.xml'
build	11-Nov-2024 16:09:52	
build	11-Nov-2024 16:09:52	> Task :cloverReport
build	11-Nov-2024 16:09:52	
build	11-Nov-2024 16:09:52	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	11-Nov-2024 16:09:52	
build	11-Nov-2024 16:09:52	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	11-Nov-2024 16:09:52	
build	11-Nov-2024 16:09:52	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	11-Nov-2024 16:09:52	
build	11-Nov-2024 16:09:52	BUILD SUCCESSFUL in 1m 2s
build	11-Nov-2024 16:09:52	2 actionable tasks: 2 executed
simple	11-Nov-2024 16:09:52	Finished task 'Clover Report' with result: Success
simple	11-Nov-2024 16:09:52	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	11-Nov-2024 16:09:52	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1...
simple	11-Nov-2024 16:09:52	Finished task 'TestNG Parser' with result: Success
simple	11-Nov-2024 16:09:52	Running post build plugin 'NCover Results Collector'
simple	11-Nov-2024 16:09:52	Running post build plugin 'Artifact Copier'
simple	11-Nov-2024 16:09:52	Publishing an artifact: Clover Report (System)
simple	11-Nov-2024 16:09:53	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.418 s
simple	11-Nov-2024 16:09:53	Publishing an artifact: TestNG report
error	11-Nov-2024 16:09:53	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB643-JOB1/build/reports/tests/test does not exist.
simple	11-Nov-2024 16:09:53	The artifact hasn't been successfully published after 1.343 ms
simple	11-Nov-2024 16:09:53	Running post build plugin 'Artifactory Release Management Staging'
simple	11-Nov-2024 16:09:53	Running post build plugin 'Artifactory Build Info Copier'
simple	11-Nov-2024 16:09:53	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	11-Nov-2024 16:09:53	Running post build plugin 'npm Cache Cleanup'
simple	11-Nov-2024 16:09:53	Running post build plugin 'Clover Results Collector'
simple	11-Nov-2024 16:09:53	Running post build plugin 'Docker Container Cleanup'
simple	11-Nov-2024 16:09:53	Finalising the build...
simple	11-Nov-2024 16:09:53	Stopping timer.
simple	11-Nov-2024 16:09:53	Build JB-GDB643-JOB1-1 completed.
simple	11-Nov-2024 16:09:53	Running on server: post build plugin 'NCover Results Collector'
simple	11-Nov-2024 16:09:53	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	11-Nov-2024 16:09:53	Running on server: post build plugin 'Clover Delta Calculator'
simple	11-Nov-2024 16:09:53	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	11-Nov-2024 16:09:53	All post build plugins have finished
simple	11-Nov-2024 16:09:53	Generating build results summary...
simple	11-Nov-2024 16:09:54	Saving build results to disk...
simple	11-Nov-2024 16:09:54	Logging substituted variables...
simple	11-Nov-2024 16:09:54	Indexing build results...
simple	11-Nov-2024 16:09:54	Finished building JB-GDB643-JOB1-1.