simple	12-Nov-2025 09:00:21	Build Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests #3 (JB-GDB724-JOB1-3) started building on agent Default Agent
simple	12-Nov-2025 09:00:21	
simple	12-Nov-2025 09:00:21	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1
simple	12-Nov-2025 09:00:21	Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests #3 (JB-GDB724-JOB1-3)
simple	12-Nov-2025 09:00:21	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	12-Nov-2025 09:00:21	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1
simple	12-Nov-2025 09:00:21	Updating source code to revision: 377f1f52a15db66fd5768669a50bfda03250a6c7
simple	12-Nov-2025 09:00:21	Fetching 'refs/heads/patch/JAL-4626_alphafoldVersionTracker' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	12-Nov-2025 09:00:22	Checking out revision 377f1f52a15db66fd5768669a50bfda03250a6c7.
simple	12-Nov-2025 09:00:22	Already on 'patch/JAL-4626_alphafoldVersionTracker'
simple	12-Nov-2025 09:00:22	Updated source code to revision: 377f1f52a15db66fd5768669a50bfda03250a6c7
simple	12-Nov-2025 09:00:22	Finished task 'Checkout Default Repository' with result: Success
simple	12-Nov-2025 09:00:22	Running pre-build action: VCS Version Collector
simple	12-Nov-2025 09:00:22	Running pre-build action: Artifactory Release Staging
simple	12-Nov-2025 09:00:22	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	12-Nov-2025 09:00:22	Bamboo Artifactory Plugin version: 2.6.2
command	12-Nov-2025 09:00:22	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests #3 (JB-GDB724-JOB1-3)'\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-GDB724-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4626_alphafoldVersionTracker\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4626_alphafoldVersionTracker\nbamboo_repository_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB724-JOB1-3\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-GDB724-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB724-JOB1\nbamboo_shortPlanName=patch-JAL-4626_alphafoldVersionTracker\nbamboo_repository_46498567_git_branch=patch/JAL-4626_alphafoldVersionTracker\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=3\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_46498567_git_username=\nbamboo_shortJobName=Clover and Tests\nbamboo_repository_46498567_previous_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB724-JOB1-3\nbamboo_repository_46498567_name=Jalview Gitlab\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker\nbamboo_shortPlanKey=GDB724\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_buildTimeStamp=2025-11-12T09:00:21.417Z\nbamboo_repository_previous_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_planRepository_previousRevision=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_repository_git_branch=patch/JAL-4626_alphafoldVersionTracker\nbamboo_buildResultKey=JB-GDB724-JOB1-3\nbamboo_repository_branch_name=patch/JAL-4626_alphafoldVersionTracker\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=377f1f52a15db66fd5768669a50bfda03250a6c7\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_dependenciesDisabled=false\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=patch/JAL-4626_alphafoldVersionTracker\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=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_planRepository_branchDisplayName=patch/JAL-4626_alphafoldVersionTracker\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4626_alphafoldVersionTracker\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-46302705\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_repository_46498567_branch_name=patch/JAL-4626_alphafoldVersionTracker\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_ManualBuildTriggerReason_userName=jprocter\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498567_git_repositoryUrl=https://gitlab.jalview.org/jalview/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-GDB724-JOB1\nbamboo_repository_46498567_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_planKey=JB-GDB724\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4626_alphafoldVersionTracker\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	12-Nov-2025 09:00:22	444
build	12-Nov-2025 09:00:24	Starting a Gradle Daemon (subsequent builds will be faster)
build	12-Nov-2025 09:00:31	
build	12-Nov-2025 09:00:31	> Configure project :
build	12-Nov-2025 09:00:31	Using properties from file './utils/channels/default/channel_gradle.properties'
build	12-Nov-2025 09:00:31	JALVIEW_VERSION is set to '2.11.5.1'
build	12-Nov-2025 09:00:31	HEADLESS BUILD
build	12-Nov-2025 09:00:31	J2S ENABLED
build	12-Nov-2025 09:00:32	Using a LOCAL profile.
build	12-Nov-2025 09:00:33	eclipseDir exists
build	12-Nov-2025 09:00:34	
build	12-Nov-2025 09:00:34	> Task :clean
build	12-Nov-2025 09:00:34	> Task :cleanClover
build	12-Nov-2025 09:00:34	> Task :cleanTest UP-TO-DATE
build	12-Nov-2025 09:00:36	
build	12-Nov-2025 09:00:36	> Task :cloverInstrJava
build	12-Nov-2025 09:00:36	Clover: About to instrument 1106 files
build	12-Nov-2025 09:00:36	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	12-Nov-2025 09:00:36	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover.db'.
build	12-Nov-2025 09:00:36	Processing files at 1.9 source level.
error	12-Nov-2025 09:00:40	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	12-Nov-2025 09:00:40	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	12-Nov-2025 09:00:40	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	12-Nov-2025 09:00:40	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	12-Nov-2025 09:00:40	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	12-Nov-2025 09:00:40	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	12-Nov-2025 09:00:40	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	12-Nov-2025 09:00:46	Clover all over. Instrumented 1106 files (112 packages).
build	12-Nov-2025 09:00:48	
build	12-Nov-2025 09:00:48	> Task :cloverInstrTests
build	12-Nov-2025 09:00:48	Clover: About to instrument test files
build	12-Nov-2025 09:00:48	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	12-Nov-2025 09:00:48	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover.db'.
build	12-Nov-2025 09:00:48	Processing files at 1.9 source level.
build	12-Nov-2025 09:00:52	Clover all over. Instrumented 293 files (52 packages).
build	12-Nov-2025 09:00:52	1619 test methods detected.
build	12-Nov-2025 09:00:52	
build	12-Nov-2025 09:00:52	> Task :cloverInstr
build	12-Nov-2025 09:00:54	
build	12-Nov-2025 09:00:54	> Task :compileCloverJava
build	12-Nov-2025 09:00:54	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	12-Nov-2025 09:00:54	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:00:54	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:00:54	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:00:54	Setting target compatibility to 11
error	12-Nov-2025 09:01:20	Note: Some input files use or override a deprecated API.
error	12-Nov-2025 09:01:20	Note: Recompile with -Xlint:deprecation for details.
error	12-Nov-2025 09:01:20	Note: Some input files use unchecked or unsafe operations.
error	12-Nov-2025 09:01:20	Note: Recompile with -Xlint:unchecked for details.
build	12-Nov-2025 09:01:27	
build	12-Nov-2025 09:01:27	> Task :processCloverResources NO-SOURCE
build	12-Nov-2025 09:01:27	> Task :cloverClasses
build	12-Nov-2025 09:01:28	> Task :copyHelp
build	12-Nov-2025 09:01:28	> Task :buildIndices
build	12-Nov-2025 09:01:29	> Task :copyResources
build	12-Nov-2025 09:01:29	> Task :copyChannelResources
build	12-Nov-2025 09:01:29	
build	12-Nov-2025 09:01:29	> Task :createBuildProperties
build	12-Nov-2025 09:01:29	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	12-Nov-2025 09:01:29	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:01:29	
build	12-Nov-2025 09:01:29	> Task :buildResources
build	12-Nov-2025 09:01:29	> Task :copyDocs
build	12-Nov-2025 09:01:29	
build	12-Nov-2025 09:01:29	> Task :convertMdFiles
build	12-Nov-2025 09:01:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	12-Nov-2025 09:01:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	12-Nov-2025 09:01:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	12-Nov-2025 09:01:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/building.html
build	12-Nov-2025 09:01:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	12-Nov-2025 09:01:30	
build	12-Nov-2025 09:01:30	> Task :releasesTemplates
build	12-Nov-2025 09:01:30	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	12-Nov-2025 09:01:30	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:01:30	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:01:30	Stripping rc/test/etc for TEST
build	12-Nov-2025 09:01:30	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	12-Nov-2025 09:01:30	
build	12-Nov-2025 09:01:30	> Task :prepare
build	12-Nov-2025 09:01:32	
build	12-Nov-2025 09:01:32	> Task :compileJava
build	12-Nov-2025 09:01:32	Setting target compatibility to 11
error	12-Nov-2025 09:01:38	Note: Some input files use or override a deprecated API.
error	12-Nov-2025 09:01:38	Note: Recompile with -Xlint:deprecation for details.
error	12-Nov-2025 09:01:38	Note: Some input files use unchecked or unsafe operations.
error	12-Nov-2025 09:01:38	Note: Recompile with -Xlint:unchecked for details.
build	12-Nov-2025 09:01:43	
build	12-Nov-2025 09:01:43	> Task :compileTestJava
build	12-Nov-2025 09:01:43	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	12-Nov-2025 09:01:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:01:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:01:43	Setting target compatibility to 11
error	12-Nov-2025 09:01:48	Note: Some input files use or override a deprecated API.
error	12-Nov-2025 09:01:48	Note: Recompile with -Xlint:deprecation for details.
error	12-Nov-2025 09:01:48	Note: Some input files use unchecked or unsafe operations.
error	12-Nov-2025 09:01:48	Note: Recompile with -Xlint:unchecked for details.
build	12-Nov-2025 09:01:50	
build	12-Nov-2025 09:01:50	> Task :processTestResources
build	12-Nov-2025 09:01:50	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	12-Nov-2025 09:01:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
build	12-Nov-2025 09:01:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:01:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:01:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:01:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:01:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:01:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:01:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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	12-Nov-2025 09:01:50	
build	12-Nov-2025 09:01:50	> Task :testClasses
build	12-Nov-2025 09:01:52	
build	12-Nov-2025 09:01:52	> Task :testTask0
build	12-Nov-2025 09:01:52	Running tests WITH clover
error	12-Nov-2025 09:01:55	WARNING: An illegal reflective access operation has occurred
error	12-Nov-2025 09:01:55	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	12-Nov-2025 09:01:55	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	12-Nov-2025 09:01:55	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	12-Nov-2025 09:01:55	WARNING: All illegal access operations will be denied in a future release
build	12-Nov-2025 09:06:36	
build	12-Nov-2025 09:06:36	> Task :testTask1
build	12-Nov-2025 09:06:36	Running tests WITH clover
error	12-Nov-2025 09:06:39	WARNING: An illegal reflective access operation has occurred
error	12-Nov-2025 09:06:39	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	12-Nov-2025 09:06:39	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	12-Nov-2025 09:06:39	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	12-Nov-2025 09:06:39	WARNING: All illegal access operations will be denied in a future release
build	12-Nov-2025 09:09:22	
build	12-Nov-2025 09:09:22	> Task :testTask2
build	12-Nov-2025 09:09:22	Running tests WITH clover
build	12-Nov-2025 09:09:26	
build	12-Nov-2025 09:09:26	> Task :testTask3
build	12-Nov-2025 09:09:26	Running tests WITH clover
error	12-Nov-2025 09:09:28	WARNING: An illegal reflective access operation has occurred
error	12-Nov-2025 09:09:28	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	12-Nov-2025 09:09:28	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	12-Nov-2025 09:09:28	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	12-Nov-2025 09:09:28	WARNING: All illegal access operations will be denied in a future release
build	12-Nov-2025 09:10:27	
build	12-Nov-2025 09:10:27	> Task :test NO-SOURCE
build	12-Nov-2025 09:10:27	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	12-Nov-2025 09:10:27	│jalview:testTask0 results: SUCCESS (1819 tests, 1819 successes, 0 failures, 0 skipped) in 4 minutes, 43.175 seconds   │
build	12-Nov-2025 09:10:27	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask0/index.html│
build	12-Nov-2025 09:10:27	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	12-Nov-2025 09:10:27	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 44.355 seconds       │
build	12-Nov-2025 09:10:27	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask1/index.html│
build	12-Nov-2025 09:10:27	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	12-Nov-2025 09:10:27	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.738 seconds                     │
build	12-Nov-2025 09:10:27	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask2/index.html│
build	12-Nov-2025 09:10:27	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	12-Nov-2025 09:10:27	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 3.271 seconds        │
build	12-Nov-2025 09:10:27	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask3/index.html│
build	12-Nov-2025 09:10:27	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	12-Nov-2025 09:10:27	│OVERALL: results: SUCCESS (1907 tests, 1907 successes, 0 failures, 0 skipped) in 7 minutes, 95.539 seconds            │
build	12-Nov-2025 09:10:27	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	12-Nov-2025 09:10:27	
build	12-Nov-2025 09:10:27	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	12-Nov-2025 09:10:27	
build	12-Nov-2025 09:10:27	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	12-Nov-2025 09:10:27	
build	12-Nov-2025 09:10:27	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	12-Nov-2025 09:10:27	
build	12-Nov-2025 09:10:27	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	12-Nov-2025 09:10:27	Please consult deprecation warnings for more details.
build	12-Nov-2025 09:10:27	
build	12-Nov-2025 09:10:27	BUILD SUCCESSFUL in 10m 4s
build	12-Nov-2025 09:10:27	21 actionable tasks: 20 executed, 1 up-to-date
simple	12-Nov-2025 09:10:28	Finished task 'Run tests with openclover under gradle' with result: Success
simple	12-Nov-2025 09:10:28	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	12-Nov-2025 09:10:28	Bamboo Artifactory Plugin version: 2.6.2
command	12-Nov-2025 09:10:28	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests #3 (JB-GDB724-JOB1-3)'\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-GDB724-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4626_alphafoldVersionTracker\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4626_alphafoldVersionTracker\nbamboo_repository_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB724-JOB1-3\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-GDB724-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB724-JOB1\nbamboo_shortPlanName=patch-JAL-4626_alphafoldVersionTracker\nbamboo_repository_46498567_git_branch=patch/JAL-4626_alphafoldVersionTracker\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=3\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_46498567_git_username=\nbamboo_shortJobName=Clover and Tests\nbamboo_repository_46498567_previous_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB724-JOB1-3\nbamboo_repository_46498567_name=Jalview Gitlab\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker\nbamboo_shortPlanKey=GDB724\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_buildTimeStamp=2025-11-12T09:00:21.417Z\nbamboo_repository_previous_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_planRepository_previousRevision=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_repository_git_branch=patch/JAL-4626_alphafoldVersionTracker\nbamboo_buildResultKey=JB-GDB724-JOB1-3\nbamboo_repository_branch_name=patch/JAL-4626_alphafoldVersionTracker\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=377f1f52a15db66fd5768669a50bfda03250a6c7\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\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_dependenciesDisabled=false\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=patch/JAL-4626_alphafoldVersionTracker\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=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_planRepository_branchDisplayName=patch/JAL-4626_alphafoldVersionTracker\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4626_alphafoldVersionTracker\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-46302705\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_repository_46498567_branch_name=patch/JAL-4626_alphafoldVersionTracker\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_ManualBuildTriggerReason_userName=jprocter\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498567_git_repositoryUrl=https://gitlab.jalview.org/jalview/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-GDB724-JOB1\nbamboo_repository_46498567_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_planKey=JB-GDB724\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4626_alphafoldVersionTracker\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	12-Nov-2025 09:10:28	444
build	12-Nov-2025 09:10:34	
build	12-Nov-2025 09:10:34	> Configure project :
build	12-Nov-2025 09:10:34	Using properties from file './utils/channels/default/channel_gradle.properties'
build	12-Nov-2025 09:10:34	JALVIEW_VERSION is set to '2.11.5.1'
build	12-Nov-2025 09:10:34	HEADLESS BUILD
build	12-Nov-2025 09:10:34	J2S ENABLED
build	12-Nov-2025 09:10:35	Using a LOCAL profile.
build	12-Nov-2025 09:10:36	eclipseDir exists
build	12-Nov-2025 09:10:38	
build	12-Nov-2025 09:10:38	> Task :cloverHtmlReport
build	12-Nov-2025 09:10:38	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	12-Nov-2025 09:10:40	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/clover'
error	12-Nov-2025 09:10:47	ERROR: Invalid Java source found or Clover failed to parse it: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/src/jalview/gui/AlignFrame.java
build	12-Nov-2025 09:11:33	Done. Processed 116 packages in 53211ms (458ms per package).
build	12-Nov-2025 09:11:39	
build	12-Nov-2025 09:11:39	> Task :cloverXmlReport
build	12-Nov-2025 09:11:39	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	12-Nov-2025 09:11:41	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/clover/clover.xml'
build	12-Nov-2025 09:11:41	
build	12-Nov-2025 09:11:41	> Task :cloverReport
build	12-Nov-2025 09:11:41	
build	12-Nov-2025 09:11:41	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	12-Nov-2025 09:11:41	
build	12-Nov-2025 09:11:41	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	12-Nov-2025 09:11:41	
build	12-Nov-2025 09:11:41	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	12-Nov-2025 09:11:41	
build	12-Nov-2025 09:11:41	BUILD SUCCESSFUL in 1m 13s
build	12-Nov-2025 09:11:41	2 actionable tasks: 2 executed
simple	12-Nov-2025 09:11:41	Finished task 'Clover Report' with result: Success
simple	12-Nov-2025 09:11:41	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	12-Nov-2025 09:11:41	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1...
simple	12-Nov-2025 09:11:41	Finished task 'TestNG Parser' with result: Success
simple	12-Nov-2025 09:11:41	Running post build plugin 'NCover Results Collector'
simple	12-Nov-2025 09:11:41	Running post build plugin 'Artifact Copier'
simple	12-Nov-2025 09:11:41	Publishing an artifact: Clover Report (System)
simple	12-Nov-2025 09:11:46	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 5.136 s
simple	12-Nov-2025 09:11:46	Publishing an artifact: TestNG report
error	12-Nov-2025 09:11:46	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/test does not exist.
simple	12-Nov-2025 09:11:46	The artifact hasn't been successfully published after 3.816 ms
simple	12-Nov-2025 09:11:46	Running post build plugin 'Artifactory Release Management Staging'
simple	12-Nov-2025 09:11:46	Running post build plugin 'Artifactory Build Info Copier'
simple	12-Nov-2025 09:11:46	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	12-Nov-2025 09:11:46	Running post build plugin 'npm Cache Cleanup'
simple	12-Nov-2025 09:11:46	Running post build plugin 'Clover Results Collector'
simple	12-Nov-2025 09:11:46	Running post build plugin 'Docker Container Cleanup'
simple	12-Nov-2025 09:11:46	Finalising the build...
simple	12-Nov-2025 09:11:46	Stopping timer.
simple	12-Nov-2025 09:11:46	Build JB-GDB724-JOB1-3 completed.
simple	12-Nov-2025 09:11:46	Running on server: post build plugin 'NCover Results Collector'
simple	12-Nov-2025 09:11:46	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	12-Nov-2025 09:11:46	Running on server: post build plugin 'Clover Delta Calculator'
simple	12-Nov-2025 09:11:46	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	12-Nov-2025 09:11:46	All post build plugins have finished
simple	12-Nov-2025 09:11:46	Generating build results summary...
simple	12-Nov-2025 09:11:47	Saving build results to disk...
simple	12-Nov-2025 09:11:47	Logging substituted variables...
simple	12-Nov-2025 09:11:47	Indexing build results...
simple	12-Nov-2025 09:11:47	Finished building JB-GDB724-JOB1-3.