simple	19-Jun-2026 06:20:25	Build Jalview Builds - Gradle Develop Build - patch-JAL-4672_for_2115_pdbe_query - Clover and Tests #2 (JB-GDB756-JOB1-2) started building on agent Default Agent
simple	19-Jun-2026 06:20:25	
simple	19-Jun-2026 06:20:25	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1
simple	19-Jun-2026 06:20:25	Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4672_for_2115_pdbe_query - Clover and Tests #2 (JB-GDB756-JOB1-2)
simple	19-Jun-2026 06:20:25	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	19-Jun-2026 06:20:25	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1
simple	19-Jun-2026 06:20:25	Updating source code to revision: ccc4465aaa5da5a9ba83fecdf1027486866a5db7
simple	19-Jun-2026 06:20:25	Fetching 'refs/heads/patch/JAL-4672_for_2115_pdbe_query' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	19-Jun-2026 06:20:25	Checking out revision ccc4465aaa5da5a9ba83fecdf1027486866a5db7.
simple	19-Jun-2026 06:20:25	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	19-Jun-2026 06:20:25	   334cafc..ccc4465  patch/JAL-4672_for_2115_pdbe_query -> origin/patch/JAL-4672_for_2115_pdbe_query
simple	19-Jun-2026 06:20:25	   f1b34f8..4b44180  epic/JAL-4320_JAL-4671_swingjs_gradle_plugin_for_jalviewjs -> origin/epic/JAL-4320_JAL-4671_swingjs_gradle_plugin_for_jalviewjs
simple	19-Jun-2026 06:20:27	Already on 'patch/JAL-4672_for_2115_pdbe_query'
simple	19-Jun-2026 06:20:27	Your branch is behind 'origin/patch/JAL-4672_for_2115_pdbe_query' by 1 commit, and can be fast-forwarded.
simple	19-Jun-2026 06:20:27	  (use "git pull" to update your local branch)
simple	19-Jun-2026 06:20:27	HEAD is now at ccc4465 JAL-4672 update mocked query strings
simple	19-Jun-2026 06:20:27	Updated source code to revision: ccc4465aaa5da5a9ba83fecdf1027486866a5db7
simple	19-Jun-2026 06:20:27	Finished task 'Checkout Default Repository' with result: Success
simple	19-Jun-2026 06:20:27	Running pre-build action: VCS Version Collector
simple	19-Jun-2026 06:20:27	Running pre-build action: Artifactory Release Staging
simple	19-Jun-2026 06:20:27	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	19-Jun-2026 06:20:27	Bamboo Artifactory Plugin version: 2.6.2
command	19-Jun-2026 06:20:27	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4672_for_2115_pdbe_query - Clover and Tests #2 (JB-GDB756-JOB1-2)'\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-GDB756-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4672_for_2115_pdbe_query\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4672_for_2115_pdbe_query\nbamboo_repository_48169084_previous_revision_number=334cafc6119496e0b2f51e5769259493c182cebd\nbamboo_repository_revision_number=ccc4465aaa5da5a9ba83fecdf1027486866a5db7\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB756-JOB1-2\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-GDB756-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB756-JOB1\nbamboo_shortPlanName=patch-JAL-4672_for_2115_pdbe_query\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_48169084_branch_name=patch/JAL-4672_for_2115_pdbe_query\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB756-JOB1-2\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_48169084_name=Jalview Gitlab\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4672_for_2115_pdbe_query\nbamboo_shortPlanKey=GDB756\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=ccc4465aaa5da5a9ba83fecdf1027486866a5db7\nbamboo_repository_48169084_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_buildTimeStamp=2026-06-19T06:20:25.225+01:00\nbamboo_repository_previous_revision_number=334cafc6119496e0b2f51e5769259493c182cebd\nbamboo_planRepository_previousRevision=334cafc6119496e0b2f51e5769259493c182cebd\nbamboo_repository_48169084_git_branch=patch/JAL-4672_for_2115_pdbe_query\nbamboo_repository_git_branch=patch/JAL-4672_for_2115_pdbe_query\nbamboo_buildResultKey=JB-GDB756-JOB1-2\nbamboo_repository_branch_name=patch/JAL-4672_for_2115_pdbe_query\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4672_for_2115_pdbe_query - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=ccc4465aaa5da5a9ba83fecdf1027486866a5db7\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/\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-4672_for_2115_pdbe_query\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=334cafc6119496e0b2f51e5769259493c182cebd\nbamboo_planRepository_branchDisplayName=patch/JAL-4672_for_2115_pdbe_query\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4672_for_2115_pdbe_query\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-47972599\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=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169084_revision_number=ccc4465aaa5da5a9ba83fecdf1027486866a5db7\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-GDB756-JOB1\nbamboo_planKey=JB-GDB756\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_48169084_git_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4672_for_2115_pdbe_query\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	19-Jun-2026 06:20:27	2414
build	19-Jun-2026 06:20:27	Starting a Gradle Daemon (subsequent builds will be faster)
build	19-Jun-2026 06:20:33	
build	19-Jun-2026 06:20:33	> Configure project :
build	19-Jun-2026 06:20:33	Using properties from file './utils/channels/default/channel_gradle.properties'
build	19-Jun-2026 06:20:33	JALVIEW_VERSION is set to '2.11.5.1'
build	19-Jun-2026 06:20:33	HEADLESS BUILD
build	19-Jun-2026 06:20:33	J2S ENABLED
build	19-Jun-2026 06:20:33	Using a LOCAL profile.
build	19-Jun-2026 06:20:34	eclipseDir exists
build	19-Jun-2026 06:20:35	
build	19-Jun-2026 06:20:35	> Task :clean
build	19-Jun-2026 06:20:35	> Task :cleanClover
build	19-Jun-2026 06:20:35	> Task :cleanTest UP-TO-DATE
build	19-Jun-2026 06:20:37	
build	19-Jun-2026 06:20:37	> Task :cloverInstrJava
build	19-Jun-2026 06:20:37	Clover: About to instrument 1109 files
build	19-Jun-2026 06:20:37	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Jun-2026 06:20:37	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/clover/clover.db'.
build	19-Jun-2026 06:20:37	Processing files at 1.9 source level.
error	19-Jun-2026 06:20:39	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	19-Jun-2026 06:20:39	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	19-Jun-2026 06:20:39	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	19-Jun-2026 06:20:39	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	19-Jun-2026 06:20:39	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	19-Jun-2026 06:20:39	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	19-Jun-2026 06:20:39	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	19-Jun-2026 06:20:45	Clover all over. Instrumented 1109 files (113 packages).
build	19-Jun-2026 06:20:47	
build	19-Jun-2026 06:20:47	> Task :cloverInstrTests
build	19-Jun-2026 06:20:47	Clover: About to instrument test files
build	19-Jun-2026 06:20:47	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Jun-2026 06:20:47	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/clover/clover.db'.
build	19-Jun-2026 06:20:47	Processing files at 1.9 source level.
build	19-Jun-2026 06:20:50	Clover all over. Instrumented 293 files (52 packages).
build	19-Jun-2026 06:20:50	1627 test methods detected.
build	19-Jun-2026 06:20:50	
build	19-Jun-2026 06:20:50	> Task :cloverInstr
build	19-Jun-2026 06:20:52	
build	19-Jun-2026 06:20:52	> Task :compileCloverJava
build	19-Jun-2026 06:20:52	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	19-Jun-2026 06:20:52	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:20:52	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:20:52	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:20:52	Setting target compatibility to 11
error	19-Jun-2026 06:21:12	Note: Some input files use or override a deprecated API.
error	19-Jun-2026 06:21:12	Note: Recompile with -Xlint:deprecation for details.
error	19-Jun-2026 06:21:12	Note: Some input files use unchecked or unsafe operations.
error	19-Jun-2026 06:21:12	Note: Recompile with -Xlint:unchecked for details.
build	19-Jun-2026 06:21:18	
build	19-Jun-2026 06:21:18	> Task :processCloverResources NO-SOURCE
build	19-Jun-2026 06:21:18	> Task :cloverClasses
build	19-Jun-2026 06:21:18	> Task :copyHelp
build	19-Jun-2026 06:21:19	> Task :buildIndices
build	19-Jun-2026 06:21:19	> Task :copyResources
build	19-Jun-2026 06:21:19	> Task :copyChannelResources
build	19-Jun-2026 06:21:19	
build	19-Jun-2026 06:21:19	> Task :createBuildProperties
build	19-Jun-2026 06:21:19	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	19-Jun-2026 06:21:19	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:21:19	
build	19-Jun-2026 06:21:19	> Task :buildResources
build	19-Jun-2026 06:21:19	> Task :copyDocs
build	19-Jun-2026 06:21:20	
build	19-Jun-2026 06:21:20	> Task :convertMdFiles
build	19-Jun-2026 06:21:20	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	19-Jun-2026 06:21:20	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	19-Jun-2026 06:21:20	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	19-Jun-2026 06:21:20	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/resources/doc_build/doc/building.html
build	19-Jun-2026 06:21:20	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	19-Jun-2026 06:21:20	
build	19-Jun-2026 06:21:20	> Task :releasesTemplates
build	19-Jun-2026 06:21:20	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	19-Jun-2026 06:21:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:21:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:21:20	Stripping rc/test/etc for TEST
build	19-Jun-2026 06:21:20	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	19-Jun-2026 06:21:20	
build	19-Jun-2026 06:21:20	> Task :prepare
build	19-Jun-2026 06:21:22	
build	19-Jun-2026 06:21:22	> Task :compileJava
build	19-Jun-2026 06:21:22	Setting target compatibility to 11
error	19-Jun-2026 06:21:27	Note: Some input files use or override a deprecated API.
error	19-Jun-2026 06:21:27	Note: Recompile with -Xlint:deprecation for details.
error	19-Jun-2026 06:21:27	Note: Some input files use unchecked or unsafe operations.
error	19-Jun-2026 06:21:27	Note: Recompile with -Xlint:unchecked for details.
build	19-Jun-2026 06:21:31	
build	19-Jun-2026 06:21:31	> Task :compileTestJava
build	19-Jun-2026 06:21:31	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	19-Jun-2026 06:21:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:21:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:21:31	Setting target compatibility to 11
error	19-Jun-2026 06:21:35	Note: Some input files use or override a deprecated API.
error	19-Jun-2026 06:21:35	Note: Recompile with -Xlint:deprecation for details.
error	19-Jun-2026 06:21:35	Note: Some input files use unchecked or unsafe operations.
error	19-Jun-2026 06:21:35	Note: Recompile with -Xlint:unchecked for details.
build	19-Jun-2026 06:21:36	
build	19-Jun-2026 06:21:36	> Task :processTestResources
build	19-Jun-2026 06:21:36	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	19-Jun-2026 06:21:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:21:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:21:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:21:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:21:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:21:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:21:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:21:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-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	19-Jun-2026 06:21:36	
build	19-Jun-2026 06:21:36	> Task :testClasses
build	19-Jun-2026 06:21:38	
build	19-Jun-2026 06:21:38	> Task :testTask0
build	19-Jun-2026 06:21:38	Running tests WITH clover
error	19-Jun-2026 06:21:40	WARNING: An illegal reflective access operation has occurred
error	19-Jun-2026 06:21:40	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	19-Jun-2026 06:21:40	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	19-Jun-2026 06:21:40	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	19-Jun-2026 06:21:40	WARNING: All illegal access operations will be denied in a future release
build	19-Jun-2026 06:25:38	
build	19-Jun-2026 06:25:38	> Task :testTask1
build	19-Jun-2026 06:25:38	Running tests WITH clover
error	19-Jun-2026 06:25:39	WARNING: An illegal reflective access operation has occurred
error	19-Jun-2026 06:25:39	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	19-Jun-2026 06:25:39	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	19-Jun-2026 06:25:39	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	19-Jun-2026 06:25:39	WARNING: All illegal access operations will be denied in a future release
build	19-Jun-2026 06:27:47	
build	19-Jun-2026 06:27:47	> Task :testTask2
build	19-Jun-2026 06:27:47	Running tests WITH clover
build	19-Jun-2026 06:27:50	
build	19-Jun-2026 06:27:50	> Task :testTask3
build	19-Jun-2026 06:27:50	Running tests WITH clover
error	19-Jun-2026 06:27:52	WARNING: An illegal reflective access operation has occurred
error	19-Jun-2026 06:27:52	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	19-Jun-2026 06:27:52	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	19-Jun-2026 06:27:52	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	19-Jun-2026 06:27:52	WARNING: All illegal access operations will be denied in a future release
build	19-Jun-2026 06:28:38	
build	19-Jun-2026 06:28:38	> Task :test NO-SOURCE
build	19-Jun-2026 06:28:38	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	19-Jun-2026 06:28:38	│jalview:testTask0 results: SUCCESS (1836 tests, 1836 successes, 0 failures, 0 skipped) in 3 minutes, 58.411 seconds   │
build	19-Jun-2026 06:28:38	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/reports/tests/testTask0/index.html│
build	19-Jun-2026 06:28:38	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Jun-2026 06:28:38	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 9.389 seconds        │
build	19-Jun-2026 06:28:38	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/reports/tests/testTask1/index.html│
build	19-Jun-2026 06:28:38	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Jun-2026 06:28:38	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 2.973 seconds                     │
build	19-Jun-2026 06:28:38	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/reports/tests/testTask2/index.html│
build	19-Jun-2026 06:28:38	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Jun-2026 06:28:38	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 49.966 seconds                  │
build	19-Jun-2026 06:28:38	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/reports/tests/testTask3/index.html│
build	19-Jun-2026 06:28:38	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	19-Jun-2026 06:28:38	│OVERALL: results: SUCCESS (1924 tests, 1924 successes, 0 failures, 0 skipped) in 5 minutes, 120.739 seconds           │
build	19-Jun-2026 06:28:38	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	19-Jun-2026 06:28:38	
build	19-Jun-2026 06:28:38	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	19-Jun-2026 06:28:38	
build	19-Jun-2026 06:28:38	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	19-Jun-2026 06:28:38	
build	19-Jun-2026 06:28:38	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	19-Jun-2026 06:28:38	
build	19-Jun-2026 06:28:38	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	19-Jun-2026 06:28:38	Please consult deprecation warnings for more details.
build	19-Jun-2026 06:28:38	
build	19-Jun-2026 06:28:38	BUILD SUCCESSFUL in 8m 11s
build	19-Jun-2026 06:28:38	21 actionable tasks: 20 executed, 1 up-to-date
simple	19-Jun-2026 06:28:39	Finished task 'Run tests with openclover under gradle' with result: Success
simple	19-Jun-2026 06:28:39	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	19-Jun-2026 06:28:39	Bamboo Artifactory Plugin version: 2.6.2
command	19-Jun-2026 06:28:39	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4672_for_2115_pdbe_query - Clover and Tests #2 (JB-GDB756-JOB1-2)'\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-GDB756-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4672_for_2115_pdbe_query\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4672_for_2115_pdbe_query\nbamboo_repository_48169084_previous_revision_number=334cafc6119496e0b2f51e5769259493c182cebd\nbamboo_repository_revision_number=ccc4465aaa5da5a9ba83fecdf1027486866a5db7\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB756-JOB1-2\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-GDB756-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB756-JOB1\nbamboo_shortPlanName=patch-JAL-4672_for_2115_pdbe_query\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_48169084_branch_name=patch/JAL-4672_for_2115_pdbe_query\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB756-JOB1-2\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_48169084_name=Jalview Gitlab\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4672_for_2115_pdbe_query\nbamboo_shortPlanKey=GDB756\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=ccc4465aaa5da5a9ba83fecdf1027486866a5db7\nbamboo_repository_48169084_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_buildTimeStamp=2026-06-19T06:20:25.225+01:00\nbamboo_repository_previous_revision_number=334cafc6119496e0b2f51e5769259493c182cebd\nbamboo_planRepository_previousRevision=334cafc6119496e0b2f51e5769259493c182cebd\nbamboo_repository_48169084_git_branch=patch/JAL-4672_for_2115_pdbe_query\nbamboo_repository_git_branch=patch/JAL-4672_for_2115_pdbe_query\nbamboo_buildResultKey=JB-GDB756-JOB1-2\nbamboo_repository_branch_name=patch/JAL-4672_for_2115_pdbe_query\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4672_for_2115_pdbe_query - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=ccc4465aaa5da5a9ba83fecdf1027486866a5db7\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/\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-4672_for_2115_pdbe_query\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=334cafc6119496e0b2f51e5769259493c182cebd\nbamboo_planRepository_branchDisplayName=patch/JAL-4672_for_2115_pdbe_query\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4672_for_2115_pdbe_query\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-47972599\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=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169084_revision_number=ccc4465aaa5da5a9ba83fecdf1027486866a5db7\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-GDB756-JOB1\nbamboo_planKey=JB-GDB756\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_48169084_git_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4672_for_2115_pdbe_query\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	19-Jun-2026 06:28:39	2414
build	19-Jun-2026 06:28:44	
build	19-Jun-2026 06:28:44	> Configure project :
build	19-Jun-2026 06:28:44	Using properties from file './utils/channels/default/channel_gradle.properties'
build	19-Jun-2026 06:28:44	JALVIEW_VERSION is set to '2.11.5.1'
build	19-Jun-2026 06:28:44	HEADLESS BUILD
build	19-Jun-2026 06:28:44	J2S ENABLED
build	19-Jun-2026 06:28:44	Using a LOCAL profile.
build	19-Jun-2026 06:28:45	eclipseDir exists
build	19-Jun-2026 06:28:47	
build	19-Jun-2026 06:28:47	> Task :cloverHtmlReport
build	19-Jun-2026 06:28:47	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Jun-2026 06:28:48	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/reports/clover'
build	19-Jun-2026 06:29:34	Done. Processed 117 packages in 46033ms (393ms per package).
build	19-Jun-2026 06:29:42	
build	19-Jun-2026 06:29:42	> Task :cloverXmlReport
build	19-Jun-2026 06:29:42	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	19-Jun-2026 06:29:44	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/reports/clover/clover.xml'
build	19-Jun-2026 06:29:44	
build	19-Jun-2026 06:29:44	> Task :cloverReport
build	19-Jun-2026 06:29:44	
build	19-Jun-2026 06:29:44	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	19-Jun-2026 06:29:44	
build	19-Jun-2026 06:29:44	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	19-Jun-2026 06:29:44	
build	19-Jun-2026 06:29:44	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	19-Jun-2026 06:29:44	
build	19-Jun-2026 06:29:44	BUILD SUCCESSFUL in 1m 5s
build	19-Jun-2026 06:29:44	2 actionable tasks: 2 executed
simple	19-Jun-2026 06:29:44	Finished task 'Clover Report' with result: Success
simple	19-Jun-2026 06:29:44	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	19-Jun-2026 06:29:44	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1...
simple	19-Jun-2026 06:29:44	Finished task 'TestNG Parser' with result: Success
simple	19-Jun-2026 06:29:44	Running post build plugin 'NCover Results Collector'
simple	19-Jun-2026 06:29:44	Running post build plugin 'Artifact Copier'
simple	19-Jun-2026 06:29:44	Publishing an artifact: Clover Report (System)
simple	19-Jun-2026 06:29:46	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.627 s
simple	19-Jun-2026 06:29:46	Publishing an artifact: TestNG report
error	19-Jun-2026 06:29:46	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB756-JOB1/build/reports/tests/test does not exist.
simple	19-Jun-2026 06:29:46	The artifact hasn't been successfully published after 3.101 ms
simple	19-Jun-2026 06:29:46	Running post build plugin 'Artifactory Release Management Staging'
simple	19-Jun-2026 06:29:46	Running post build plugin 'Artifactory Build Info Copier'
simple	19-Jun-2026 06:29:46	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	19-Jun-2026 06:29:46	Running post build plugin 'npm Cache Cleanup'
simple	19-Jun-2026 06:29:46	Running post build plugin 'Clover Results Collector'
simple	19-Jun-2026 06:29:46	Running post build plugin 'Docker Container Cleanup'
simple	19-Jun-2026 06:29:46	Finalising the build...
simple	19-Jun-2026 06:29:46	Stopping timer.
simple	19-Jun-2026 06:29:46	Build JB-GDB756-JOB1-2 completed.
simple	19-Jun-2026 06:29:46	Running on server: post build plugin 'NCover Results Collector'
simple	19-Jun-2026 06:29:46	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	19-Jun-2026 06:29:46	Running on server: post build plugin 'Clover Delta Calculator'
simple	19-Jun-2026 06:29:46	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	19-Jun-2026 06:29:46	All post build plugins have finished
simple	19-Jun-2026 06:29:46	Generating build results summary...
simple	19-Jun-2026 06:29:46	Saving build results to disk...
simple	19-Jun-2026 06:29:46	Logging substituted variables...
simple	19-Jun-2026 06:29:46	Indexing build results...
simple	19-Jun-2026 06:29:46	Finished building JB-GDB756-JOB1-2.