simple	03-Dec-2025 15:58:10	Build Jalview Builds - Gradle Develop Build - bug-JAL-4603_Export_files_missing_part_of_sequence - Clover and Tests #4 (JB-GDB733-JOB1-4) started building on agent Default Agent
simple	03-Dec-2025 15:58:10	
simple	03-Dec-2025 15:58:10	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1
simple	03-Dec-2025 15:58:10	Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4603_Export_files_missing_part_of_sequence - Clover and Tests #4 (JB-GDB733-JOB1-4)
simple	03-Dec-2025 15:58:10	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	03-Dec-2025 15:58:10	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1
simple	03-Dec-2025 15:58:10	Updating source code to revision: db868848b73d9a08f5ee1b08a269436a41323446
simple	03-Dec-2025 15:58:10	Fetching 'refs/heads/bug/JAL-4603_Export_files_missing_part_of_sequence' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	03-Dec-2025 15:58:10	Checking out revision db868848b73d9a08f5ee1b08a269436a41323446.
simple	03-Dec-2025 15:58:10	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	03-Dec-2025 15:58:10	   6343fb6..db86884  bug/JAL-4603_Export_files_missing_part_of_sequence -> origin/bug/JAL-4603_Export_files_missing_part_of_sequence
simple	03-Dec-2025 15:58:10	   1c6a6fa..fae9009  development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch
simple	03-Dec-2025 15:58:10	   a66e20b..c586364  releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch
simple	03-Dec-2025 15:58:11	Already on 'bug/JAL-4603_Export_files_missing_part_of_sequence'
simple	03-Dec-2025 15:58:11	Your branch is behind 'origin/bug/JAL-4603_Export_files_missing_part_of_sequence' by 1 commit, and can be fast-forwarded.
simple	03-Dec-2025 15:58:11	  (use "git pull" to update your local branch)
simple	03-Dec-2025 15:58:11	HEAD is now at db86884 JAL-4603 Fixed failed tests in SeqCanvasTest
simple	03-Dec-2025 15:58:11	Updated source code to revision: db868848b73d9a08f5ee1b08a269436a41323446
simple	03-Dec-2025 15:58:11	Finished task 'Checkout Default Repository' with result: Success
simple	03-Dec-2025 15:58:11	Running pre-build action: VCS Version Collector
simple	03-Dec-2025 15:58:11	Running pre-build action: Artifactory Release Staging
simple	03-Dec-2025 15:58:11	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	03-Dec-2025 15:58:11	Bamboo Artifactory Plugin version: 2.6.2
command	03-Dec-2025 15:58:11	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4603_Export_files_missing_part_of_sequence - Clover and Tests #4 (JB-GDB733-JOB1-4)'\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-GDB733-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_repository_revision_number=db868848b73d9a08f5ee1b08a269436a41323446\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB733-JOB1-4\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-GDB733-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB733-JOB1\nbamboo_shortPlanName=bug-JAL-4603_Export_files_missing_part_of_sequence\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=4\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-GDB733-JOB1-4\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4603_Export_files_missing_part_of_sequence\nbamboo_shortPlanKey=GDB733\nbamboo_repository_46498613_revision_number=db868848b73d9a08f5ee1b08a269436a41323446\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498613_git_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=db868848b73d9a08f5ee1b08a269436a41323446\nbamboo_buildTimeStamp=2025-12-03T15:58:10.388Z\nbamboo_repository_previous_revision_number=6343fb679e94dec0d94366f19ed793109bc79aed\nbamboo_planRepository_previousRevision=6343fb679e94dec0d94366f19ed793109bc79aed\nbamboo_repository_git_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_buildResultKey=JB-GDB733-JOB1-4\nbamboo_repository_branch_name=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4603_Export_files_missing_part_of_sequence - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=db868848b73d9a08f5ee1b08a269436a41323446\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_repository_46498613_git_username=\nbamboo_repository_46498613_previous_revision_number=6343fb679e94dec0d94366f19ed793109bc79aed\nbamboo_planRepository_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_46498613_branch_name=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=6343fb679e94dec0d94366f19ed793109bc79aed\nbamboo_planRepository_branchDisplayName=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4603_Export_files_missing_part_of_sequence\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-46302795\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46498613_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\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_46498613_name=Jalview Gitlab\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-GDB733-JOB1\nbamboo_planKey=JB-GDB733\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4603_Export_files_missing_part_of_sequence\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	03-Dec-2025 15:58:11	444
build	03-Dec-2025 15:58:15	
build	03-Dec-2025 15:58:15	> Configure project :
build	03-Dec-2025 15:58:15	Using properties from file './utils/channels/default/channel_gradle.properties'
build	03-Dec-2025 15:58:15	JALVIEW_VERSION is set to '2.11.5.1'
build	03-Dec-2025 15:58:15	HEADLESS BUILD
build	03-Dec-2025 15:58:15	J2S ENABLED
build	03-Dec-2025 15:58:15	Using a LOCAL profile.
build	03-Dec-2025 15:58:15	eclipseDir exists
build	03-Dec-2025 15:58:15	
build	03-Dec-2025 15:58:15	> Task :clean
build	03-Dec-2025 15:58:15	> Task :cleanClover
build	03-Dec-2025 15:58:15	> Task :cleanTest UP-TO-DATE
build	03-Dec-2025 15:58:19	
build	03-Dec-2025 15:58:19	> Task :cloverInstrJava
build	03-Dec-2025 15:58:19	Clover: About to instrument 1109 files
build	03-Dec-2025 15:58:19	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	03-Dec-2025 15:58:19	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/clover/clover.db'.
build	03-Dec-2025 15:58:19	Processing files at 1.9 source level.
error	03-Dec-2025 15:58:23	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	03-Dec-2025 15:58:23	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	03-Dec-2025 15:58:23	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	03-Dec-2025 15:58:23	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	03-Dec-2025 15:58:23	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	03-Dec-2025 15:58:23	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	03-Dec-2025 15:58:23	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	03-Dec-2025 15:58:31	Clover all over. Instrumented 1109 files (113 packages).
build	03-Dec-2025 15:58:32	
build	03-Dec-2025 15:58:32	> Task :cloverInstrTests
build	03-Dec-2025 15:58:32	Clover: About to instrument test files
build	03-Dec-2025 15:58:32	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	03-Dec-2025 15:58:32	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/clover/clover.db'.
build	03-Dec-2025 15:58:32	Processing files at 1.9 source level.
build	03-Dec-2025 15:58:36	Clover all over. Instrumented 293 files (52 packages).
build	03-Dec-2025 15:58:36	1627 test methods detected.
build	03-Dec-2025 15:58:36	
build	03-Dec-2025 15:58:36	> Task :cloverInstr
build	03-Dec-2025 15:58:38	
build	03-Dec-2025 15:58:38	> Task :compileCloverJava
build	03-Dec-2025 15:58:38	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	03-Dec-2025 15:58:38	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:58:38	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:58:38	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:58:38	Setting target compatibility to 11
error	03-Dec-2025 15:58:54	Note: Some input files use or override a deprecated API.
error	03-Dec-2025 15:58:54	Note: Recompile with -Xlint:deprecation for details.
error	03-Dec-2025 15:58:54	Note: Some input files use unchecked or unsafe operations.
error	03-Dec-2025 15:58:54	Note: Recompile with -Xlint:unchecked for details.
build	03-Dec-2025 15:59:02	
build	03-Dec-2025 15:59:02	> Task :processCloverResources NO-SOURCE
build	03-Dec-2025 15:59:02	> Task :cloverClasses
build	03-Dec-2025 15:59:02	> Task :copyHelp
build	03-Dec-2025 15:59:03	> Task :buildIndices
build	03-Dec-2025 15:59:03	> Task :copyResources
build	03-Dec-2025 15:59:03	> Task :copyChannelResources
build	03-Dec-2025 15:59:03	
build	03-Dec-2025 15:59:03	> Task :createBuildProperties
build	03-Dec-2025 15:59:03	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	03-Dec-2025 15:59:03	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:59:03	
build	03-Dec-2025 15:59:03	> Task :buildResources
build	03-Dec-2025 15:59:03	> Task :copyDocs
build	03-Dec-2025 15:59:04	
build	03-Dec-2025 15:59:04	> Task :convertMdFiles
build	03-Dec-2025 15:59:04	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	03-Dec-2025 15:59:04	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	03-Dec-2025 15:59:04	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	03-Dec-2025 15:59:04	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/resources/doc_build/doc/building.html
build	03-Dec-2025 15:59:04	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	03-Dec-2025 15:59:04	
build	03-Dec-2025 15:59:04	> Task :releasesTemplates
build	03-Dec-2025 15:59:04	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	03-Dec-2025 15:59:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:59:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:59:04	Stripping rc/test/etc for TEST
build	03-Dec-2025 15:59:04	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	03-Dec-2025 15:59:04	
build	03-Dec-2025 15:59:04	> Task :prepare
build	03-Dec-2025 15:59:06	
build	03-Dec-2025 15:59:06	> Task :compileJava
build	03-Dec-2025 15:59:06	Setting target compatibility to 11
error	03-Dec-2025 15:59:13	Note: Some input files use or override a deprecated API.
error	03-Dec-2025 15:59:13	Note: Recompile with -Xlint:deprecation for details.
error	03-Dec-2025 15:59:13	Note: Some input files use unchecked or unsafe operations.
error	03-Dec-2025 15:59:13	Note: Recompile with -Xlint:unchecked for details.
build	03-Dec-2025 15:59:14	
build	03-Dec-2025 15:59:14	> Task :compileTestJava
build	03-Dec-2025 15:59:14	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	03-Dec-2025 15:59:14	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:59:14	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:59:14	Setting target compatibility to 11
error	03-Dec-2025 15:59:20	Note: Some input files use or override a deprecated API.
error	03-Dec-2025 15:59:20	Note: Recompile with -Xlint:deprecation for details.
error	03-Dec-2025 15:59:20	Note: Some input files use unchecked or unsafe operations.
error	03-Dec-2025 15:59:20	Note: Recompile with -Xlint:unchecked for details.
build	03-Dec-2025 15:59:22	
build	03-Dec-2025 15:59:22	> Task :processTestResources
build	03-Dec-2025 15:59:22	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	03-Dec-2025 15:59:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:59:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:59:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:59:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:59:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:59:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:59:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:59:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-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	03-Dec-2025 15:59:22	
build	03-Dec-2025 15:59:22	> Task :testClasses
build	03-Dec-2025 15:59:23	
build	03-Dec-2025 15:59:23	> Task :testTask0
build	03-Dec-2025 15:59:23	Running tests WITH clover
error	03-Dec-2025 15:59:26	WARNING: An illegal reflective access operation has occurred
error	03-Dec-2025 15:59:26	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	03-Dec-2025 15:59:26	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	03-Dec-2025 15:59:26	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	03-Dec-2025 15:59:26	WARNING: All illegal access operations will be denied in a future release
build	03-Dec-2025 16:04:33	
build	03-Dec-2025 16:04:33	> Task :testTask1
build	03-Dec-2025 16:04:33	Running tests WITH clover
error	03-Dec-2025 16:04:34	WARNING: An illegal reflective access operation has occurred
error	03-Dec-2025 16:04:34	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	03-Dec-2025 16:04:34	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	03-Dec-2025 16:04:34	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	03-Dec-2025 16:04:34	WARNING: All illegal access operations will be denied in a future release
build	03-Dec-2025 16:07:25	
build	03-Dec-2025 16:07:25	> Task :testTask2
build	03-Dec-2025 16:07:25	Running tests WITH clover
build	03-Dec-2025 16:07:30	
build	03-Dec-2025 16:07:30	> Task :testTask3
build	03-Dec-2025 16:07:30	Running tests WITH clover
error	03-Dec-2025 16:07:33	WARNING: An illegal reflective access operation has occurred
error	03-Dec-2025 16:07:33	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	03-Dec-2025 16:07:33	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	03-Dec-2025 16:07:33	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	03-Dec-2025 16:07:33	WARNING: All illegal access operations will be denied in a future release
build	03-Dec-2025 16:08:33	
build	03-Dec-2025 16:08:33	> Task :test NO-SOURCE
build	03-Dec-2025 16:08:33	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	03-Dec-2025 16:08:33	│jalview:testTask0 results: SUCCESS (1834 tests, 1834 successes, 0 failures, 0 skipped) in 5 minutes, 7.620 seconds    │
build	03-Dec-2025 16:08:33	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/reports/tests/testTask0/index.html│
build	03-Dec-2025 16:08:33	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	03-Dec-2025 16:08:33	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 53.259 seconds       │
build	03-Dec-2025 16:08:33	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/reports/tests/testTask1/index.html│
build	03-Dec-2025 16:08:33	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	03-Dec-2025 16:08:33	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 5.211 seconds                     │
build	03-Dec-2025 16:08:33	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/reports/tests/testTask2/index.html│
build	03-Dec-2025 16:08:33	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	03-Dec-2025 16:08:33	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 4.138 seconds        │
build	03-Dec-2025 16:08:33	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/reports/tests/testTask3/index.html│
build	03-Dec-2025 16:08:33	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	03-Dec-2025 16:08:33	│OVERALL: results: SUCCESS (1922 tests, 1922 successes, 0 failures, 0 skipped) in 8 minutes, 70.228 seconds            │
build	03-Dec-2025 16:08:33	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	03-Dec-2025 16:08:33	
build	03-Dec-2025 16:08:33	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	03-Dec-2025 16:08:33	
build	03-Dec-2025 16:08:33	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	03-Dec-2025 16:08:33	
build	03-Dec-2025 16:08:33	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	03-Dec-2025 16:08:33	
build	03-Dec-2025 16:08:33	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	03-Dec-2025 16:08:33	Please consult deprecation warnings for more details.
build	03-Dec-2025 16:08:33	
build	03-Dec-2025 16:08:33	BUILD SUCCESSFUL in 10m 21s
build	03-Dec-2025 16:08:33	21 actionable tasks: 20 executed, 1 up-to-date
simple	03-Dec-2025 16:08:33	Finished task 'Run tests with openclover under gradle' with result: Success
simple	03-Dec-2025 16:08:33	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	03-Dec-2025 16:08:33	Bamboo Artifactory Plugin version: 2.6.2
command	03-Dec-2025 16:08:33	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4603_Export_files_missing_part_of_sequence - Clover and Tests #4 (JB-GDB733-JOB1-4)'\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-GDB733-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_repository_revision_number=db868848b73d9a08f5ee1b08a269436a41323446\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB733-JOB1-4\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-GDB733-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB733-JOB1\nbamboo_shortPlanName=bug-JAL-4603_Export_files_missing_part_of_sequence\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=4\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-GDB733-JOB1-4\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4603_Export_files_missing_part_of_sequence\nbamboo_shortPlanKey=GDB733\nbamboo_repository_46498613_revision_number=db868848b73d9a08f5ee1b08a269436a41323446\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498613_git_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=db868848b73d9a08f5ee1b08a269436a41323446\nbamboo_buildTimeStamp=2025-12-03T15:58:10.388Z\nbamboo_repository_previous_revision_number=6343fb679e94dec0d94366f19ed793109bc79aed\nbamboo_planRepository_previousRevision=6343fb679e94dec0d94366f19ed793109bc79aed\nbamboo_repository_git_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_buildResultKey=JB-GDB733-JOB1-4\nbamboo_repository_branch_name=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4603_Export_files_missing_part_of_sequence - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=db868848b73d9a08f5ee1b08a269436a41323446\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_repository_46498613_git_username=\nbamboo_repository_46498613_previous_revision_number=6343fb679e94dec0d94366f19ed793109bc79aed\nbamboo_planRepository_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_46498613_branch_name=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=6343fb679e94dec0d94366f19ed793109bc79aed\nbamboo_planRepository_branchDisplayName=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4603_Export_files_missing_part_of_sequence\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-46302795\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46498613_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\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_46498613_name=Jalview Gitlab\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-GDB733-JOB1\nbamboo_planKey=JB-GDB733\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4603_Export_files_missing_part_of_sequence\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	03-Dec-2025 16:08:33	444
build	03-Dec-2025 16:08:42	
build	03-Dec-2025 16:08:42	> Configure project :
build	03-Dec-2025 16:08:42	Using properties from file './utils/channels/default/channel_gradle.properties'
build	03-Dec-2025 16:08:42	JALVIEW_VERSION is set to '2.11.5.1'
build	03-Dec-2025 16:08:42	HEADLESS BUILD
build	03-Dec-2025 16:08:42	J2S ENABLED
build	03-Dec-2025 16:08:42	Using a LOCAL profile.
build	03-Dec-2025 16:08:43	eclipseDir exists
build	03-Dec-2025 16:08:46	
build	03-Dec-2025 16:08:46	> Task :cloverHtmlReport
build	03-Dec-2025 16:08:46	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	03-Dec-2025 16:08:48	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/reports/clover'
build	03-Dec-2025 16:09:43	Done. Processed 117 packages in 55369ms (473ms per package).
build	03-Dec-2025 16:09:49	
build	03-Dec-2025 16:09:49	> Task :cloverXmlReport
build	03-Dec-2025 16:09:49	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	03-Dec-2025 16:09:52	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/reports/clover/clover.xml'
build	03-Dec-2025 16:09:52	
build	03-Dec-2025 16:09:52	> Task :cloverReport
build	03-Dec-2025 16:09:52	
build	03-Dec-2025 16:09:52	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	03-Dec-2025 16:09:52	
build	03-Dec-2025 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	03-Dec-2025 16:09:52	
build	03-Dec-2025 16:09:52	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	03-Dec-2025 16:09:52	
build	03-Dec-2025 16:09:52	BUILD SUCCESSFUL in 1m 18s
build	03-Dec-2025 16:09:52	2 actionable tasks: 2 executed
simple	03-Dec-2025 16:09:52	Finished task 'Clover Report' with result: Success
simple	03-Dec-2025 16:09:52	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	03-Dec-2025 16:09:52	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1...
simple	03-Dec-2025 16:09:52	Finished task 'TestNG Parser' with result: Success
simple	03-Dec-2025 16:09:52	Running post build plugin 'NCover Results Collector'
simple	03-Dec-2025 16:09:52	Running post build plugin 'Artifact Copier'
simple	03-Dec-2025 16:09:52	Publishing an artifact: Clover Report (System)
simple	03-Dec-2025 16:09:58	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 5.966 s
simple	03-Dec-2025 16:09:58	Publishing an artifact: TestNG report
error	03-Dec-2025 16:09:58	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB733-JOB1/build/reports/tests/test does not exist.
simple	03-Dec-2025 16:09:58	The artifact hasn't been successfully published after 3.941 ms
simple	03-Dec-2025 16:09:58	Running post build plugin 'Artifactory Release Management Staging'
simple	03-Dec-2025 16:09:58	Running post build plugin 'Artifactory Build Info Copier'
simple	03-Dec-2025 16:09:58	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	03-Dec-2025 16:09:58	Running post build plugin 'npm Cache Cleanup'
simple	03-Dec-2025 16:09:58	Running post build plugin 'Clover Results Collector'
simple	03-Dec-2025 16:09:58	Running post build plugin 'Docker Container Cleanup'
simple	03-Dec-2025 16:09:58	Finalising the build...
simple	03-Dec-2025 16:09:58	Stopping timer.
simple	03-Dec-2025 16:09:58	Build JB-GDB733-JOB1-4 completed.
simple	03-Dec-2025 16:09:58	Running on server: post build plugin 'NCover Results Collector'
simple	03-Dec-2025 16:09:58	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	03-Dec-2025 16:09:58	Running on server: post build plugin 'Clover Delta Calculator'
simple	03-Dec-2025 16:09:58	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	03-Dec-2025 16:09:58	All post build plugins have finished
simple	03-Dec-2025 16:09:58	Generating build results summary...
simple	03-Dec-2025 16:09:59	Saving build results to disk...
simple	03-Dec-2025 16:09:59	Logging substituted variables...
simple	03-Dec-2025 16:10:00	Indexing build results...
simple	03-Dec-2025 16:10:00	Finished building JB-GDB733-JOB1-4.