simple 03-Dec-2025 16:46:51 Build Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #4 (JB-GDB731-JOB1-4) started building on agent Default Agent simple 03-Dec-2025 16:46:51 simple 03-Dec-2025 16:46:51 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1 simple 03-Dec-2025 16:46:51 Executing build Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #4 (JB-GDB731-JOB1-4) simple 03-Dec-2025 16:46:51 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 03-Dec-2025 16:46:51 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1 simple 03-Dec-2025 16:46:51 Updating source code to revision: 4d0c90d7e29c7842bd1b903abe465f22d9853a4f simple 03-Dec-2025 16:46:51 Fetching 'refs/heads/development/Release_2_11_5_Branch' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 03-Dec-2025 16:46:52 Checking out revision 4d0c90d7e29c7842bd1b903abe465f22d9853a4f. simple 03-Dec-2025 16:46:52 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 03-Dec-2025 16:46:52 fae9009..4d0c90d development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch simple 03-Dec-2025 16:46:52 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 16:46:52 aca2c5f..7d35e28 development/Release_2_12_Branch -> origin/development/Release_2_12_Branch simple 03-Dec-2025 16:46:52 a66e20b..c586364 releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch simple 03-Dec-2025 16:46:52 Already on 'development/Release_2_11_5_Branch' simple 03-Dec-2025 16:46:52 Your branch is behind 'origin/development/Release_2_11_5_Branch' by 8 commits, and can be fast-forwarded. simple 03-Dec-2025 16:46:52 (use "git pull" to update your local branch) simple 03-Dec-2025 16:46:53 HEAD is now at 4d0c90d JAL-4603 added addional patch and relocated the test data simple 03-Dec-2025 16:46:53 Updated source code to revision: 4d0c90d7e29c7842bd1b903abe465f22d9853a4f simple 03-Dec-2025 16:46:53 Finished task 'Checkout Default Repository' with result: Success simple 03-Dec-2025 16:46:53 Running pre-build action: VCS Version Collector simple 03-Dec-2025 16:46:53 Running pre-build action: Artifactory Release Staging simple 03-Dec-2025 16:46:53 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 03-Dec-2025 16:46:53 Bamboo Artifactory Plugin version: 2.6.2 command 03-Dec-2025 16:46:53 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #4 (JB-GDB731-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-GDB731-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_11_5_Branch\nbamboo_repository_46498610_previous_revision_number=fae900933e918d9f3670c0c005d2c2a75190058e\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_repository_revision_number=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB731-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-GDB731-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB731-JOB1\nbamboo_repository_46498610_git_username=\nbamboo_shortPlanName=development-Release_2_11_5_Branch\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-GDB731-JOB1-4\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498610_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch\nbamboo_repository_46498610_revision_number=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\nbamboo_shortPlanKey=GDB731\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\nbamboo_buildTimeStamp=2025-12-03T16:36:58.097Z\nbamboo_repository_previous_revision_number=fae900933e918d9f3670c0c005d2c2a75190058e\nbamboo_planRepository_previousRevision=fae900933e918d9f3670c0c005d2c2a75190058e\nbamboo_repository_git_branch=development/Release_2_11_5_Branch\nbamboo_buildResultKey=JB-GDB731-JOB1-4\nbamboo_repository_branch_name=development/Release_2_11_5_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\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_46498610_branch_name=development/Release_2_11_5_Branch\nbamboo_planRepository_branch=development/Release_2_11_5_Branch\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=fae900933e918d9f3670c0c005d2c2a75190058e\nbamboo_repository_46498610_git_branch=development/Release_2_11_5_Branch\nbamboo_planRepository_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=development/Release_2_11_5_Branch\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-46302791\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_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-GDB731-JOB1\nbamboo_planKey=JB-GDB731\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498610_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=development/Release_2_11_5_Branch\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 16:46:53 444 build 03-Dec-2025 16:46:54 build 03-Dec-2025 16:46:54 > Configure project : build 03-Dec-2025 16:46:54 Using properties from file './utils/channels/default/channel_gradle.properties' build 03-Dec-2025 16:46:54 JALVIEW_VERSION is set to '2.11.5.1' build 03-Dec-2025 16:46:54 HEADLESS BUILD build 03-Dec-2025 16:46:54 J2S ENABLED build 03-Dec-2025 16:46:54 Using a LOCAL profile. build 03-Dec-2025 16:46:54 eclipseDir exists build 03-Dec-2025 16:46:56 build 03-Dec-2025 16:46:56 > Task :clean build 03-Dec-2025 16:46:56 > Task :cleanClover build 03-Dec-2025 16:46:56 > Task :cleanTest UP-TO-DATE build 03-Dec-2025 16:46:58 build 03-Dec-2025 16:46:58 > Task :cloverInstrJava build 03-Dec-2025 16:46:58 Clover: About to instrument 1109 files build 03-Dec-2025 16:46:58 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Dec-2025 16:46:58 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover.db'. build 03-Dec-2025 16:46:58 Processing files at 1.9 source level. error 03-Dec-2025 16:47:02 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 16:47:02 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 16:47:02 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 16:47:02 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 16:47:02 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 16:47:02 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 16:47:02 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 16:47:10 Clover all over. Instrumented 1109 files (113 packages). build 03-Dec-2025 16:47:12 build 03-Dec-2025 16:47:12 > Task :cloverInstrTests build 03-Dec-2025 16:47:12 Clover: About to instrument test files build 03-Dec-2025 16:47:12 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Dec-2025 16:47:12 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover.db'. build 03-Dec-2025 16:47:12 Processing files at 1.9 source level. build 03-Dec-2025 16:47:16 Clover all over. Instrumented 293 files (52 packages). build 03-Dec-2025 16:47:16 1627 test methods detected. build 03-Dec-2025 16:47:16 build 03-Dec-2025 16:47:16 > Task :cloverInstr build 03-Dec-2025 16:47:18 build 03-Dec-2025 16:47:18 > Task :compileCloverJava build 03-Dec-2025 16:47:18 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 03-Dec-2025 16:47:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:47:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:47:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:47:18 Setting target compatibility to 11 error 03-Dec-2025 16:47:35 Note: Some input files use or override a deprecated API. error 03-Dec-2025 16:47:35 Note: Recompile with -Xlint:deprecation for details. error 03-Dec-2025 16:47:35 Note: Some input files use unchecked or unsafe operations. error 03-Dec-2025 16:47:35 Note: Recompile with -Xlint:unchecked for details. build 03-Dec-2025 16:47:42 build 03-Dec-2025 16:47:42 > Task :processCloverResources NO-SOURCE build 03-Dec-2025 16:47:42 > Task :cloverClasses build 03-Dec-2025 16:47:42 > Task :copyHelp build 03-Dec-2025 16:47:44 > Task :buildIndices build 03-Dec-2025 16:47:44 > Task :copyResources build 03-Dec-2025 16:47:44 > Task :copyChannelResources build 03-Dec-2025 16:47:44 build 03-Dec-2025 16:47:44 > Task :createBuildProperties build 03-Dec-2025 16:47:44 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 03-Dec-2025 16:47:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:47:44 build 03-Dec-2025 16:47:44 > Task :buildResources build 03-Dec-2025 16:47:44 > Task :copyDocs build 03-Dec-2025 16:47:44 build 03-Dec-2025 16:47:44 > Task :convertMdFiles build 03-Dec-2025 16:47:44 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 03-Dec-2025 16:47:44 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/releaseprocess.html build 03-Dec-2025 16:47:44 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 03-Dec-2025 16:47:44 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/building.html build 03-Dec-2025 16:47:44 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/resources/doc_build/doc/jalview-projects.html build 03-Dec-2025 16:47:45 build 03-Dec-2025 16:47:45 > Task :releasesTemplates build 03-Dec-2025 16:47:45 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 03-Dec-2025 16:47:45 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:47:45 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:47:45 Stripping rc/test/etc for TEST build 03-Dec-2025 16:47:45 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 03-Dec-2025 16:47:45 build 03-Dec-2025 16:47:45 > Task :prepare build 03-Dec-2025 16:47:47 build 03-Dec-2025 16:47:47 > Task :compileJava build 03-Dec-2025 16:47:47 Setting target compatibility to 11 error 03-Dec-2025 16:47:53 Note: Some input files use or override a deprecated API. error 03-Dec-2025 16:47:53 Note: Recompile with -Xlint:deprecation for details. error 03-Dec-2025 16:47:53 Note: Some input files use unchecked or unsafe operations. error 03-Dec-2025 16:47:53 Note: Recompile with -Xlint:unchecked for details. build 03-Dec-2025 16:47:55 build 03-Dec-2025 16:47:55 > Task :compileTestJava build 03-Dec-2025 16:47:55 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 03-Dec-2025 16:47:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:47:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:47:55 Setting target compatibility to 11 error 03-Dec-2025 16:48:01 Note: Some input files use or override a deprecated API. error 03-Dec-2025 16:48:01 Note: Recompile with -Xlint:deprecation for details. error 03-Dec-2025 16:48:01 Note: Some input files use unchecked or unsafe operations. error 03-Dec-2025 16:48:01 Note: Recompile with -Xlint:unchecked for details. build 03-Dec-2025 16:48:02 build 03-Dec-2025 16:48:02 > Task :processTestResources build 03-Dec-2025 16:48:02 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 03-Dec-2025 16:48:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:48:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:48:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:48:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:48:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:48:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:48:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:48:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-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 16:48:02 build 03-Dec-2025 16:48:02 > Task :testClasses build 03-Dec-2025 16:48:04 build 03-Dec-2025 16:48:04 > Task :testTask0 build 03-Dec-2025 16:48:04 Running tests WITH clover error 03-Dec-2025 16:48:08 WARNING: An illegal reflective access operation has occurred error 03-Dec-2025 16:48:08 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 03-Dec-2025 16:48:08 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 03-Dec-2025 16:48:08 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 03-Dec-2025 16:48:08 WARNING: All illegal access operations will be denied in a future release build 03-Dec-2025 16:53:01 build 03-Dec-2025 16:53:01 > Task :testTask1 build 03-Dec-2025 16:53:01 Running tests WITH clover error 03-Dec-2025 16:53:03 WARNING: An illegal reflective access operation has occurred error 03-Dec-2025 16:53:03 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 03-Dec-2025 16:53:03 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 03-Dec-2025 16:53:03 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 03-Dec-2025 16:53:03 WARNING: All illegal access operations will be denied in a future release build 03-Dec-2025 16:55:38 build 03-Dec-2025 16:55:38 > Task :testTask2 build 03-Dec-2025 16:55:38 Running tests WITH clover build 03-Dec-2025 16:55:43 build 03-Dec-2025 16:55:43 > Task :testTask3 build 03-Dec-2025 16:55:43 Running tests WITH clover error 03-Dec-2025 16:55:44 WARNING: An illegal reflective access operation has occurred error 03-Dec-2025 16:55:44 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 03-Dec-2025 16:55:44 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 03-Dec-2025 16:55:44 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 03-Dec-2025 16:55:44 WARNING: All illegal access operations will be denied in a future release build 03-Dec-2025 16:56:44 build 03-Dec-2025 16:56:44 > Task :test NO-SOURCE build 03-Dec-2025 16:56:44 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 03-Dec-2025 16:56:44 │jalview:testTask0 results: SUCCESS (1834 tests, 1834 successes, 0 failures, 0 skipped) in 4 minutes, 55.985 seconds │ build 03-Dec-2025 16:56:44 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask0/index.html│ build 03-Dec-2025 16:56:44 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Dec-2025 16:56:44 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 37.624 seconds │ build 03-Dec-2025 16:56:44 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask1/index.html│ build 03-Dec-2025 16:56:44 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Dec-2025 16:56:44 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.272 seconds │ build 03-Dec-2025 16:56:44 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask2/index.html│ build 03-Dec-2025 16:56:44 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Dec-2025 16:56:44 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 2.996 seconds │ build 03-Dec-2025 16:56:44 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/testTask3/index.html│ build 03-Dec-2025 16:56:44 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Dec-2025 16:56:44 │OVERALL: results: SUCCESS (1922 tests, 1922 successes, 0 failures, 0 skipped) in 7 minutes, 100.877 seconds │ build 03-Dec-2025 16:56:44 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 03-Dec-2025 16:56:44 build 03-Dec-2025 16:56:44 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 03-Dec-2025 16:56:44 build 03-Dec-2025 16:56:44 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 03-Dec-2025 16:56:44 build 03-Dec-2025 16:56:44 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 03-Dec-2025 16:56:44 build 03-Dec-2025 16:56:44 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 03-Dec-2025 16:56:44 Please consult deprecation warnings for more details. build 03-Dec-2025 16:56:44 build 03-Dec-2025 16:56:44 BUILD SUCCESSFUL in 9m 51s build 03-Dec-2025 16:56:44 21 actionable tasks: 20 executed, 1 up-to-date simple 03-Dec-2025 16:56:45 Finished task 'Run tests with openclover under gradle' with result: Success simple 03-Dec-2025 16:56:45 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 03-Dec-2025 16:56:45 Bamboo Artifactory Plugin version: 2.6.2 command 03-Dec-2025 16:56:45 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests #4 (JB-GDB731-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-GDB731-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_11_5_Branch\nbamboo_repository_46498610_previous_revision_number=fae900933e918d9f3670c0c005d2c2a75190058e\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_repository_revision_number=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB731-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-GDB731-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB731-JOB1\nbamboo_repository_46498610_git_username=\nbamboo_shortPlanName=development-Release_2_11_5_Branch\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-GDB731-JOB1-4\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498610_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch\nbamboo_repository_46498610_revision_number=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\nbamboo_shortPlanKey=GDB731\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\nbamboo_buildTimeStamp=2025-12-03T16:36:58.097Z\nbamboo_repository_previous_revision_number=fae900933e918d9f3670c0c005d2c2a75190058e\nbamboo_planRepository_previousRevision=fae900933e918d9f3670c0c005d2c2a75190058e\nbamboo_repository_git_branch=development/Release_2_11_5_Branch\nbamboo_buildResultKey=JB-GDB731-JOB1-4\nbamboo_repository_branch_name=development/Release_2_11_5_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - development-Release_2_11_5_Branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=4d0c90d7e29c7842bd1b903abe465f22d9853a4f\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_46498610_branch_name=development/Release_2_11_5_Branch\nbamboo_planRepository_branch=development/Release_2_11_5_Branch\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=fae900933e918d9f3670c0c005d2c2a75190058e\nbamboo_repository_46498610_git_branch=development/Release_2_11_5_Branch\nbamboo_planRepository_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=development/Release_2_11_5_Branch\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-46302791\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_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-GDB731-JOB1\nbamboo_planKey=JB-GDB731\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498610_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=development/Release_2_11_5_Branch\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 16:56:45 444 build 03-Dec-2025 16:56:53 build 03-Dec-2025 16:56:53 > Configure project : build 03-Dec-2025 16:56:53 Using properties from file './utils/channels/default/channel_gradle.properties' build 03-Dec-2025 16:56:53 JALVIEW_VERSION is set to '2.11.5.1' build 03-Dec-2025 16:56:53 HEADLESS BUILD build 03-Dec-2025 16:56:53 J2S ENABLED build 03-Dec-2025 16:56:53 Using a LOCAL profile. build 03-Dec-2025 16:56:54 eclipseDir exists build 03-Dec-2025 16:56:56 build 03-Dec-2025 16:56:56 > Task :cloverHtmlReport build 03-Dec-2025 16:56:56 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Dec-2025 16:56:58 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/clover' build 03-Dec-2025 16:57:57 Done. Processed 117 packages in 57895ms (494ms per package). build 03-Dec-2025 16:58:04 build 03-Dec-2025 16:58:04 > Task :cloverXmlReport build 03-Dec-2025 16:58:04 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Dec-2025 16:58:08 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/clover/clover.xml' build 03-Dec-2025 16:58:08 build 03-Dec-2025 16:58:08 > Task :cloverReport build 03-Dec-2025 16:58:08 build 03-Dec-2025 16:58:08 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 03-Dec-2025 16:58:08 build 03-Dec-2025 16:58:08 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 16:58:08 build 03-Dec-2025 16:58:08 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 03-Dec-2025 16:58:08 build 03-Dec-2025 16:58:08 BUILD SUCCESSFUL in 1m 23s build 03-Dec-2025 16:58:08 2 actionable tasks: 2 executed simple 03-Dec-2025 16:58:08 Finished task 'Clover Report' with result: Success simple 03-Dec-2025 16:58:08 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 03-Dec-2025 16:58:08 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1... simple 03-Dec-2025 16:58:08 Finished task 'TestNG Parser' with result: Success simple 03-Dec-2025 16:58:08 Running post build plugin 'NCover Results Collector' simple 03-Dec-2025 16:58:08 Running post build plugin 'Artifact Copier' simple 03-Dec-2025 16:58:08 Publishing an artifact: Clover Report (System) simple 03-Dec-2025 16:58:14 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 6.493 s simple 03-Dec-2025 16:58:14 Publishing an artifact: TestNG report error 03-Dec-2025 16:58:14 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB731-JOB1/build/reports/tests/test does not exist. simple 03-Dec-2025 16:58:14 The artifact hasn't been successfully published after 4.727 ms simple 03-Dec-2025 16:58:14 Running post build plugin 'Artifactory Release Management Staging' simple 03-Dec-2025 16:58:14 Running post build plugin 'Artifactory Build Info Copier' simple 03-Dec-2025 16:58:14 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 03-Dec-2025 16:58:14 Running post build plugin 'npm Cache Cleanup' simple 03-Dec-2025 16:58:14 Running post build plugin 'Clover Results Collector' simple 03-Dec-2025 16:58:14 Running post build plugin 'Docker Container Cleanup' simple 03-Dec-2025 16:58:14 Finalising the build... simple 03-Dec-2025 16:58:14 Stopping timer. simple 03-Dec-2025 16:58:14 Build JB-GDB731-JOB1-4 completed. simple 03-Dec-2025 16:58:14 Running on server: post build plugin 'NCover Results Collector' simple 03-Dec-2025 16:58:14 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 03-Dec-2025 16:58:14 Running on server: post build plugin 'Clover Delta Calculator' simple 03-Dec-2025 16:58:15 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 03-Dec-2025 16:58:15 All post build plugins have finished simple 03-Dec-2025 16:58:15 Generating build results summary... simple 03-Dec-2025 16:58:16 Saving build results to disk... simple 03-Dec-2025 16:58:16 Logging substituted variables... simple 03-Dec-2025 16:58:16 Indexing build results... simple 03-Dec-2025 16:58:16 Finished building JB-GDB731-JOB1-4.