simple 27-Nov-2025 16:51:07 Build Jalview Builds - Gradle Develop Build - patch-JAL-4601_stk_ss_annots_showhide - Clover and Tests #1 (JB-GDB730-JOB1-1) started building on agent Default Agent simple 27-Nov-2025 16:51:07 simple 27-Nov-2025 16:51:08 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1 simple 27-Nov-2025 16:51:08 Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4601_stk_ss_annots_showhide - Clover and Tests #1 (JB-GDB730-JOB1-1) simple 27-Nov-2025 16:51:08 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 27-Nov-2025 16:51:08 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1 simple 27-Nov-2025 16:51:08 Updating source code to revision: 3640cfb3a1a72b0a7514f5406b223cad955aa1fc simple 27-Nov-2025 16:51:08 Fetching 'refs/heads/patch/JAL-4601_stk_ss_annots_showhide' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 27-Nov-2025 16:51:09 Checking out revision 3640cfb3a1a72b0a7514f5406b223cad955aa1fc. simple 27-Nov-2025 16:51:09 Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/.git'. simple 27-Nov-2025 16:51:09 Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1'... simple 27-Nov-2025 16:51:09 done. simple 27-Nov-2025 16:51:16 Branch patch/JAL-4601_stk_ss_annots_showhide set up to track remote branch patch/JAL-4601_stk_ss_annots_showhide from origin. simple 27-Nov-2025 16:51:16 Switched to a new branch 'patch/JAL-4601_stk_ss_annots_showhide' simple 27-Nov-2025 16:51:16 Updated source code to revision: 3640cfb3a1a72b0a7514f5406b223cad955aa1fc simple 27-Nov-2025 16:51:16 Finished task 'Checkout Default Repository' with result: Success simple 27-Nov-2025 16:51:16 Running pre-build action: VCS Version Collector simple 27-Nov-2025 16:51:16 Running pre-build action: Artifactory Release Staging simple 27-Nov-2025 16:51:16 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 27-Nov-2025 16:51:16 Bamboo Artifactory Plugin version: 2.6.2 command 27-Nov-2025 16:51:16 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4601_stk_ss_annots_showhide - Clover and Tests #1 (JB-GDB730-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4601_stk_ss_annots_showhide\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4601_stk_ss_annots_showhide\nbamboo_repository_revision_number=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB730-JOB1-1\nbamboo_repository_46498605_git_branch=patch/JAL-4601_stk_ss_annots_showhide\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_46498605_branch_name=patch/JAL-4601_stk_ss_annots_showhide\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB730-JOB1\nbamboo_shortPlanName=patch-JAL-4601_stk_ss_annots_showhide\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB730-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4601_stk_ss_annots_showhide\nbamboo_shortPlanKey=GDB730\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\nbamboo_repository_previous_revision_number=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\nbamboo_buildTimeStamp=2025-11-27T16:51:07.875Z\nbamboo_planRepository_previousRevision=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\nbamboo_repository_git_branch=patch/JAL-4601_stk_ss_annots_showhide\nbamboo_buildResultKey=JB-GDB730-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4601_stk_ss_annots_showhide\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4601_stk_ss_annots_showhide - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498605_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_1_revision=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\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-4601_stk_ss_annots_showhide\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=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\nbamboo_planRepository_branchDisplayName=patch/JAL-4601_stk_ss_annots_showhide\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4601_stk_ss_annots_showhide\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-46302781\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_46498605_git_username=\nbamboo_repository_46498605_previous_revision_number=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\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-GDB730-JOB1\nbamboo_planKey=JB-GDB730\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498605_revision_number=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\nbamboo_repository_46498605_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4601_stk_ss_annots_showhide\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 27-Nov-2025 16:51:16 444 build 27-Nov-2025 16:51:20 build 27-Nov-2025 16:51:20 > Configure project : build 27-Nov-2025 16:51:20 Using properties from file './utils/channels/default/channel_gradle.properties' build 27-Nov-2025 16:51:20 JALVIEW_VERSION is set to '2.11.5.1' build 27-Nov-2025 16:51:20 HEADLESS BUILD build 27-Nov-2025 16:51:20 J2S ENABLED build 27-Nov-2025 16:51:20 Using a LOCAL profile. build 27-Nov-2025 16:51:20 eclipseDir exists build 27-Nov-2025 16:51:20 build 27-Nov-2025 16:51:20 > Task :clean build 27-Nov-2025 16:51:20 > Task :cleanClover build 27-Nov-2025 16:51:20 > Task :cleanTest UP-TO-DATE build 27-Nov-2025 16:51:22 build 27-Nov-2025 16:51:22 > Task :cloverInstrJava build 27-Nov-2025 16:51:22 Clover: About to instrument 1107 files build 27-Nov-2025 16:51:22 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 27-Nov-2025 16:51:22 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/clover/clover.db'. build 27-Nov-2025 16:51:22 Processing files at 1.9 source level. error 27-Nov-2025 16:51:27 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 27-Nov-2025 16:51:27 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 27-Nov-2025 16:51:27 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 27-Nov-2025 16:51:27 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 27-Nov-2025 16:51:27 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 27-Nov-2025 16:51:27 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 27-Nov-2025 16:51:27 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 27-Nov-2025 16:51:34 Clover all over. Instrumented 1107 files (112 packages). build 27-Nov-2025 16:51:36 build 27-Nov-2025 16:51:36 > Task :cloverInstrTests build 27-Nov-2025 16:51:36 Clover: About to instrument test files build 27-Nov-2025 16:51:36 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 27-Nov-2025 16:51:36 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/clover/clover.db'. build 27-Nov-2025 16:51:36 Processing files at 1.9 source level. build 27-Nov-2025 16:51:39 Clover all over. Instrumented 293 files (52 packages). build 27-Nov-2025 16:51:39 1624 test methods detected. build 27-Nov-2025 16:51:39 build 27-Nov-2025 16:51:39 > Task :cloverInstr build 27-Nov-2025 16:51:43 build 27-Nov-2025 16:51:43 > Task :compileCloverJava build 27-Nov-2025 16:51:43 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 27-Nov-2025 16:51:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:51:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:51:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:51:43 Setting target compatibility to 11 error 27-Nov-2025 16:52:02 Note: Some input files use or override a deprecated API. error 27-Nov-2025 16:52:02 Note: Recompile with -Xlint:deprecation for details. error 27-Nov-2025 16:52:02 Note: Some input files use unchecked or unsafe operations. error 27-Nov-2025 16:52:02 Note: Recompile with -Xlint:unchecked for details. build 27-Nov-2025 16:52:09 build 27-Nov-2025 16:52:09 > Task :processCloverResources NO-SOURCE build 27-Nov-2025 16:52:09 > Task :cloverClasses build 27-Nov-2025 16:52:09 > Task :copyHelp build 27-Nov-2025 16:52:11 > Task :buildIndices build 27-Nov-2025 16:52:11 > Task :copyResources build 27-Nov-2025 16:52:11 > Task :copyChannelResources build 27-Nov-2025 16:52:11 build 27-Nov-2025 16:52:11 > Task :createBuildProperties build 27-Nov-2025 16:52:11 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 27-Nov-2025 16:52:11 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:52:11 build 27-Nov-2025 16:52:11 > Task :buildResources build 27-Nov-2025 16:52:11 > Task :copyDocs build 27-Nov-2025 16:52:11 build 27-Nov-2025 16:52:11 > Task :convertMdFiles build 27-Nov-2025 16:52:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 27-Nov-2025 16:52:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/resources/doc_build/doc/releaseprocess.html build 27-Nov-2025 16:52:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 27-Nov-2025 16:52:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/resources/doc_build/doc/building.html build 27-Nov-2025 16:52:11 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/resources/doc_build/doc/jalview-projects.html build 27-Nov-2025 16:52:11 build 27-Nov-2025 16:52:11 > Task :releasesTemplates build 27-Nov-2025 16:52:11 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 27-Nov-2025 16:52:11 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:52:11 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:52:11 Stripping rc/test/etc for TEST build 27-Nov-2025 16:52:11 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 27-Nov-2025 16:52:11 build 27-Nov-2025 16:52:11 > Task :prepare build 27-Nov-2025 16:52:13 build 27-Nov-2025 16:52:13 > Task :compileJava build 27-Nov-2025 16:52:13 Setting target compatibility to 11 error 27-Nov-2025 16:52:19 Note: Some input files use or override a deprecated API. error 27-Nov-2025 16:52:19 Note: Recompile with -Xlint:deprecation for details. error 27-Nov-2025 16:52:19 Note: Some input files use unchecked or unsafe operations. error 27-Nov-2025 16:52:19 Note: Recompile with -Xlint:unchecked for details. build 27-Nov-2025 16:52:22 build 27-Nov-2025 16:52:22 > Task :compileTestJava build 27-Nov-2025 16:52:22 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 27-Nov-2025 16:52:22 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:52:22 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:52:22 Setting target compatibility to 11 error 27-Nov-2025 16:52:27 Note: Some input files use or override a deprecated API. error 27-Nov-2025 16:52:27 Note: Recompile with -Xlint:deprecation for details. error 27-Nov-2025 16:52:27 Note: Some input files use unchecked or unsafe operations. error 27-Nov-2025 16:52:27 Note: Recompile with -Xlint:unchecked for details. build 27-Nov-2025 16:52:28 build 27-Nov-2025 16:52:28 > Task :processTestResources build 27-Nov-2025 16:52:28 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 27-Nov-2025 16:52:28 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:52:28 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:52:28 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:52:28 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:52:28 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:52:28 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:52:28 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-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 27-Nov-2025 16:52:28 build 27-Nov-2025 16:52:28 > Task :testClasses build 27-Nov-2025 16:52:30 build 27-Nov-2025 16:52:30 > Task :testTask0 build 27-Nov-2025 16:52:30 Running tests WITH clover error 27-Nov-2025 16:52:33 WARNING: An illegal reflective access operation has occurred error 27-Nov-2025 16:52:33 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 27-Nov-2025 16:52:33 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 27-Nov-2025 16:52:33 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 27-Nov-2025 16:52:33 WARNING: All illegal access operations will be denied in a future release build 27-Nov-2025 16:57:22 build 27-Nov-2025 16:57:22 > Task :testTask1 build 27-Nov-2025 16:57:22 Running tests WITH clover error 27-Nov-2025 16:57:24 WARNING: An illegal reflective access operation has occurred error 27-Nov-2025 16:57:24 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 27-Nov-2025 16:57:24 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 27-Nov-2025 16:57:24 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 27-Nov-2025 16:57:24 WARNING: All illegal access operations will be denied in a future release build 27-Nov-2025 16:57:28 build 27-Nov-2025 16:57:28 Gradle suite > Gradle test > jalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges[0](./test/files/annotation_label_width/sample.a2m, false, 50, 70, 100, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb, ./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json, true, pLDDT, null, 114, 117) FAILED build 27-Nov-2025 16:57:28 java.lang.AssertionError: idWidth is not set to the manually set width 100 expected [100] but found [68] build 27-Nov-2025 16:57:28 at org.testng.Assert.fail(Assert.java:94) build 27-Nov-2025 16:57:28 at org.testng.Assert.failNotEquals(Assert.java:496) build 27-Nov-2025 16:57:28 at org.testng.Assert.assertEquals(Assert.java:125) build 27-Nov-2025 16:57:28 at org.testng.Assert.assertEquals(Assert.java:372) build 27-Nov-2025 16:57:28 at jalview.gui.AnnotationLabelsTest2.__CLR4_4_1roan143tio(AnnotationLabelsTest2.java:202) build 27-Nov-2025 16:57:28 at jalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges(AnnotationLabelsTest2.java:171) error 27-Nov-2025 17:00:04 error 27-Nov-2025 17:00:04 62 tests completed, 1 failed build 27-Nov-2025 17:00:04 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/tests/testTask1/index.html build 27-Nov-2025 17:00:06 build 27-Nov-2025 17:00:06 > Task :testTask2 build 27-Nov-2025 17:00:06 Running tests WITH clover build 27-Nov-2025 17:00:11 build 27-Nov-2025 17:00:11 > Task :testTask3 build 27-Nov-2025 17:00:11 Running tests WITH clover error 27-Nov-2025 17:00:14 WARNING: An illegal reflective access operation has occurred error 27-Nov-2025 17:00:14 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 27-Nov-2025 17:00:14 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 27-Nov-2025 17:00:14 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 27-Nov-2025 17:00:14 WARNING: All illegal access operations will be denied in a future release build 27-Nov-2025 17:01:12 build 27-Nov-2025 17:01:12 > Task :test NO-SOURCE error 27-Nov-2025 17:01:12 error 27-Nov-2025 17:01:12 FAILURE: Build failed with an exception. error 27-Nov-2025 17:01:12 error 27-Nov-2025 17:01:12 * Where: error 27-Nov-2025 17:01:12 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build.gradle' line: 1967 error 27-Nov-2025 17:01:12 error 27-Nov-2025 17:01:12 * What went wrong: error 27-Nov-2025 17:01:12 Failed tests! error 27-Nov-2025 17:01:12 error 27-Nov-2025 17:01:12 * Try: error 27-Nov-2025 17:01:12 > Run with --stacktrace option to get the stack trace. error 27-Nov-2025 17:01:12 > Run with --info or --debug option to get more log output. error 27-Nov-2025 17:01:12 > Run with --scan to get full insights. error 27-Nov-2025 17:01:12 error 27-Nov-2025 17:01:12 * Get more help at https://help.gradle.org error 27-Nov-2025 17:01:12 error 27-Nov-2025 17:01:12 BUILD FAILED in 9m 55s build 27-Nov-2025 17:01:12 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 27-Nov-2025 17:01:12 │jalview:testTask0 results: SUCCESS (1824 tests, 1824 successes, 0 failures, 0 skipped) in 4 minutes, 50.988 seconds │ build 27-Nov-2025 17:01:12 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/tests/testTask0/index.html│ build 27-Nov-2025 17:01:12 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 27-Nov-2025 17:01:12 │jalview:testTask1 results: FAILURE (62 tests, 61 successes, 1 failures, 0 skipped) in 2 minutes, 43.876 seconds │ build 27-Nov-2025 17:01:12 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/tests/testTask1/index.html│ build 27-Nov-2025 17:01:12 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 27-Nov-2025 17:01:12 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.882 seconds │ build 27-Nov-2025 17:01:12 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/tests/testTask2/index.html│ build 27-Nov-2025 17:01:12 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 27-Nov-2025 17:01:12 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 3.400 seconds │ build 27-Nov-2025 17:01:12 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/tests/testTask3/index.html│ build 27-Nov-2025 17:01:12 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 27-Nov-2025 17:01:12 │OVERALL: results: FAILURE (1912 tests, 1911 successes, 1 failures, 0 skipped) in 7 minutes, 103.146 seconds │ build 27-Nov-2025 17:01:12 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 27-Nov-2025 17:01:12 build 27-Nov-2025 17:01:12 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 27-Nov-2025 17:01:12 build 27-Nov-2025 17:01:12 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 27-Nov-2025 17:01:12 build 27-Nov-2025 17:01:12 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 27-Nov-2025 17:01:12 build 27-Nov-2025 17:01:12 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 27-Nov-2025 17:01:12 Please consult deprecation warnings for more details. build 27-Nov-2025 17:01:12 21 actionable tasks: 20 executed, 1 up-to-date simple 27-Nov-2025 17:01:12 simple 27-Nov-2025 17:01:12 Failing task since return code of [/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test] was 1 while expected 0 simple 27-Nov-2025 17:01:12 Finished task 'Run tests with openclover under gradle' with result: Failed simple 27-Nov-2025 17:01:12 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 27-Nov-2025 17:01:12 Bamboo Artifactory Plugin version: 2.6.2 command 27-Nov-2025 17:01:12 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4601_stk_ss_annots_showhide - Clover and Tests #1 (JB-GDB730-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4601_stk_ss_annots_showhide\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4601_stk_ss_annots_showhide\nbamboo_repository_revision_number=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB730-JOB1-1\nbamboo_repository_46498605_git_branch=patch/JAL-4601_stk_ss_annots_showhide\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_46498605_branch_name=patch/JAL-4601_stk_ss_annots_showhide\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB730-JOB1\nbamboo_shortPlanName=patch-JAL-4601_stk_ss_annots_showhide\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB730-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4601_stk_ss_annots_showhide\nbamboo_shortPlanKey=GDB730\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\nbamboo_repository_previous_revision_number=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\nbamboo_buildTimeStamp=2025-11-27T16:51:07.875Z\nbamboo_planRepository_previousRevision=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\nbamboo_repository_git_branch=patch/JAL-4601_stk_ss_annots_showhide\nbamboo_buildResultKey=JB-GDB730-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4601_stk_ss_annots_showhide\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4601_stk_ss_annots_showhide - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498605_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_1_revision=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\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=true\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=patch/JAL-4601_stk_ss_annots_showhide\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\nbamboo_planRepository_branchDisplayName=patch/JAL-4601_stk_ss_annots_showhide\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4601_stk_ss_annots_showhide\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-46302781\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_46498605_git_username=\nbamboo_repository_46498605_previous_revision_number=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\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-GDB730-JOB1\nbamboo_planKey=JB-GDB730\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498605_revision_number=3640cfb3a1a72b0a7514f5406b223cad955aa1fc\nbamboo_repository_46498605_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4601_stk_ss_annots_showhide\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 27-Nov-2025 17:01:12 444 build 27-Nov-2025 17:01:20 build 27-Nov-2025 17:01:20 > Configure project : build 27-Nov-2025 17:01:20 Using properties from file './utils/channels/default/channel_gradle.properties' build 27-Nov-2025 17:01:20 JALVIEW_VERSION is set to '2.11.5.1' build 27-Nov-2025 17:01:21 HEADLESS BUILD build 27-Nov-2025 17:01:21 J2S ENABLED build 27-Nov-2025 17:01:21 Using a LOCAL profile. build 27-Nov-2025 17:01:22 eclipseDir exists build 27-Nov-2025 17:01:24 build 27-Nov-2025 17:01:24 > Task :cloverHtmlReport build 27-Nov-2025 17:01:24 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 27-Nov-2025 17:01:26 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/clover' build 27-Nov-2025 17:02:22 Done. Processed 116 packages in 55787ms (480ms per package). build 27-Nov-2025 17:02:31 build 27-Nov-2025 17:02:31 > Task :cloverXmlReport build 27-Nov-2025 17:02:31 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 27-Nov-2025 17:02:33 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/clover/clover.xml' build 27-Nov-2025 17:02:34 build 27-Nov-2025 17:02:34 > Task :cloverReport build 27-Nov-2025 17:02:34 build 27-Nov-2025 17:02:34 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 27-Nov-2025 17:02:34 build 27-Nov-2025 17:02:34 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 27-Nov-2025 17:02:34 build 27-Nov-2025 17:02:34 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 27-Nov-2025 17:02:34 build 27-Nov-2025 17:02:34 BUILD SUCCESSFUL in 1m 21s build 27-Nov-2025 17:02:34 2 actionable tasks: 2 executed simple 27-Nov-2025 17:02:34 Finished task 'Clover Report' with result: Success simple 27-Nov-2025 17:02:34 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 27-Nov-2025 17:02:34 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1... simple 27-Nov-2025 17:02:35 Failing task since 1 failing test cases were found. simple 27-Nov-2025 17:02:35 Finished task 'TestNG Parser' with result: Failed simple 27-Nov-2025 17:02:35 Running post build plugin 'NCover Results Collector' simple 27-Nov-2025 17:02:35 Running post build plugin 'Artifact Copier' simple 27-Nov-2025 17:02:35 Publishing an artifact: Clover Report (System) simple 27-Nov-2025 17:02:41 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 6.719 s simple 27-Nov-2025 17:02:41 Publishing an artifact: TestNG report error 27-Nov-2025 17:02:41 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB730-JOB1/build/reports/tests/test does not exist. simple 27-Nov-2025 17:02:41 The artifact hasn't been successfully published after 4.169 ms simple 27-Nov-2025 17:02:41 Running post build plugin 'Artifactory Release Management Staging' simple 27-Nov-2025 17:02:41 Running post build plugin 'Artifactory Build Info Copier' simple 27-Nov-2025 17:02:41 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 27-Nov-2025 17:02:41 Running post build plugin 'npm Cache Cleanup' simple 27-Nov-2025 17:02:41 Running post build plugin 'Clover Results Collector' simple 27-Nov-2025 17:02:41 Running post build plugin 'Docker Container Cleanup' simple 27-Nov-2025 17:02:41 Finalising the build... simple 27-Nov-2025 17:02:41 Stopping timer. simple 27-Nov-2025 17:02:41 Build JB-GDB730-JOB1-1 completed. simple 27-Nov-2025 17:02:41 Running on server: post build plugin 'NCover Results Collector' simple 27-Nov-2025 17:02:41 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 27-Nov-2025 17:02:41 Running on server: post build plugin 'Clover Delta Calculator' simple 27-Nov-2025 17:02:41 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 27-Nov-2025 17:02:41 All post build plugins have finished simple 27-Nov-2025 17:02:41 Generating build results summary... simple 27-Nov-2025 17:02:41 Saving build results to disk... simple 27-Nov-2025 17:02:42 Logging substituted variables... simple 27-Nov-2025 17:02:42 Indexing build results... simple 27-Nov-2025 17:02:42 Finished building JB-GDB730-JOB1-1.