simple 01-Dec-2025 15:35:14 Build Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests #9 (JB-GDB722-JOB1-9) started building on agent Default Agent simple 01-Dec-2025 15:35:14 simple 01-Dec-2025 15:35:14 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1 simple 01-Dec-2025 15:35:14 Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests #9 (JB-GDB722-JOB1-9) simple 01-Dec-2025 15:35:14 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 01-Dec-2025 15:35:14 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1 simple 01-Dec-2025 15:35:14 Updating source code to revision: aa9b04d454c094e49d21b391333c4abf661ee162 simple 01-Dec-2025 15:35:14 Fetching 'refs/heads/bug/JAL-4603_export_svg_files_missing_part_of_sequence' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 01-Dec-2025 15:35:14 Checking out revision aa9b04d454c094e49d21b391333c4abf661ee162. simple 01-Dec-2025 15:35:14 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 01-Dec-2025 15:35:14 cc05d28..aa9b04d bug/JAL-4603_export_svg_files_missing_part_of_sequence -> origin/bug/JAL-4603_export_svg_files_missing_part_of_sequence simple 01-Dec-2025 15:35:14 Already on 'bug/JAL-4603_export_svg_files_missing_part_of_sequence' simple 01-Dec-2025 15:35:14 Your branch is behind 'origin/bug/JAL-4603_export_svg_files_missing_part_of_sequence' by 1 commit, and can be fast-forwarded. simple 01-Dec-2025 15:35:14 (use "git pull" to update your local branch) simple 01-Dec-2025 15:35:15 HEAD is now at aa9b04d JAL-4635 redo patching of zeus URL to fix failing test simple 01-Dec-2025 15:35:15 Updated source code to revision: aa9b04d454c094e49d21b391333c4abf661ee162 simple 01-Dec-2025 15:35:15 Finished task 'Checkout Default Repository' with result: Success simple 01-Dec-2025 15:35:15 Running pre-build action: VCS Version Collector simple 01-Dec-2025 15:35:15 Running pre-build action: Artifactory Release Staging simple 01-Dec-2025 15:35:15 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 01-Dec-2025 15:35:15 Bamboo Artifactory Plugin version: 2.6.2 command 01-Dec-2025 15:35:15 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests #9 (JB-GDB722-JOB1-9)'\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-GDB722-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4603_export_svg_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_svg_files_missing_part_of_sequence\nbamboo_repository_revision_number=aa9b04d454c094e49d21b391333c4abf661ee162\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB722-JOB1-9\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-GDB722-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB722-JOB1\nbamboo_repository_46498555_previous_revision_number=cc05d28187e3100fd060e6b7e3b1795477c23e62\nbamboo_shortPlanName=bug-JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=9\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-GDB722-JOB1-9\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498555_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_shortPlanKey=GDB722\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=aa9b04d454c094e49d21b391333c4abf661ee162\nbamboo_buildTimeStamp=2025-12-01T15:35:14.380Z\nbamboo_repository_previous_revision_number=cc05d28187e3100fd060e6b7e3b1795477c23e62\nbamboo_planRepository_previousRevision=cc05d28187e3100fd060e6b7e3b1795477c23e62\nbamboo_repository_git_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_buildResultKey=JB-GDB722-JOB1-9\nbamboo_repository_branch_name=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_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=aa9b04d454c094e49d21b391333c4abf661ee162\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498555_git_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\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=bug/JAL-4603_export_svg_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_git_username=\nbamboo_planRepository_1_previousRevision=cc05d28187e3100fd060e6b7e3b1795477c23e62\nbamboo_planRepository_branchDisplayName=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4603_export_svg_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_repository_46498555_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302681\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-GDB722-JOB1\nbamboo_planKey=JB-GDB722\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498555_name=Jalview Gitlab\nbamboo_repository_46498555_revision_number=aa9b04d454c094e49d21b391333c4abf661ee162\nbamboo_repository_46498555_branch_name=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4603_export_svg_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 01-Dec-2025 15:35:15 444 build 01-Dec-2025 15:35:17 build 01-Dec-2025 15:35:17 > Configure project : build 01-Dec-2025 15:35:17 Using properties from file './utils/channels/default/channel_gradle.properties' build 01-Dec-2025 15:35:17 JALVIEW_VERSION is set to '2.11.5.1' build 01-Dec-2025 15:35:17 HEADLESS BUILD build 01-Dec-2025 15:35:17 J2S ENABLED build 01-Dec-2025 15:35:17 Using a LOCAL profile. build 01-Dec-2025 15:35:17 eclipseDir exists build 01-Dec-2025 15:35:18 build 01-Dec-2025 15:35:18 > Task :clean build 01-Dec-2025 15:35:18 > Task :cleanClover build 01-Dec-2025 15:35:18 > Task :cleanTest UP-TO-DATE build 01-Dec-2025 15:35:20 build 01-Dec-2025 15:35:20 > Task :cloverInstrJava build 01-Dec-2025 15:35:20 Clover: About to instrument 1109 files build 01-Dec-2025 15:35:20 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 01-Dec-2025 15:35:20 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover.db'. build 01-Dec-2025 15:35:20 Processing files at 1.9 source level. error 01-Dec-2025 15:35:24 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 01-Dec-2025 15:35:24 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 01-Dec-2025 15:35:24 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 01-Dec-2025 15:35:24 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 01-Dec-2025 15:35:24 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 01-Dec-2025 15:35:24 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 01-Dec-2025 15:35:24 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 01-Dec-2025 15:35:31 Clover all over. Instrumented 1109 files (113 packages). build 01-Dec-2025 15:35:33 build 01-Dec-2025 15:35:33 > Task :cloverInstrTests build 01-Dec-2025 15:35:33 Clover: About to instrument test files build 01-Dec-2025 15:35:33 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 01-Dec-2025 15:35:33 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover.db'. build 01-Dec-2025 15:35:33 Processing files at 1.9 source level. build 01-Dec-2025 15:35:36 Clover all over. Instrumented 293 files (52 packages). build 01-Dec-2025 15:35:36 1625 test methods detected. build 01-Dec-2025 15:35:36 build 01-Dec-2025 15:35:36 > Task :cloverInstr build 01-Dec-2025 15:35:38 build 01-Dec-2025 15:35:38 > Task :compileCloverJava build 01-Dec-2025 15:35:38 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 01-Dec-2025 15:35:38 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:35:38 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:35:38 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:35:38 Setting target compatibility to 11 error 01-Dec-2025 15:35:55 Note: Some input files use or override a deprecated API. error 01-Dec-2025 15:35:55 Note: Recompile with -Xlint:deprecation for details. error 01-Dec-2025 15:35:55 Note: Some input files use unchecked or unsafe operations. error 01-Dec-2025 15:35:55 Note: Recompile with -Xlint:unchecked for details. build 01-Dec-2025 15:36:02 build 01-Dec-2025 15:36:02 > Task :processCloverResources NO-SOURCE build 01-Dec-2025 15:36:02 > Task :cloverClasses build 01-Dec-2025 15:36:02 > Task :copyHelp build 01-Dec-2025 15:36:03 > Task :buildIndices build 01-Dec-2025 15:36:03 > Task :copyResources build 01-Dec-2025 15:36:03 > Task :copyChannelResources build 01-Dec-2025 15:36:03 build 01-Dec-2025 15:36:03 > Task :createBuildProperties build 01-Dec-2025 15:36:03 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 01-Dec-2025 15:36:03 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:36:03 build 01-Dec-2025 15:36:03 > Task :buildResources build 01-Dec-2025 15:36:03 > Task :copyDocs build 01-Dec-2025 15:36:03 build 01-Dec-2025 15:36:03 > Task :convertMdFiles build 01-Dec-2025 15:36:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 01-Dec-2025 15:36:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/releaseprocess.html build 01-Dec-2025 15:36:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 01-Dec-2025 15:36:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/building.html build 01-Dec-2025 15:36:03 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/jalview-projects.html build 01-Dec-2025 15:36:04 build 01-Dec-2025 15:36:04 > Task :releasesTemplates build 01-Dec-2025 15:36:04 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 01-Dec-2025 15:36:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:36:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:36:04 Stripping rc/test/etc for TEST build 01-Dec-2025 15:36:04 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 01-Dec-2025 15:36:04 build 01-Dec-2025 15:36:04 > Task :prepare build 01-Dec-2025 15:36:06 build 01-Dec-2025 15:36:06 > Task :compileJava build 01-Dec-2025 15:36:06 Setting target compatibility to 11 error 01-Dec-2025 15:36:12 Note: Some input files use or override a deprecated API. error 01-Dec-2025 15:36:12 Note: Recompile with -Xlint:deprecation for details. error 01-Dec-2025 15:36:12 Note: Some input files use unchecked or unsafe operations. error 01-Dec-2025 15:36:12 Note: Recompile with -Xlint:unchecked for details. build 01-Dec-2025 15:36:14 build 01-Dec-2025 15:36:14 > Task :compileTestJava build 01-Dec-2025 15:36:14 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 01-Dec-2025 15:36:14 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:36:14 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:36:14 Setting target compatibility to 11 error 01-Dec-2025 15:36:19 Note: Some input files use or override a deprecated API. error 01-Dec-2025 15:36:19 Note: Recompile with -Xlint:deprecation for details. error 01-Dec-2025 15:36:19 Note: Some input files use unchecked or unsafe operations. error 01-Dec-2025 15:36:19 Note: Recompile with -Xlint:unchecked for details. build 01-Dec-2025 15:36:20 build 01-Dec-2025 15:36:20 > Task :processTestResources build 01-Dec-2025 15:36:20 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 01-Dec-2025 15:36:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:36:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:36:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:36:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:36:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:36:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:36:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:36:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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 01-Dec-2025 15:36:20 build 01-Dec-2025 15:36:20 > Task :testClasses build 01-Dec-2025 15:36:22 build 01-Dec-2025 15:36:22 > Task :testTask0 build 01-Dec-2025 15:36:22 Running tests WITH clover error 01-Dec-2025 15:36:26 WARNING: An illegal reflective access operation has occurred error 01-Dec-2025 15:36:26 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 01-Dec-2025 15:36:26 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 01-Dec-2025 15:36:26 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 01-Dec-2025 15:36:26 WARNING: All illegal access operations will be denied in a future release build 01-Dec-2025 15:37:30 build 01-Dec-2025 15:37:30 Gradle suite > Gradle test > jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy FAILED build 01-Dec-2025 15:37:30 java.lang.AssertionError: Expected occupancy to be non-null in column 5 expected object to not be null build 01-Dec-2025 15:37:30 at org.testng.Assert.fail(Assert.java:94) build 01-Dec-2025 15:37:30 at org.testng.Assert.assertNotNull(Assert.java:406) build 01-Dec-2025 15:37:30 at jalview.gui.AlignViewportTest.__CLR4_4_1lfq8443us9(AlignViewportTest.java:478) build 01-Dec-2025 15:37:30 at jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy(AlignViewportTest.java:446) build 01-Dec-2025 15:40:57 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask0/index.html error 01-Dec-2025 15:40:57 error 01-Dec-2025 15:40:57 1829 tests completed, 1 failed build 01-Dec-2025 15:41:00 build 01-Dec-2025 15:41:00 > Task :testTask1 build 01-Dec-2025 15:41:00 Running tests WITH clover error 01-Dec-2025 15:41:02 WARNING: An illegal reflective access operation has occurred error 01-Dec-2025 15:41:02 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 01-Dec-2025 15:41:02 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 01-Dec-2025 15:41:02 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 01-Dec-2025 15:41:02 WARNING: All illegal access operations will be denied in a future release build 01-Dec-2025 15:43:39 build 01-Dec-2025 15:43:39 > Task :testTask2 build 01-Dec-2025 15:43:39 Running tests WITH clover build 01-Dec-2025 15:43:43 build 01-Dec-2025 15:43:43 > Task :testTask3 build 01-Dec-2025 15:43:43 Running tests WITH clover error 01-Dec-2025 15:43:46 WARNING: An illegal reflective access operation has occurred error 01-Dec-2025 15:43:46 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 01-Dec-2025 15:43:46 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 01-Dec-2025 15:43:46 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 01-Dec-2025 15:43:46 WARNING: All illegal access operations will be denied in a future release error 01-Dec-2025 15:44:43 error 01-Dec-2025 15:44:43 FAILURE: Build failed with an exception. error 01-Dec-2025 15:44:43 error 01-Dec-2025 15:44:43 * Where: error 01-Dec-2025 15:44:43 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build.gradle' line: 1967 error 01-Dec-2025 15:44:43 error 01-Dec-2025 15:44:43 * What went wrong: error 01-Dec-2025 15:44:43 Failed tests! error 01-Dec-2025 15:44:43 error 01-Dec-2025 15:44:43 * Try: error 01-Dec-2025 15:44:43 > Run with --stacktrace option to get the stack trace. error 01-Dec-2025 15:44:43 > Run with --info or --debug option to get more log output. error 01-Dec-2025 15:44:43 > Run with --scan to get full insights. error 01-Dec-2025 15:44:43 error 01-Dec-2025 15:44:43 * Get more help at https://help.gradle.org error 01-Dec-2025 15:44:43 error 01-Dec-2025 15:44:43 BUILD FAILED in 9m 27s build 01-Dec-2025 15:44:43 build 01-Dec-2025 15:44:43 > Task :test NO-SOURCE build 01-Dec-2025 15:44:43 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 01-Dec-2025 15:44:43 │jalview:testTask0 results: FAILURE (1829 tests, 1828 successes, 1 failures, 0 skipped) in 4 minutes, 36.028 seconds │ build 01-Dec-2025 15:44:43 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask0/index.html│ build 01-Dec-2025 15:44:43 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 01-Dec-2025 15:44:43 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 39.296 seconds │ build 01-Dec-2025 15:44:43 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask1/index.html│ build 01-Dec-2025 15:44:43 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 01-Dec-2025 15:44:43 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.323 seconds │ build 01-Dec-2025 15:44:43 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask2/index.html│ build 01-Dec-2025 15:44:43 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 01-Dec-2025 15:44:43 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 0.611 seconds │ build 01-Dec-2025 15:44:43 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask3/index.html│ build 01-Dec-2025 15:44:43 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 01-Dec-2025 15:44:43 │OVERALL: results: FAILURE (1917 tests, 1916 successes, 1 failures, 0 skipped) in 7 minutes, 80.258 seconds │ build 01-Dec-2025 15:44:43 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 01-Dec-2025 15:44:43 build 01-Dec-2025 15:44:43 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 01-Dec-2025 15:44:43 build 01-Dec-2025 15:44:43 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 01-Dec-2025 15:44:43 build 01-Dec-2025 15:44:43 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 01-Dec-2025 15:44:43 build 01-Dec-2025 15:44:43 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 01-Dec-2025 15:44:43 Please consult deprecation warnings for more details. build 01-Dec-2025 15:44:43 21 actionable tasks: 20 executed, 1 up-to-date simple 01-Dec-2025 15:44:43 simple 01-Dec-2025 15:44:43 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 01-Dec-2025 15:44:43 Finished task 'Run tests with openclover under gradle' with result: Failed simple 01-Dec-2025 15:44:43 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 01-Dec-2025 15:44:43 Bamboo Artifactory Plugin version: 2.6.2 command 01-Dec-2025 15:44:43 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests #9 (JB-GDB722-JOB1-9)'\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-GDB722-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4603_export_svg_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_svg_files_missing_part_of_sequence\nbamboo_repository_revision_number=aa9b04d454c094e49d21b391333c4abf661ee162\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB722-JOB1-9\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-GDB722-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB722-JOB1\nbamboo_repository_46498555_previous_revision_number=cc05d28187e3100fd060e6b7e3b1795477c23e62\nbamboo_shortPlanName=bug-JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=9\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-GDB722-JOB1-9\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498555_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_shortPlanKey=GDB722\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=aa9b04d454c094e49d21b391333c4abf661ee162\nbamboo_buildTimeStamp=2025-12-01T15:35:14.380Z\nbamboo_repository_previous_revision_number=cc05d28187e3100fd060e6b7e3b1795477c23e62\nbamboo_planRepository_previousRevision=cc05d28187e3100fd060e6b7e3b1795477c23e62\nbamboo_repository_git_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_buildResultKey=JB-GDB722-JOB1-9\nbamboo_repository_branch_name=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_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=aa9b04d454c094e49d21b391333c4abf661ee162\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498555_git_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\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=bug/JAL-4603_export_svg_files_missing_part_of_sequence\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=cc05d28187e3100fd060e6b7e3b1795477c23e62\nbamboo_planRepository_branchDisplayName=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4603_export_svg_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_repository_46498555_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302681\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-GDB722-JOB1\nbamboo_planKey=JB-GDB722\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498555_name=Jalview Gitlab\nbamboo_repository_46498555_revision_number=aa9b04d454c094e49d21b391333c4abf661ee162\nbamboo_repository_46498555_branch_name=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4603_export_svg_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 01-Dec-2025 15:44:43 444 build 01-Dec-2025 15:44:50 build 01-Dec-2025 15:44:50 > Configure project : build 01-Dec-2025 15:44:50 Using properties from file './utils/channels/default/channel_gradle.properties' build 01-Dec-2025 15:44:50 JALVIEW_VERSION is set to '2.11.5.1' build 01-Dec-2025 15:44:50 HEADLESS BUILD build 01-Dec-2025 15:44:50 J2S ENABLED build 01-Dec-2025 15:44:50 Using a LOCAL profile. build 01-Dec-2025 15:44:52 eclipseDir exists build 01-Dec-2025 15:44:54 build 01-Dec-2025 15:44:54 > Task :cloverHtmlReport build 01-Dec-2025 15:44:54 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 01-Dec-2025 15:44:57 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/clover' build 01-Dec-2025 15:45:52 Done. Processed 117 packages in 55895ms (477ms per package). build 01-Dec-2025 15:45:59 build 01-Dec-2025 15:45:59 > Task :cloverXmlReport build 01-Dec-2025 15:45:59 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 01-Dec-2025 15:46:03 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/clover/clover.xml' build 01-Dec-2025 15:46:04 build 01-Dec-2025 15:46:04 > Task :cloverReport build 01-Dec-2025 15:46:04 build 01-Dec-2025 15:46:04 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 01-Dec-2025 15:46:04 build 01-Dec-2025 15:46:04 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 01-Dec-2025 15:46:04 build 01-Dec-2025 15:46:04 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 01-Dec-2025 15:46:04 build 01-Dec-2025 15:46:04 BUILD SUCCESSFUL in 1m 19s build 01-Dec-2025 15:46:04 2 actionable tasks: 2 executed simple 01-Dec-2025 15:46:04 Finished task 'Clover Report' with result: Success simple 01-Dec-2025 15:46:04 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 01-Dec-2025 15:46:04 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1... simple 01-Dec-2025 15:46:04 Failing task since 1 failing test cases were found. simple 01-Dec-2025 15:46:04 Finished task 'TestNG Parser' with result: Failed simple 01-Dec-2025 15:46:04 Running post build plugin 'NCover Results Collector' simple 01-Dec-2025 15:46:04 Running post build plugin 'Artifact Copier' simple 01-Dec-2025 15:46:04 Publishing an artifact: Clover Report (System) simple 01-Dec-2025 15:46:09 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 5.142 s simple 01-Dec-2025 15:46:09 Publishing an artifact: TestNG report error 01-Dec-2025 15:46:09 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/test does not exist. simple 01-Dec-2025 15:46:09 The artifact hasn't been successfully published after 3.949 ms simple 01-Dec-2025 15:46:09 Running post build plugin 'Artifactory Release Management Staging' simple 01-Dec-2025 15:46:09 Running post build plugin 'Artifactory Build Info Copier' simple 01-Dec-2025 15:46:09 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 01-Dec-2025 15:46:09 Running post build plugin 'npm Cache Cleanup' simple 01-Dec-2025 15:46:09 Running post build plugin 'Clover Results Collector' simple 01-Dec-2025 15:46:09 Running post build plugin 'Docker Container Cleanup' simple 01-Dec-2025 15:46:09 Finalising the build... simple 01-Dec-2025 15:46:09 Stopping timer. simple 01-Dec-2025 15:46:09 Build JB-GDB722-JOB1-9 completed. simple 01-Dec-2025 15:46:09 Running on server: post build plugin 'NCover Results Collector' simple 01-Dec-2025 15:46:09 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 01-Dec-2025 15:46:09 Running on server: post build plugin 'Clover Delta Calculator' simple 01-Dec-2025 15:46:09 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 01-Dec-2025 15:46:09 All post build plugins have finished simple 01-Dec-2025 15:46:09 Generating build results summary... simple 01-Dec-2025 15:46:09 Saving build results to disk... simple 01-Dec-2025 15:46:10 Logging substituted variables... simple 01-Dec-2025 15:46:10 Indexing build results... simple 01-Dec-2025 15:46:10 Finished building JB-GDB722-JOB1-9.