simple 11-Nov-2025 17:12:15 Build Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests #2 (JB-GDB724-JOB1-2) started building on agent Default Agent simple 11-Nov-2025 17:12:15 simple 11-Nov-2025 17:12:15 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1 simple 11-Nov-2025 17:12:15 Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests #2 (JB-GDB724-JOB1-2) simple 11-Nov-2025 17:12:15 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 11-Nov-2025 17:12:15 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1 simple 11-Nov-2025 17:12:15 Updating source code to revision: 377f1f52a15db66fd5768669a50bfda03250a6c7 simple 11-Nov-2025 17:12:15 Fetching 'refs/heads/patch/JAL-4626_alphafoldVersionTracker' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 11-Nov-2025 17:12:15 Checking out revision 377f1f52a15db66fd5768669a50bfda03250a6c7. simple 11-Nov-2025 17:12:15 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 11-Nov-2025 17:12:15 9c98e9d..377f1f5 patch/JAL-4626_alphafoldVersionTracker -> origin/patch/JAL-4626_alphafoldVersionTracker simple 11-Nov-2025 17:12:17 Your branch is behind 'origin/patch/JAL-4626_alphafoldVersionTracker' by 5 commits, and can be fast-forwarded. simple 11-Nov-2025 17:12:17 (use "git pull" to update your local branch) simple 11-Nov-2025 17:12:17 Already on 'patch/JAL-4626_alphafoldVersionTracker' simple 11-Nov-2025 17:12:17 HEAD is now at 377f1f5 Merge branch 'development/Release_2_11_5_Branch' into patch/JAL-4626_alphafoldVersionTracker simple 11-Nov-2025 17:12:17 Updated source code to revision: 377f1f52a15db66fd5768669a50bfda03250a6c7 simple 11-Nov-2025 17:12:17 Finished task 'Checkout Default Repository' with result: Success simple 11-Nov-2025 17:12:17 Running pre-build action: VCS Version Collector simple 11-Nov-2025 17:12:17 Running pre-build action: Artifactory Release Staging simple 11-Nov-2025 17:12:17 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 11-Nov-2025 17:12:17 Bamboo Artifactory Plugin version: 2.6.2 command 11-Nov-2025 17:12:17 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests #2 (JB-GDB724-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4626_alphafoldVersionTracker\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4626_alphafoldVersionTracker\nbamboo_repository_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB724-JOB1-2\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB724-JOB1\nbamboo_shortPlanName=patch-JAL-4626_alphafoldVersionTracker\nbamboo_repository_46498567_git_branch=patch/JAL-4626_alphafoldVersionTracker\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_46498567_git_username=\nbamboo_shortJobName=Clover and Tests\nbamboo_repository_46498567_previous_revision_number=9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB724-JOB1-2\nbamboo_repository_46498567_name=Jalview Gitlab\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-4626_alphafoldVersionTracker\nbamboo_shortPlanKey=GDB724\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_buildTimeStamp=2025-11-11T17:12:15.523Z\nbamboo_repository_previous_revision_number=9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616\nbamboo_planRepository_previousRevision=9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616\nbamboo_repository_git_branch=patch/JAL-4626_alphafoldVersionTracker\nbamboo_buildResultKey=JB-GDB724-JOB1-2\nbamboo_repository_branch_name=patch/JAL-4626_alphafoldVersionTracker\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=377f1f52a15db66fd5768669a50bfda03250a6c7\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-4626_alphafoldVersionTracker\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=9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616\nbamboo_planRepository_branchDisplayName=patch/JAL-4626_alphafoldVersionTracker\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4626_alphafoldVersionTracker\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-46302705\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_repository_46498567_branch_name=patch/JAL-4626_alphafoldVersionTracker\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_46498567_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-GDB724-JOB1\nbamboo_repository_46498567_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_planKey=JB-GDB724\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4626_alphafoldVersionTracker\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 11-Nov-2025 17:12:17 444 build 11-Nov-2025 17:12:19 build 11-Nov-2025 17:12:19 > Configure project : build 11-Nov-2025 17:12:19 Using properties from file './utils/channels/default/channel_gradle.properties' build 11-Nov-2025 17:12:19 JALVIEW_VERSION is set to '2.11.5.1' build 11-Nov-2025 17:12:19 HEADLESS BUILD build 11-Nov-2025 17:12:19 J2S ENABLED build 11-Nov-2025 17:12:19 Using a LOCAL profile. build 11-Nov-2025 17:12:19 eclipseDir exists build 11-Nov-2025 17:12:20 build 11-Nov-2025 17:12:20 > Task :clean build 11-Nov-2025 17:12:20 > Task :cleanClover build 11-Nov-2025 17:12:20 > Task :cleanTest UP-TO-DATE build 11-Nov-2025 17:12:22 build 11-Nov-2025 17:12:22 > Task :cloverInstrJava build 11-Nov-2025 17:12:22 Clover: About to instrument 1106 files build 11-Nov-2025 17:12:22 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 11-Nov-2025 17:12:22 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover.db'. build 11-Nov-2025 17:12:22 Processing files at 1.9 source level. error 11-Nov-2025 17:12:25 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 11-Nov-2025 17:12:25 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 11-Nov-2025 17:12:25 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 11-Nov-2025 17:12:25 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 11-Nov-2025 17:12:25 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 11-Nov-2025 17:12:25 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 11-Nov-2025 17:12:25 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 11-Nov-2025 17:12:31 Clover all over. Instrumented 1106 files (112 packages). build 11-Nov-2025 17:12:34 build 11-Nov-2025 17:12:34 > Task :cloverInstrTests build 11-Nov-2025 17:12:34 Clover: About to instrument test files build 11-Nov-2025 17:12:34 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 11-Nov-2025 17:12:34 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover.db'. build 11-Nov-2025 17:12:34 Processing files at 1.9 source level. build 11-Nov-2025 17:12:37 Clover all over. Instrumented 293 files (52 packages). build 11-Nov-2025 17:12:37 1619 test methods detected. build 11-Nov-2025 17:12:38 build 11-Nov-2025 17:12:38 > Task :cloverInstr build 11-Nov-2025 17:12:39 build 11-Nov-2025 17:12:39 > Task :compileCloverJava build 11-Nov-2025 17:12:39 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 11-Nov-2025 17:12:39 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:12:39 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:12:39 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:12:39 Setting target compatibility to 11 error 11-Nov-2025 17:12:55 Note: Some input files use or override a deprecated API. error 11-Nov-2025 17:12:55 Note: Recompile with -Xlint:deprecation for details. error 11-Nov-2025 17:12:55 Note: Some input files use unchecked or unsafe operations. error 11-Nov-2025 17:12:55 Note: Recompile with -Xlint:unchecked for details. build 11-Nov-2025 17:13:01 build 11-Nov-2025 17:13:01 > Task :processCloverResources NO-SOURCE build 11-Nov-2025 17:13:01 > Task :cloverClasses build 11-Nov-2025 17:13:02 > Task :copyHelp build 11-Nov-2025 17:13:04 > Task :buildIndices build 11-Nov-2025 17:13:04 > Task :copyResources build 11-Nov-2025 17:13:04 > Task :copyChannelResources build 11-Nov-2025 17:13:04 build 11-Nov-2025 17:13:04 > Task :createBuildProperties build 11-Nov-2025 17:13:04 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 11-Nov-2025 17:13:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:13:04 build 11-Nov-2025 17:13:04 > Task :buildResources build 11-Nov-2025 17:13:04 > Task :copyDocs build 11-Nov-2025 17:13:04 build 11-Nov-2025 17:13:04 > Task :convertMdFiles build 11-Nov-2025 17:13:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 11-Nov-2025 17:13:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/releaseprocess.html build 11-Nov-2025 17:13:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 11-Nov-2025 17:13:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/building.html build 11-Nov-2025 17:13:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/resources/doc_build/doc/jalview-projects.html build 11-Nov-2025 17:13:04 build 11-Nov-2025 17:13:04 > Task :releasesTemplates build 11-Nov-2025 17:13:04 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 11-Nov-2025 17:13:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:13:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:13:04 Stripping rc/test/etc for TEST build 11-Nov-2025 17:13:04 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 11-Nov-2025 17:13:04 build 11-Nov-2025 17:13:04 > Task :prepare build 11-Nov-2025 17:13:06 build 11-Nov-2025 17:13:06 > Task :compileJava build 11-Nov-2025 17:13:06 Setting target compatibility to 11 error 11-Nov-2025 17:13:12 Note: Some input files use or override a deprecated API. error 11-Nov-2025 17:13:12 Note: Recompile with -Xlint:deprecation for details. error 11-Nov-2025 17:13:12 Note: Some input files use unchecked or unsafe operations. error 11-Nov-2025 17:13:12 Note: Recompile with -Xlint:unchecked for details. build 11-Nov-2025 17:13:14 build 11-Nov-2025 17:13:14 > Task :compileTestJava build 11-Nov-2025 17:13:14 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 11-Nov-2025 17:13:14 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:13:14 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:13:14 Setting target compatibility to 11 error 11-Nov-2025 17:13:19 Note: Some input files use or override a deprecated API. error 11-Nov-2025 17:13:19 Note: Recompile with -Xlint:deprecation for details. error 11-Nov-2025 17:13:19 Note: Some input files use unchecked or unsafe operations. error 11-Nov-2025 17:13:19 Note: Recompile with -Xlint:unchecked for details. build 11-Nov-2025 17:13:20 build 11-Nov-2025 17:13:20 > Task :processTestResources build 11-Nov-2025 17:13:20 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 11-Nov-2025 17:13:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:13:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:13:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:13:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:13:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:13:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:13:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:13:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-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 11-Nov-2025 17:13:20 build 11-Nov-2025 17:13:20 > Task :testClasses build 11-Nov-2025 17:13:22 build 11-Nov-2025 17:13:22 > Task :testTask0 build 11-Nov-2025 17:13:22 Running tests WITH clover error 11-Nov-2025 17:13:25 WARNING: An illegal reflective access operation has occurred error 11-Nov-2025 17:13:25 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 11-Nov-2025 17:13:25 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 11-Nov-2025 17:13:25 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 11-Nov-2025 17:13:25 WARNING: All illegal access operations will be denied in a future release build 11-Nov-2025 17:18:18 build 11-Nov-2025 17:18:18 > Task :testTask1 build 11-Nov-2025 17:18:18 Running tests WITH clover error 11-Nov-2025 17:18:20 WARNING: An illegal reflective access operation has occurred error 11-Nov-2025 17:18:20 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 11-Nov-2025 17:18:20 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 11-Nov-2025 17:18:20 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 11-Nov-2025 17:18:20 WARNING: All illegal access operations will be denied in a future release build 11-Nov-2025 17:19:47 build 11-Nov-2025 17:19:47 Gradle suite > Gradle test > jalview.bin.CommandLineOperationsNG.testHeadlessModeOutputToStdout[6](./test/jalview/bin/argparser/testfiles/test1.fa ./test/jalview/bin/argparser/testfiles/test2.fa ./test/jalview/bin/argparser/testfiles/test3.fa --all --output -, test/jalview/bin/test1-3.fa, 13000) FAILED build 11-Nov-2025 17:19:47 java.lang.AssertionError: STDOUT from jalview command did not match the comparison file expected [>TEST1/1-4 build 11-Nov-2025 17:19:47 AAAA build 11-Nov-2025 17:19:47 >TEST2/1-4 build 11-Nov-2025 17:19:47 LLLL build 11-Nov-2025 17:19:47 >TEST3/1-5 build 11-Nov-2025 17:19:47 AAARG build 11-Nov-2025 17:19:47 ] but found [>TEST1/1-4 build 11-Nov-2025 17:19:47 AAAA build 11-Nov-2025 17:19:47 >TEST2/1-4 build 11-Nov-2025 17:19:47 LLLL build 11-Nov-2025 17:19:47 ] build 11-Nov-2025 17:19:47 at org.testng.Assert.fail(Assert.java:94) build 11-Nov-2025 17:19:47 at org.testng.Assert.failNotEquals(Assert.java:496) build 11-Nov-2025 17:19:47 at org.testng.Assert.assertEquals(Assert.java:125) build 11-Nov-2025 17:19:47 at org.testng.Assert.assertEquals(Assert.java:178) build 11-Nov-2025 17:19:47 at jalview.bin.CommandLineOperationsNG.testHeadlessModeOutputToStdout(CommandLineOperationsNG.java:410) error 11-Nov-2025 17:21:05 error 11-Nov-2025 17:21:05 62 tests completed, 1 failed build 11-Nov-2025 17:21:05 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask1/index.html build 11-Nov-2025 17:21:07 build 11-Nov-2025 17:21:07 > Task :testTask2 build 11-Nov-2025 17:21:07 Running tests WITH clover build 11-Nov-2025 17:21:11 build 11-Nov-2025 17:21:11 > Task :testTask3 build 11-Nov-2025 17:21:11 Running tests WITH clover error 11-Nov-2025 17:21:14 WARNING: An illegal reflective access operation has occurred error 11-Nov-2025 17:21:14 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 11-Nov-2025 17:21:14 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 11-Nov-2025 17:21:14 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 11-Nov-2025 17:21:14 WARNING: All illegal access operations will be denied in a future release build 11-Nov-2025 17:22:08 build 11-Nov-2025 17:22:08 > Task :test NO-SOURCE build 11-Nov-2025 17:22:08 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 11-Nov-2025 17:22:08 │jalview:testTask0 results: SUCCESS (1819 tests, 1819 successes, 0 failures, 0 skipped) in 4 minutes, 54.973 seconds │ build 11-Nov-2025 17:22:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask0/index.html│ build 11-Nov-2025 17:22:08 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Nov-2025 17:22:08 │jalview:testTask1 results: FAILURE (62 tests, 61 successes, 1 failures, 0 skipped) in 2 minutes, 49.218 seconds │ build 11-Nov-2025 17:22:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask1/index.html│ build 11-Nov-2025 17:22:08 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Nov-2025 17:22:08 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.411 seconds │ build 11-Nov-2025 17:22:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask2/index.html│ build 11-Nov-2025 17:22:08 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Nov-2025 17:22:08 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 59.005 seconds │ build 11-Nov-2025 17:22:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/testTask3/index.html│ build 11-Nov-2025 17:22:08 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Nov-2025 17:22:08 │OVERALL: results: FAILURE (1907 tests, 1906 successes, 1 failures, 0 skipped) in 6 minutes, 167.607 seconds │ build 11-Nov-2025 17:22:08 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 11-Nov-2025 17:22:08 build 11-Nov-2025 17:22:08 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 11-Nov-2025 17:22:08 build 11-Nov-2025 17:22:08 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 11-Nov-2025 17:22:08 build 11-Nov-2025 17:22:08 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 11-Nov-2025 17:22:08 build 11-Nov-2025 17:22:08 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 11-Nov-2025 17:22:08 Please consult deprecation warnings for more details. build 11-Nov-2025 17:22:08 21 actionable tasks: 20 executed, 1 up-to-date error 11-Nov-2025 17:22:08 error 11-Nov-2025 17:22:08 FAILURE: Build failed with an exception. error 11-Nov-2025 17:22:08 error 11-Nov-2025 17:22:08 * Where: error 11-Nov-2025 17:22:08 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build.gradle' line: 1967 error 11-Nov-2025 17:22:08 error 11-Nov-2025 17:22:08 * What went wrong: error 11-Nov-2025 17:22:08 Failed tests! error 11-Nov-2025 17:22:08 error 11-Nov-2025 17:22:08 * Try: error 11-Nov-2025 17:22:08 > Run with --stacktrace option to get the stack trace. error 11-Nov-2025 17:22:08 > Run with --info or --debug option to get more log output. error 11-Nov-2025 17:22:08 > Run with --scan to get full insights. error 11-Nov-2025 17:22:08 error 11-Nov-2025 17:22:08 * Get more help at https://help.gradle.org error 11-Nov-2025 17:22:08 error 11-Nov-2025 17:22:08 BUILD FAILED in 9m 51s simple 11-Nov-2025 17:22:09 simple 11-Nov-2025 17:22:09 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 11-Nov-2025 17:22:09 Finished task 'Run tests with openclover under gradle' with result: Failed simple 11-Nov-2025 17:22:09 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 11-Nov-2025 17:22:09 Bamboo Artifactory Plugin version: 2.6.2 command 11-Nov-2025 17:22:09 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests #2 (JB-GDB724-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4626_alphafoldVersionTracker\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4626_alphafoldVersionTracker\nbamboo_repository_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB724-JOB1-2\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB724-JOB1\nbamboo_shortPlanName=patch-JAL-4626_alphafoldVersionTracker\nbamboo_repository_46498567_git_branch=patch/JAL-4626_alphafoldVersionTracker\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_46498567_git_username=\nbamboo_shortJobName=Clover and Tests\nbamboo_repository_46498567_previous_revision_number=9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB724-JOB1-2\nbamboo_repository_46498567_name=Jalview Gitlab\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-4626_alphafoldVersionTracker\nbamboo_shortPlanKey=GDB724\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_buildTimeStamp=2025-11-11T17:12:15.523Z\nbamboo_repository_previous_revision_number=9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616\nbamboo_planRepository_previousRevision=9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616\nbamboo_repository_git_branch=patch/JAL-4626_alphafoldVersionTracker\nbamboo_buildResultKey=JB-GDB724-JOB1-2\nbamboo_repository_branch_name=patch/JAL-4626_alphafoldVersionTracker\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4626_alphafoldVersionTracker - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=377f1f52a15db66fd5768669a50bfda03250a6c7\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-4626_alphafoldVersionTracker\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=9c98e9d9d1171c8085ed2ca1db4ffeb8b606c616\nbamboo_planRepository_branchDisplayName=patch/JAL-4626_alphafoldVersionTracker\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4626_alphafoldVersionTracker\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-46302705\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_repository_46498567_branch_name=patch/JAL-4626_alphafoldVersionTracker\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_46498567_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-GDB724-JOB1\nbamboo_repository_46498567_revision_number=377f1f52a15db66fd5768669a50bfda03250a6c7\nbamboo_planKey=JB-GDB724\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4626_alphafoldVersionTracker\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 11-Nov-2025 17:22:09 444 build 11-Nov-2025 17:22:16 build 11-Nov-2025 17:22:16 > Configure project : build 11-Nov-2025 17:22:16 Using properties from file './utils/channels/default/channel_gradle.properties' build 11-Nov-2025 17:22:16 JALVIEW_VERSION is set to '2.11.5.1' build 11-Nov-2025 17:22:16 HEADLESS BUILD build 11-Nov-2025 17:22:16 J2S ENABLED build 11-Nov-2025 17:22:17 Using a LOCAL profile. build 11-Nov-2025 17:22:18 eclipseDir exists build 11-Nov-2025 17:22:21 build 11-Nov-2025 17:22:21 > Task :cloverHtmlReport build 11-Nov-2025 17:22:21 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 11-Nov-2025 17:22:23 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/clover' build 11-Nov-2025 17:23:18 Done. Processed 116 packages in 56002ms (482ms per package). build 11-Nov-2025 17:23:24 build 11-Nov-2025 17:23:24 > Task :cloverXmlReport build 11-Nov-2025 17:23:24 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 11-Nov-2025 17:23:26 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/clover/clover.xml' build 11-Nov-2025 17:23:26 build 11-Nov-2025 17:23:26 > Task :cloverReport build 11-Nov-2025 17:23:26 build 11-Nov-2025 17:23:26 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 11-Nov-2025 17:23:26 build 11-Nov-2025 17:23:26 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 11-Nov-2025 17:23:26 build 11-Nov-2025 17:23:26 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 11-Nov-2025 17:23:26 build 11-Nov-2025 17:23:26 BUILD SUCCESSFUL in 1m 17s build 11-Nov-2025 17:23:26 2 actionable tasks: 2 executed simple 11-Nov-2025 17:23:27 Finished task 'Clover Report' with result: Success simple 11-Nov-2025 17:23:27 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 11-Nov-2025 17:23:27 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1... simple 11-Nov-2025 17:23:27 Failing task since 1 failing test cases were found. simple 11-Nov-2025 17:23:27 Finished task 'TestNG Parser' with result: Failed simple 11-Nov-2025 17:23:27 Running post build plugin 'NCover Results Collector' simple 11-Nov-2025 17:23:27 Running post build plugin 'Artifact Copier' simple 11-Nov-2025 17:23:27 Publishing an artifact: Clover Report (System) simple 11-Nov-2025 17:23:32 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 5.700 s simple 11-Nov-2025 17:23:32 Publishing an artifact: TestNG report error 11-Nov-2025 17:23:32 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB724-JOB1/build/reports/tests/test does not exist. simple 11-Nov-2025 17:23:32 The artifact hasn't been successfully published after 4.223 ms simple 11-Nov-2025 17:23:32 Running post build plugin 'Artifactory Release Management Staging' simple 11-Nov-2025 17:23:32 Running post build plugin 'Artifactory Build Info Copier' simple 11-Nov-2025 17:23:32 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 11-Nov-2025 17:23:32 Running post build plugin 'npm Cache Cleanup' simple 11-Nov-2025 17:23:32 Running post build plugin 'Clover Results Collector' simple 11-Nov-2025 17:23:32 Running post build plugin 'Docker Container Cleanup' simple 11-Nov-2025 17:23:32 Finalising the build... simple 11-Nov-2025 17:23:32 Stopping timer. simple 11-Nov-2025 17:23:32 Build JB-GDB724-JOB1-2 completed. simple 11-Nov-2025 17:23:32 Running on server: post build plugin 'NCover Results Collector' simple 11-Nov-2025 17:23:32 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 11-Nov-2025 17:23:32 Running on server: post build plugin 'Clover Delta Calculator' simple 11-Nov-2025 17:23:32 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 11-Nov-2025 17:23:32 All post build plugins have finished simple 11-Nov-2025 17:23:32 Generating build results summary... simple 11-Nov-2025 17:23:33 Saving build results to disk... simple 11-Nov-2025 17:23:33 Logging substituted variables... simple 11-Nov-2025 17:23:34 Indexing build results... simple 11-Nov-2025 17:23:34 Finished building JB-GDB724-JOB1-2.