simple 27-Nov-2025 17:21:20 Build Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Clover and Tests #3 (JB-GDB727-JOB1-3) started building on agent Default Agent simple 27-Nov-2025 17:21:20 simple 27-Nov-2025 17:21:20 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1 simple 27-Nov-2025 17:21:20 Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Clover and Tests #3 (JB-GDB727-JOB1-3) simple 27-Nov-2025 17:21:20 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 27-Nov-2025 17:21:20 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1 simple 27-Nov-2025 17:21:20 Updating source code to revision: c0746f1378bd64b7cf72b082eca210d21f86feff simple 27-Nov-2025 17:21:21 Fetching 'refs/heads/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 27-Nov-2025 17:21:23 Checking out revision c0746f1378bd64b7cf72b082eca210d21f86feff. simple 27-Nov-2025 17:21:23 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 27-Nov-2025 17:21:23 d92ec98..c0746f1 bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest -> origin/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest simple 27-Nov-2025 17:21:23 * [new branch] bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus -> origin/bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus simple 27-Nov-2025 17:21:23 b0fd08a..d96cd12 development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch simple 27-Nov-2025 17:21:23 * [new branch] patch/JAL-4601_stk_ss_annots_showhide -> origin/patch/JAL-4601_stk_ss_annots_showhide simple 27-Nov-2025 17:21:23 86d2c84..a66e20b releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch simple 27-Nov-2025 17:21:23 Already on 'bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest' simple 27-Nov-2025 17:21:23 Your branch is behind 'origin/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest' by 1 commit, and can be fast-forwarded. simple 27-Nov-2025 17:21:23 (use "git pull" to update your local branch) simple 27-Nov-2025 17:21:23 HEAD is now at c0746f1 JAL-4581. Added an MD5 hash for jalview.ext.htsjdk.HtsContigDb. Made jalview.util.DigestUtils for MD5 and SHA256 digest. Adapted net.meyfa.sha256.Sha256 to not use java.nio.IntBuffer and java.nio.ByteBuffer (not supported by SwingJS). simple 27-Nov-2025 17:21:23 Updated source code to revision: c0746f1378bd64b7cf72b082eca210d21f86feff simple 27-Nov-2025 17:21:23 Finished task 'Checkout Default Repository' with result: Success simple 27-Nov-2025 17:21:23 Running pre-build action: VCS Version Collector simple 27-Nov-2025 17:21:23 Running pre-build action: Artifactory Release Staging simple 27-Nov-2025 17:21:23 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 27-Nov-2025 17:21:23 Bamboo Artifactory Plugin version: 2.6.2 command 27-Nov-2025 17:21:23 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Clover and Tests #3 (JB-GDB727-JOB1-3)'\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-GDB727-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_repository_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB727-JOB1-3\nbamboo_repository_46498584_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff\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-GDB727-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB727-JOB1\nbamboo_repository_46498584_git_username=\nbamboo_shortPlanName=bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_repository_46498584_previous_revision_number=d92ec98a32dc75a9fd0c635c803d00d60ce92f97\nLOGNAME=bamboo\nbamboo_buildNumber=3\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-GDB727-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_repository_46498584_name=Jalview Gitlab\nbamboo_shortPlanKey=GDB727\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=c0746f1378bd64b7cf72b082eca210d21f86feff\nbamboo_buildTimeStamp=2025-11-27T17:14:12.825Z\nbamboo_repository_previous_revision_number=d92ec98a32dc75a9fd0c635c803d00d60ce92f97\nbamboo_planRepository_previousRevision=d92ec98a32dc75a9fd0c635c803d00d60ce92f97\nbamboo_repository_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_buildResultKey=JB-GDB727-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498584_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_1_revision=c0746f1378bd64b7cf72b082eca210d21f86feff\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=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\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=d92ec98a32dc75a9fd0c635c803d00d60ce92f97\nbamboo_planRepository_branchDisplayName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\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-46302739\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-GDB727-JOB1\nbamboo_planKey=JB-GDB727\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498584_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_repository_46498584_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\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 17:21:23 444 build 27-Nov-2025 17:21:25 build 27-Nov-2025 17:21:25 > Configure project : build 27-Nov-2025 17:21:25 Using properties from file './utils/channels/default/channel_gradle.properties' build 27-Nov-2025 17:21:25 JALVIEW_VERSION is set to '2.11.5.1' build 27-Nov-2025 17:21:25 HEADLESS BUILD build 27-Nov-2025 17:21:25 J2S ENABLED build 27-Nov-2025 17:21:25 Using a LOCAL profile. build 27-Nov-2025 17:21:25 eclipseDir exists build 27-Nov-2025 17:21:25 build 27-Nov-2025 17:21:25 > Task :clean build 27-Nov-2025 17:21:25 > Task :cleanClover build 27-Nov-2025 17:21:25 > Task :cleanTest UP-TO-DATE build 27-Nov-2025 17:21:28 build 27-Nov-2025 17:21:28 > Task :cloverInstrJava build 27-Nov-2025 17:21:28 Clover: About to instrument 1108 files build 27-Nov-2025 17:21:28 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 27-Nov-2025 17:21:28 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover.db'. build 27-Nov-2025 17:21:28 Processing files at 1.9 source level. error 27-Nov-2025 17:21:31 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 17:21:31 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 17:21:31 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 17:21:31 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 17:21:31 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 17:21:31 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 17:21:31 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 17:21:40 Clover all over. Instrumented 1108 files (113 packages). build 27-Nov-2025 17:21:42 build 27-Nov-2025 17:21:42 > Task :cloverInstrTests build 27-Nov-2025 17:21:42 Clover: About to instrument test files build 27-Nov-2025 17:21:42 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 27-Nov-2025 17:21:42 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover.db'. build 27-Nov-2025 17:21:42 Processing files at 1.9 source level. build 27-Nov-2025 17:21:45 Clover all over. Instrumented 293 files (52 packages). build 27-Nov-2025 17:21:45 1619 test methods detected. build 27-Nov-2025 17:21:45 build 27-Nov-2025 17:21:45 > Task :cloverInstr build 27-Nov-2025 17:21:47 build 27-Nov-2025 17:21:47 > Task :compileCloverJava build 27-Nov-2025 17:21:47 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 27-Nov-2025 17:21:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:21:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:21:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:21:47 Setting target compatibility to 11 error 27-Nov-2025 17:22:04 Note: Some input files use or override a deprecated API. error 27-Nov-2025 17:22:04 Note: Recompile with -Xlint:deprecation for details. error 27-Nov-2025 17:22:04 Note: Some input files use unchecked or unsafe operations. error 27-Nov-2025 17:22:04 Note: Recompile with -Xlint:unchecked for details. build 27-Nov-2025 17:22:11 build 27-Nov-2025 17:22:11 > Task :processCloverResources NO-SOURCE build 27-Nov-2025 17:22:11 > Task :cloverClasses build 27-Nov-2025 17:22:11 > Task :copyHelp build 27-Nov-2025 17:22:12 > Task :buildIndices build 27-Nov-2025 17:22:12 > Task :copyResources build 27-Nov-2025 17:22:13 > Task :copyChannelResources build 27-Nov-2025 17:22:13 build 27-Nov-2025 17:22:13 > Task :createBuildProperties build 27-Nov-2025 17:22:13 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 27-Nov-2025 17:22:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:22:13 build 27-Nov-2025 17:22:13 > Task :buildResources build 27-Nov-2025 17:22:13 > Task :copyDocs build 27-Nov-2025 17:22:13 build 27-Nov-2025 17:22:13 > Task :convertMdFiles build 27-Nov-2025 17:22:13 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 27-Nov-2025 17:22:13 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/doc_build/doc/releaseprocess.html build 27-Nov-2025 17:22:13 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 27-Nov-2025 17:22:13 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/doc_build/doc/building.html build 27-Nov-2025 17:22:13 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/doc_build/doc/jalview-projects.html build 27-Nov-2025 17:22:13 build 27-Nov-2025 17:22:13 > Task :releasesTemplates build 27-Nov-2025 17:22:13 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 27-Nov-2025 17:22:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:22:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:22:13 Stripping rc/test/etc for TEST build 27-Nov-2025 17:22:13 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 27-Nov-2025 17:22:13 build 27-Nov-2025 17:22:13 > Task :prepare build 27-Nov-2025 17:22:15 build 27-Nov-2025 17:22:15 > Task :compileJava build 27-Nov-2025 17:22:15 Setting target compatibility to 11 error 27-Nov-2025 17:22:21 Note: Some input files use or override a deprecated API. error 27-Nov-2025 17:22:21 Note: Recompile with -Xlint:deprecation for details. error 27-Nov-2025 17:22:21 Note: Some input files use unchecked or unsafe operations. error 27-Nov-2025 17:22:21 Note: Recompile with -Xlint:unchecked for details. build 27-Nov-2025 17:22:23 build 27-Nov-2025 17:22:23 > Task :compileTestJava build 27-Nov-2025 17:22:23 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 27-Nov-2025 17:22:23 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:22:23 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:22:23 Setting target compatibility to 11 error 27-Nov-2025 17:22:28 Note: Some input files use or override a deprecated API. error 27-Nov-2025 17:22:28 Note: Recompile with -Xlint:deprecation for details. error 27-Nov-2025 17:22:28 Note: Some input files use unchecked or unsafe operations. error 27-Nov-2025 17:22:28 Note: Recompile with -Xlint:unchecked for details. build 27-Nov-2025 17:22:31 build 27-Nov-2025 17:22:31 > Task :processTestResources build 27-Nov-2025 17:22:31 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 27-Nov-2025 17:22:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 27-Nov-2025 17:22:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:22:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:22:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:22:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:22:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:22:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:22:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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 17:22:31 build 27-Nov-2025 17:22:31 > Task :testClasses build 27-Nov-2025 17:22:32 build 27-Nov-2025 17:22:32 > Task :testTask0 build 27-Nov-2025 17:22:32 Running tests WITH clover error 27-Nov-2025 17:22:35 WARNING: An illegal reflective access operation has occurred error 27-Nov-2025 17:22:35 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 27-Nov-2025 17:22:35 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 27-Nov-2025 17:22:35 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 27-Nov-2025 17:22:35 WARNING: All illegal access operations will be denied in a future release build 27-Nov-2025 17:27:17 build 27-Nov-2025 17:27:17 > Task :testTask1 build 27-Nov-2025 17:27:17 Running tests WITH clover error 27-Nov-2025 17:27:19 WARNING: An illegal reflective access operation has occurred error 27-Nov-2025 17:27:19 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 27-Nov-2025 17:27:19 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 27-Nov-2025 17:27:19 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 27-Nov-2025 17:27:19 WARNING: All illegal access operations will be denied in a future release build 27-Nov-2025 17:29:57 build 27-Nov-2025 17:29:57 > Task :testTask2 build 27-Nov-2025 17:29:57 Running tests WITH clover build 27-Nov-2025 17:30:01 build 27-Nov-2025 17:30:01 > Task :testTask3 build 27-Nov-2025 17:30:01 Running tests WITH clover error 27-Nov-2025 17:30:04 WARNING: An illegal reflective access operation has occurred error 27-Nov-2025 17:30:04 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 27-Nov-2025 17:30:04 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 27-Nov-2025 17:30:04 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 27-Nov-2025 17:30:04 WARNING: All illegal access operations will be denied in a future release build 27-Nov-2025 17:31:05 build 27-Nov-2025 17:31:05 > Task :test NO-SOURCE build 27-Nov-2025 17:31:05 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 27-Nov-2025 17:31:05 │jalview:testTask0 results: SUCCESS (1824 tests, 1824 successes, 0 failures, 0 skipped) in 4 minutes, 44.674 seconds │ build 27-Nov-2025 17:31:05 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/tests/testTask0/index.html│ build 27-Nov-2025 17:31:05 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 27-Nov-2025 17:31:05 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 39.682 seconds │ build 27-Nov-2025 17:31:05 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/tests/testTask1/index.html│ build 27-Nov-2025 17:31:05 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 27-Nov-2025 17:31:05 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.052 seconds │ build 27-Nov-2025 17:31:05 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/tests/testTask2/index.html│ build 27-Nov-2025 17:31:05 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 27-Nov-2025 17:31:05 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 5.701 seconds │ build 27-Nov-2025 17:31:05 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/tests/testTask3/index.html│ build 27-Nov-2025 17:31:05 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 27-Nov-2025 17:31:05 │OVERALL: results: SUCCESS (1912 tests, 1912 successes, 0 failures, 0 skipped) in 7 minutes, 94.109 seconds │ build 27-Nov-2025 17:31:05 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 27-Nov-2025 17:31:05 build 27-Nov-2025 17:31:05 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 27-Nov-2025 17:31:05 build 27-Nov-2025 17:31:05 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 17:31:05 build 27-Nov-2025 17:31:05 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 27-Nov-2025 17:31:05 build 27-Nov-2025 17:31:05 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 27-Nov-2025 17:31:05 Please consult deprecation warnings for more details. build 27-Nov-2025 17:31:05 build 27-Nov-2025 17:31:05 BUILD SUCCESSFUL in 9m 41s build 27-Nov-2025 17:31:05 21 actionable tasks: 20 executed, 1 up-to-date simple 27-Nov-2025 17:31:05 Finished task 'Run tests with openclover under gradle' with result: Success simple 27-Nov-2025 17:31:05 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 27-Nov-2025 17:31:05 Bamboo Artifactory Plugin version: 2.6.2 command 27-Nov-2025 17:31:05 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Clover and Tests #3 (JB-GDB727-JOB1-3)'\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-GDB727-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_repository_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB727-JOB1-3\nbamboo_repository_46498584_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff\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-GDB727-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB727-JOB1\nbamboo_repository_46498584_git_username=\nbamboo_shortPlanName=bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_repository_46498584_previous_revision_number=d92ec98a32dc75a9fd0c635c803d00d60ce92f97\nLOGNAME=bamboo\nbamboo_buildNumber=3\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-GDB727-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_repository_46498584_name=Jalview Gitlab\nbamboo_shortPlanKey=GDB727\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=c0746f1378bd64b7cf72b082eca210d21f86feff\nbamboo_buildTimeStamp=2025-11-27T17:14:12.825Z\nbamboo_repository_previous_revision_number=d92ec98a32dc75a9fd0c635c803d00d60ce92f97\nbamboo_planRepository_previousRevision=d92ec98a32dc75a9fd0c635c803d00d60ce92f97\nbamboo_repository_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_buildResultKey=JB-GDB727-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498584_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_1_revision=c0746f1378bd64b7cf72b082eca210d21f86feff\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=d92ec98a32dc75a9fd0c635c803d00d60ce92f97\nbamboo_planRepository_branchDisplayName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\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-46302739\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-GDB727-JOB1\nbamboo_planKey=JB-GDB727\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498584_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_repository_46498584_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\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 17:31:05 444 build 27-Nov-2025 17:31:12 build 27-Nov-2025 17:31:12 > Configure project : build 27-Nov-2025 17:31:12 Using properties from file './utils/channels/default/channel_gradle.properties' build 27-Nov-2025 17:31:12 JALVIEW_VERSION is set to '2.11.5.1' build 27-Nov-2025 17:31:12 HEADLESS BUILD build 27-Nov-2025 17:31:12 J2S ENABLED build 27-Nov-2025 17:31:13 Using a LOCAL profile. build 27-Nov-2025 17:31:15 eclipseDir exists build 27-Nov-2025 17:31:17 build 27-Nov-2025 17:31:17 > Task :cloverHtmlReport build 27-Nov-2025 17:31:17 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 27-Nov-2025 17:31:18 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/clover' error 27-Nov-2025 17:32:06 ERROR: Invalid Java source found or Clover failed to parse it: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/src/jalview/schemes/ResidueProperties.java build 27-Nov-2025 17:32:13 Done. Processed 117 packages in 54563ms (466ms per package). build 27-Nov-2025 17:32:21 build 27-Nov-2025 17:32:21 > Task :cloverXmlReport build 27-Nov-2025 17:32:21 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 27-Nov-2025 17:32:25 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/clover/clover.xml' build 27-Nov-2025 17:32:25 build 27-Nov-2025 17:32:25 > Task :cloverReport build 27-Nov-2025 17:32:25 build 27-Nov-2025 17:32:25 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 27-Nov-2025 17:32:25 build 27-Nov-2025 17:32:25 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 17:32:25 build 27-Nov-2025 17:32:25 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 27-Nov-2025 17:32:25 build 27-Nov-2025 17:32:25 BUILD SUCCESSFUL in 1m 19s build 27-Nov-2025 17:32:25 2 actionable tasks: 2 executed simple 27-Nov-2025 17:32:25 Finished task 'Clover Report' with result: Success simple 27-Nov-2025 17:32:25 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 27-Nov-2025 17:32:25 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1... simple 27-Nov-2025 17:32:26 Finished task 'TestNG Parser' with result: Success simple 27-Nov-2025 17:32:26 Running post build plugin 'NCover Results Collector' simple 27-Nov-2025 17:32:26 Running post build plugin 'Artifact Copier' simple 27-Nov-2025 17:32:26 Publishing an artifact: Clover Report (System) simple 27-Nov-2025 17:32:31 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 5.878 s simple 27-Nov-2025 17:32:31 Publishing an artifact: TestNG report error 27-Nov-2025 17:32:31 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/tests/test does not exist. simple 27-Nov-2025 17:32:31 The artifact hasn't been successfully published after 4.337 ms simple 27-Nov-2025 17:32:31 Running post build plugin 'Artifactory Release Management Staging' simple 27-Nov-2025 17:32:31 Running post build plugin 'Artifactory Build Info Copier' simple 27-Nov-2025 17:32:31 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 27-Nov-2025 17:32:31 Running post build plugin 'npm Cache Cleanup' simple 27-Nov-2025 17:32:31 Running post build plugin 'Clover Results Collector' simple 27-Nov-2025 17:32:31 Running post build plugin 'Docker Container Cleanup' simple 27-Nov-2025 17:32:31 Finalising the build... simple 27-Nov-2025 17:32:31 Stopping timer. simple 27-Nov-2025 17:32:31 Build JB-GDB727-JOB1-3 completed. simple 27-Nov-2025 17:32:31 Running on server: post build plugin 'NCover Results Collector' simple 27-Nov-2025 17:32:31 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 27-Nov-2025 17:32:31 Running on server: post build plugin 'Clover Delta Calculator' simple 27-Nov-2025 17:32:31 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 27-Nov-2025 17:32:31 All post build plugins have finished simple 27-Nov-2025 17:32:31 Generating build results summary... simple 27-Nov-2025 17:32:32 Saving build results to disk... simple 27-Nov-2025 17:32:32 Logging substituted variables... simple 27-Nov-2025 17:32:32 Indexing build results... simple 27-Nov-2025 17:32:32 Finished building JB-GDB727-JOB1-3.