simple 06-Jan-2025 10:27:12 Build Jalview Builds - Gradle Develop Build - Clover and Tests #699 (JB-GDB-JOB1-699) started building on agent Default Agent simple 06-Jan-2025 10:27:12 simple 06-Jan-2025 10:27:12 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1 simple 06-Jan-2025 10:27:12 Executing build Jalview Builds - Gradle Develop Build - Clover and Tests #699 (JB-GDB-JOB1-699) simple 06-Jan-2025 10:27:12 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 06-Jan-2025 10:27:12 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1 simple 06-Jan-2025 10:27:12 Updating source code to revision: 1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a simple 06-Jan-2025 10:27:13 Fetching 'refs/heads/develop' from 'http://source.jalview.org/git/jalview.git'. simple 06-Jan-2025 10:27:14 Checking out revision 1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a. simple 06-Jan-2025 10:27:15 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 06-Jan-2025 10:27:15 544bd63..1dad9dc develop -> origin/develop simple 06-Jan-2025 10:27:15 1da3b80..5275010 JAL-4474_jalview.ps1_not_working -> origin/JAL-4474_jalview.ps1_not_working simple 06-Jan-2025 10:27:15 a8875a0..72a0f1e bug/JAL-4477_unmapped_filename_characters -> origin/bug/JAL-4477_unmapped_filename_characters simple 06-Jan-2025 10:27:15 * [new branch] bug/JAL-4492_gradle_build_not_excluding_classes -> origin/bug/JAL-4492_gradle_build_not_excluding_classes simple 06-Jan-2025 10:27:15 1c79fdc..39291a3 feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels simple 06-Jan-2025 10:27:15 * [new branch] features/JAL-3914_modelqualityscores_v2115 -> origin/features/JAL-3914_modelqualityscores_v2115 simple 06-Jan-2025 10:27:15 * [new branch] patch/JAL-4333_translatecodonexception -> origin/patch/JAL-4333_translatecodonexception simple 06-Jan-2025 10:27:15 * [new branch] spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure -> origin/spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure simple 06-Jan-2025 10:27:16 Already on 'develop' simple 06-Jan-2025 10:27:16 Your branch is behind 'origin/develop' by 2 commits, and can be fast-forwarded. simple 06-Jan-2025 10:27:16 (use "git pull" to update your local branch) simple 06-Jan-2025 10:27:16 HEAD is now at 1dad9dc JAL-4503 failing test for checking location of Jmol view when restoring from project - currently disabled simple 06-Jan-2025 10:27:16 Updated source code to revision: 1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a simple 06-Jan-2025 10:27:16 Finished task 'Checkout Default Repository' with result: Success simple 06-Jan-2025 10:27:16 Running pre-build action: VCS Version Collector simple 06-Jan-2025 10:27:16 Running pre-build action: Artifactory Release Staging simple 06-Jan-2025 10:27:16 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 06-Jan-2025 10:27:16 Bamboo Artifactory Plugin version: 2.6.2 command 06-Jan-2025 10:27:16 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - Clover and Tests #699 (JB-GDB-JOB1-699)'\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-GDB-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB-JOB1-699\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-GDB-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB-JOB1\nbamboo_shortPlanName=Gradle Develop Build\nbamboo_repository_8060939_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_8060939_git_username=\nLOGNAME=bamboo\nbamboo_buildNumber=699\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-GDB-JOB1-699\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build\nbamboo_shortPlanKey=GDB\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_buildTimeStamp=2025-01-06T10:26:47.035Z\nbamboo_repository_previous_revision_number=544bd63f8e2c0122da4f309bdc415162fc1da737\nbamboo_repository_8060939_branch_name=develop\nbamboo_planRepository_previousRevision=544bd63f8e2c0122da4f309bdc415162fc1da737\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-GDB-JOB1-699\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - Clover and Tests\nbamboo_repository_8060939_name=Jalview Git\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_8060939_git_branch=develop\nbamboo_planRepository_branch=develop\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=544bd63f8e2c0122da4f309bdc415162fc1da737\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\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-7864341\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_8060939_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_repository_8060939_previous_revision_number=544bd63f8e2c0122da4f309bdc415162fc1da737\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=http://source.jalview.org/git/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-GDB-JOB1\nbamboo_planKey=JB-GDB\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 06-Jan-2025 10:27:16 444 build 06-Jan-2025 10:27:23 build 06-Jan-2025 10:27:23 > Configure project : build 06-Jan-2025 10:27:23 Using properties from file './utils/channels/default/channel_gradle.properties' build 06-Jan-2025 10:27:23 JALVIEW_VERSION is set to '2.11.4.2' build 06-Jan-2025 10:27:23 HEADLESS BUILD build 06-Jan-2025 10:27:23 J2S ENABLED build 06-Jan-2025 10:27:23 Using a LOCAL profile. build 06-Jan-2025 10:27:23 eclipseDir exists build 06-Jan-2025 10:27:25 build 06-Jan-2025 10:27:25 > Task :clean build 06-Jan-2025 10:27:25 > Task :cleanClover build 06-Jan-2025 10:27:25 > Task :cleanTest UP-TO-DATE build 06-Jan-2025 10:27:27 build 06-Jan-2025 10:27:27 > Task :cloverInstrJava build 06-Jan-2025 10:27:27 Clover: About to instrument 1103 files build 06-Jan-2025 10:27:30 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Jan-2025 10:27:30 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover.db'. build 06-Jan-2025 10:27:31 Processing files at 1.9 source level. error 06-Jan-2025 10:27:38 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 06-Jan-2025 10:27:38 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 06-Jan-2025 10:27:38 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 06-Jan-2025 10:27:38 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 06-Jan-2025 10:27:38 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 06-Jan-2025 10:27:38 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 06-Jan-2025 10:27:38 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 06-Jan-2025 10:27:49 Clover all over. Instrumented 1103 files (112 packages). build 06-Jan-2025 10:27:51 build 06-Jan-2025 10:27:51 > Task :cloverInstrTests build 06-Jan-2025 10:27:51 Clover: About to instrument test files build 06-Jan-2025 10:27:51 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Jan-2025 10:27:51 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover.db'. build 06-Jan-2025 10:27:51 Processing files at 1.9 source level. build 06-Jan-2025 10:27:57 Clover all over. Instrumented 291 files (52 packages). build 06-Jan-2025 10:27:57 1598 test methods detected. build 06-Jan-2025 10:27:57 build 06-Jan-2025 10:27:57 > Task :cloverInstr build 06-Jan-2025 10:27:59 build 06-Jan-2025 10:27:59 > Task :compileCloverJava build 06-Jan-2025 10:27:59 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 06-Jan-2025 10:27:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:27:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:27:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:27:59 Setting target compatibility to 11 error 06-Jan-2025 10:28:23 Note: Some input files use or override a deprecated API. error 06-Jan-2025 10:28:23 Note: Recompile with -Xlint:deprecation for details. error 06-Jan-2025 10:28:23 Note: Some input files use unchecked or unsafe operations. error 06-Jan-2025 10:28:23 Note: Recompile with -Xlint:unchecked for details. build 06-Jan-2025 10:29:08 build 06-Jan-2025 10:29:08 > Task :processCloverResources NO-SOURCE build 06-Jan-2025 10:29:08 > Task :cloverClasses build 06-Jan-2025 10:29:11 > Task :copyHelp build 06-Jan-2025 10:29:12 > Task :buildIndices build 06-Jan-2025 10:29:13 > Task :copyResources build 06-Jan-2025 10:29:13 > Task :copyChannelResources build 06-Jan-2025 10:29:13 build 06-Jan-2025 10:29:13 > Task :createBuildProperties build 06-Jan-2025 10:29:13 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 06-Jan-2025 10:29:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:29:13 build 06-Jan-2025 10:29:13 > Task :buildResources build 06-Jan-2025 10:29:14 > Task :copyDocs build 06-Jan-2025 10:29:15 build 06-Jan-2025 10:29:15 > Task :convertMdFiles build 06-Jan-2025 10:29:15 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 06-Jan-2025 10:29:15 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/releaseprocess.html build 06-Jan-2025 10:29:15 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 06-Jan-2025 10:29:15 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/building.html build 06-Jan-2025 10:29:15 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/jalview-projects.html build 06-Jan-2025 10:29:16 build 06-Jan-2025 10:29:16 > Task :releasesTemplates build 06-Jan-2025 10:29:16 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 06-Jan-2025 10:29:16 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:29:16 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:29:16 Stripping rc/test/etc for TEST build 06-Jan-2025 10:29:16 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 06-Jan-2025 10:29:16 build 06-Jan-2025 10:29:16 > Task :prepare build 06-Jan-2025 10:29:18 build 06-Jan-2025 10:29:18 > Task :compileJava build 06-Jan-2025 10:29:18 Setting target compatibility to 11 error 06-Jan-2025 10:29:23 Note: Some input files use or override a deprecated API. error 06-Jan-2025 10:29:23 Note: Recompile with -Xlint:deprecation for details. error 06-Jan-2025 10:29:23 Note: Some input files use unchecked or unsafe operations. error 06-Jan-2025 10:29:23 Note: Recompile with -Xlint:unchecked for details. build 06-Jan-2025 10:29:35 build 06-Jan-2025 10:29:35 > Task :compileTestJava build 06-Jan-2025 10:29:35 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 06-Jan-2025 10:29:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:29:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:29:35 Setting target compatibility to 11 error 06-Jan-2025 10:29:41 Note: Some input files use or override a deprecated API. error 06-Jan-2025 10:29:41 Note: Recompile with -Xlint:deprecation for details. error 06-Jan-2025 10:29:41 Note: Some input files use unchecked or unsafe operations. error 06-Jan-2025 10:29:41 Note: Recompile with -Xlint:unchecked for details. build 06-Jan-2025 10:29:44 build 06-Jan-2025 10:29:44 > Task :processTestResources build 06-Jan-2025 10:29:44 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 06-Jan-2025 10:29:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:29:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:29:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:29:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:29:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:29:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:29:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:29:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 06-Jan-2025 10:29:44 build 06-Jan-2025 10:29:44 > Task :testClasses build 06-Jan-2025 10:29:46 build 06-Jan-2025 10:29:46 > Task :testTask0 build 06-Jan-2025 10:29:46 Running tests WITH clover error 06-Jan-2025 10:29:51 WARNING: An illegal reflective access operation has occurred error 06-Jan-2025 10:29:51 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 06-Jan-2025 10:29:51 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 06-Jan-2025 10:29:51 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 06-Jan-2025 10:29:51 WARNING: All illegal access operations will be denied in a future release build 06-Jan-2025 10:33:43 build 06-Jan-2025 10:33:43 > Task :testTask1 build 06-Jan-2025 10:33:43 Running tests WITH clover error 06-Jan-2025 10:33:44 WARNING: An illegal reflective access operation has occurred error 06-Jan-2025 10:33:44 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 06-Jan-2025 10:33:44 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 06-Jan-2025 10:33:44 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 06-Jan-2025 10:33:44 WARNING: All illegal access operations will be denied in a future release build 06-Jan-2025 10:35:17 build 06-Jan-2025 10:35:17 > Task :testTask2 build 06-Jan-2025 10:35:17 Running tests WITH clover build 06-Jan-2025 10:35:21 build 06-Jan-2025 10:35:21 > Task :testTask3 build 06-Jan-2025 10:35:21 Running tests WITH clover error 06-Jan-2025 10:35:22 WARNING: An illegal reflective access operation has occurred error 06-Jan-2025 10:35:22 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 06-Jan-2025 10:35:22 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 06-Jan-2025 10:35:22 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 06-Jan-2025 10:35:22 WARNING: All illegal access operations will be denied in a future release build 06-Jan-2025 10:36:08 build 06-Jan-2025 10:36:08 > Task :test NO-SOURCE build 06-Jan-2025 10:36:08 ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 06-Jan-2025 10:36:08 │jalview:testTask0 results: SUCCESS (1746 tests, 1746 successes, 0 failures, 0 skipped) in 3 minutes, 55.099 seconds│ build 06-Jan-2025 10:36:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask0/index.html│ build 06-Jan-2025 10:36:08 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Jan-2025 10:36:08 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 34.427 seconds │ build 06-Jan-2025 10:36:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask1/index.html│ build 06-Jan-2025 10:36:08 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Jan-2025 10:36:08 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.425 seconds │ build 06-Jan-2025 10:36:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask2/index.html│ build 06-Jan-2025 10:36:08 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Jan-2025 10:36:08 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 49.309 seconds │ build 06-Jan-2025 10:36:08 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask3/index.html│ build 06-Jan-2025 10:36:08 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Jan-2025 10:36:08 │OVERALL: results: SUCCESS (1821 tests, 1821 successes, 0 failures, 0 skipped) in 4 minutes, 142.260 seconds │ build 06-Jan-2025 10:36:08 └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 06-Jan-2025 10:36:08 build 06-Jan-2025 10:36:08 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 06-Jan-2025 10:36:08 build 06-Jan-2025 10:36:08 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 06-Jan-2025 10:36:08 build 06-Jan-2025 10:36:08 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 06-Jan-2025 10:36:08 build 06-Jan-2025 10:36:08 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 06-Jan-2025 10:36:08 Please consult deprecation warnings for more details. build 06-Jan-2025 10:36:08 build 06-Jan-2025 10:36:08 BUILD SUCCESSFUL in 8m 51s build 06-Jan-2025 10:36:08 21 actionable tasks: 20 executed, 1 up-to-date simple 06-Jan-2025 10:36:09 Finished task 'Run tests with openclover under gradle' with result: Success simple 06-Jan-2025 10:36:09 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 06-Jan-2025 10:36:09 Bamboo Artifactory Plugin version: 2.6.2 command 06-Jan-2025 10:36:09 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - Clover and Tests #699 (JB-GDB-JOB1-699)'\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-GDB-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB-JOB1-699\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-GDB-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB-JOB1\nbamboo_shortPlanName=Gradle Develop Build\nbamboo_repository_8060939_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_8060939_git_username=\nLOGNAME=bamboo\nbamboo_buildNumber=699\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-GDB-JOB1-699\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build\nbamboo_shortPlanKey=GDB\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nbamboo_buildTimeStamp=2025-01-06T10:26:47.035Z\nbamboo_repository_previous_revision_number=544bd63f8e2c0122da4f309bdc415162fc1da737\nbamboo_repository_8060939_branch_name=develop\nbamboo_planRepository_previousRevision=544bd63f8e2c0122da4f309bdc415162fc1da737\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-GDB-JOB1-699\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - Clover and Tests\nbamboo_repository_8060939_name=Jalview Git\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_8060939_git_branch=develop\nbamboo_planRepository_branch=develop\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=544bd63f8e2c0122da4f309bdc415162fc1da737\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\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-7864341\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_8060939_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_repository_8060939_previous_revision_number=544bd63f8e2c0122da4f309bdc415162fc1da737\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=http://source.jalview.org/git/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-GDB-JOB1\nbamboo_planKey=JB-GDB\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 06-Jan-2025 10:36:09 444 build 06-Jan-2025 10:36:19 build 06-Jan-2025 10:36:19 > Configure project : build 06-Jan-2025 10:36:19 Using properties from file './utils/channels/default/channel_gradle.properties' build 06-Jan-2025 10:36:19 JALVIEW_VERSION is set to '2.11.4.2' build 06-Jan-2025 10:36:19 HEADLESS BUILD build 06-Jan-2025 10:36:19 J2S ENABLED build 06-Jan-2025 10:36:20 Using a LOCAL profile. build 06-Jan-2025 10:36:21 eclipseDir exists build 06-Jan-2025 10:36:23 build 06-Jan-2025 10:36:23 > Task :cloverHtmlReport build 06-Jan-2025 10:36:23 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Jan-2025 10:36:25 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/clover' build 06-Jan-2025 10:37:06 Done. Processed 116 packages in 40783ms (351ms per package). build 06-Jan-2025 10:37:13 build 06-Jan-2025 10:37:13 > Task :cloverXmlReport build 06-Jan-2025 10:37:13 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Jan-2025 10:37:16 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/clover/clover.xml' build 06-Jan-2025 10:37:16 build 06-Jan-2025 10:37:16 > Task :cloverReport build 06-Jan-2025 10:37:16 build 06-Jan-2025 10:37:16 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 06-Jan-2025 10:37:16 build 06-Jan-2025 10:37:16 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 06-Jan-2025 10:37:16 build 06-Jan-2025 10:37:16 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 06-Jan-2025 10:37:16 build 06-Jan-2025 10:37:16 BUILD SUCCESSFUL in 1m 7s build 06-Jan-2025 10:37:16 2 actionable tasks: 2 executed simple 06-Jan-2025 10:37:18 Finished task 'Clover Report' with result: Success simple 06-Jan-2025 10:37:18 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 06-Jan-2025 10:37:18 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1... simple 06-Jan-2025 10:37:18 Finished task 'TestNG Parser' with result: Success simple 06-Jan-2025 10:37:18 Running post build plugin 'NCover Results Collector' simple 06-Jan-2025 10:37:18 Running post build plugin 'Artifact Copier' simple 06-Jan-2025 10:37:18 Publishing an artifact: Clover Report (System) simple 06-Jan-2025 10:37:20 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.417 s simple 06-Jan-2025 10:37:20 Publishing an artifact: TestNG report error 06-Jan-2025 10:37:20 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/test does not exist. simple 06-Jan-2025 10:37:20 The artifact hasn't been successfully published after 2.290 ms simple 06-Jan-2025 10:37:20 Running post build plugin 'Artifactory Release Management Staging' simple 06-Jan-2025 10:37:20 Running post build plugin 'Artifactory Build Info Copier' simple 06-Jan-2025 10:37:20 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 06-Jan-2025 10:37:20 Running post build plugin 'npm Cache Cleanup' simple 06-Jan-2025 10:37:20 Running post build plugin 'Clover Results Collector' simple 06-Jan-2025 10:37:20 Running post build plugin 'Docker Container Cleanup' simple 06-Jan-2025 10:37:20 Finalising the build... simple 06-Jan-2025 10:37:20 Stopping timer. simple 06-Jan-2025 10:37:20 Build JB-GDB-JOB1-699 completed. simple 06-Jan-2025 10:37:20 Running on server: post build plugin 'NCover Results Collector' simple 06-Jan-2025 10:37:20 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 06-Jan-2025 10:37:20 Running on server: post build plugin 'Clover Delta Calculator' simple 06-Jan-2025 10:37:20 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 06-Jan-2025 10:37:20 All post build plugins have finished simple 06-Jan-2025 10:37:20 Generating build results summary... simple 06-Jan-2025 10:37:20 Saving build results to disk... simple 06-Jan-2025 10:37:20 Logging substituted variables... simple 06-Jan-2025 10:37:20 Indexing build results... simple 06-Jan-2025 10:37:20 Finished building JB-GDB-JOB1-699.