simple 28-Nov-2024 11:45:00 Build Jalview Builds - Gradle Develop Build - bug-JAL-4492_gradle_build_not_excluding_classes - Clover and Tests #3 (JB-GDB648-JOB1-3) started building on agent Default Agent simple 28-Nov-2024 11:45:00 simple 28-Nov-2024 11:45:00 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1 simple 28-Nov-2024 11:45:00 Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4492_gradle_build_not_excluding_classes - Clover and Tests #3 (JB-GDB648-JOB1-3) simple 28-Nov-2024 11:45:00 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 28-Nov-2024 11:45:00 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1 simple 28-Nov-2024 11:45:00 Updating source code to revision: f1f306f9af0fb1643345831b8880aebb526a5f61 simple 28-Nov-2024 11:45:00 Fetching 'refs/heads/bug/JAL-4492_gradle_build_not_excluding_classes' from 'http://source.jalview.org/git/jalview.git'. simple 28-Nov-2024 11:45:00 Checking out revision f1f306f9af0fb1643345831b8880aebb526a5f61. simple 28-Nov-2024 11:45:00 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 28-Nov-2024 11:45:00 ffe484b..f1f306f bug/JAL-4492_gradle_build_not_excluding_classes -> origin/bug/JAL-4492_gradle_build_not_excluding_classes simple 28-Nov-2024 11:45:00 Already on 'bug/JAL-4492_gradle_build_not_excluding_classes' simple 28-Nov-2024 11:45:00 Your branch is behind 'origin/bug/JAL-4492_gradle_build_not_excluding_classes' by 2 commits, and can be fast-forwarded. simple 28-Nov-2024 11:45:00 (use "git pull" to update your local branch) simple 28-Nov-2024 11:45:00 HEAD is now at f1f306f JAL-3907 Remove no longer used SecurityManager. Will replace functionality with snyk simple 28-Nov-2024 11:45:00 Updated source code to revision: f1f306f9af0fb1643345831b8880aebb526a5f61 simple 28-Nov-2024 11:45:00 Finished task 'Checkout Default Repository' with result: Success simple 28-Nov-2024 11:45:00 Running pre-build action: VCS Version Collector simple 28-Nov-2024 11:45:00 Running pre-build action: Artifactory Release Staging simple 28-Nov-2024 11:45:00 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 28-Nov-2024 11:45:00 Bamboo Artifactory Plugin version: 2.6.2 command 28-Nov-2024 11:45:00 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4492_gradle_build_not_excluding_classes - Clover and Tests #3 (JB-GDB648-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-GDB648-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_revision_number=f1f306f9af0fb1643345831b8880aebb526a5f61\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB648-JOB1-3\nbamboo_repository_46498222_git_branch=bug/JAL-4492_gradle_build_not_excluding_classes\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_46498222_branch_name=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB648-JOB1\nbamboo_shortPlanName=bug-JAL-4492_gradle_build_not_excluding_classes\nbamboo_planRepository_name=Jalview Git\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-GDB648-JOB1-3\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_46498222_name=Jalview Git\nbamboo_shortPlanKey=GDB648\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=f1f306f9af0fb1643345831b8880aebb526a5f61\nbamboo_buildTimeStamp=2024-11-28T11:45:00.392Z\nbamboo_repository_previous_revision_number=ffe484b2223e4a07ded26429b159f02faa082bb2\nbamboo_planRepository_previousRevision=ffe484b2223e4a07ded26429b159f02faa082bb2\nbamboo_repository_git_branch=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_buildResultKey=JB-GDB648-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4492_gradle_build_not_excluding_classes - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=f1f306f9af0fb1643345831b8880aebb526a5f61\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498222_git_username=\nbamboo_repository_name=Jalview Git\nbamboo_repository_46498222_revision_number=f1f306f9af0fb1643345831b8880aebb526a5f61\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_46498222_previous_revision_number=ffe484b2223e4a07ded26429b159f02faa082bb2\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_46498222_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branch=bug/JAL-4492_gradle_build_not_excluding_classes\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=ffe484b2223e4a07ded26429b159f02faa082bb2\nbamboo_planRepository_branchDisplayName=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4492_gradle_build_not_excluding_classes\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-46302043\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=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-GDB648-JOB1\nbamboo_planKey=JB-GDB648\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4492_gradle_build_not_excluding_classes\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 28-Nov-2024 11:45:00 444 build 28-Nov-2024 11:45:02 Starting a Gradle Daemon (subsequent builds will be faster) build 28-Nov-2024 11:45:15 build 28-Nov-2024 11:45:15 > Configure project : build 28-Nov-2024 11:45:15 Using properties from file './utils/channels/default/channel_gradle.properties' build 28-Nov-2024 11:45:15 JALVIEW_VERSION is set to '2.11.4.2' build 28-Nov-2024 11:45:15 HEADLESS BUILD build 28-Nov-2024 11:45:15 J2S ENABLED build 28-Nov-2024 11:45:15 Using a LOCAL profile. build 28-Nov-2024 11:45:17 eclipseDir exists build 28-Nov-2024 11:45:18 build 28-Nov-2024 11:45:18 > Task :clean build 28-Nov-2024 11:45:18 > Task :cleanClover build 28-Nov-2024 11:45:18 > Task :cleanTest UP-TO-DATE build 28-Nov-2024 11:45:20 build 28-Nov-2024 11:45:20 > Task :cloverInstrJava build 28-Nov-2024 11:45:20 Clover: About to instrument 1050 files build 28-Nov-2024 11:45:20 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 28-Nov-2024 11:45:20 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/clover/clover.db'. build 28-Nov-2024 11:45:20 Processing files at 1.9 source level. error 28-Nov-2024 11:45:22 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 28-Nov-2024 11:45:22 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 28-Nov-2024 11:45:22 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 28-Nov-2024 11:45:22 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 28-Nov-2024 11:45:22 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 28-Nov-2024 11:45:22 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 28-Nov-2024 11:45:22 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 28-Nov-2024 11:45:29 Clover all over. Instrumented 1050 files (109 packages). build 28-Nov-2024 11:45:32 build 28-Nov-2024 11:45:32 > Task :cloverInstrTests build 28-Nov-2024 11:45:32 Clover: About to instrument test files build 28-Nov-2024 11:45:32 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 28-Nov-2024 11:45:32 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/clover/clover.db'. build 28-Nov-2024 11:45:32 Processing files at 1.9 source level. build 28-Nov-2024 11:45:34 Clover all over. Instrumented 291 files (52 packages). build 28-Nov-2024 11:45:34 1597 test methods detected. build 28-Nov-2024 11:45:35 build 28-Nov-2024 11:45:35 > Task :cloverInstr build 28-Nov-2024 11:45:37 build 28-Nov-2024 11:45:37 > Task :compileCloverJava build 28-Nov-2024 11:45:37 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 28-Nov-2024 11:45:37 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:45:37 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:45:37 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:45:37 Setting target compatibility to 11 error 28-Nov-2024 11:45:57 Note: Some input files use or override a deprecated API. error 28-Nov-2024 11:45:57 Note: Recompile with -Xlint:deprecation for details. error 28-Nov-2024 11:45:57 Note: Some input files use unchecked or unsafe operations. error 28-Nov-2024 11:45:57 Note: Recompile with -Xlint:unchecked for details. build 28-Nov-2024 11:46:04 build 28-Nov-2024 11:46:04 > Task :processCloverResources NO-SOURCE build 28-Nov-2024 11:46:04 > Task :cloverClasses build 28-Nov-2024 11:46:04 > Task :copyHelp build 28-Nov-2024 11:46:05 > Task :buildIndices build 28-Nov-2024 11:46:05 > Task :copyResources build 28-Nov-2024 11:46:05 > Task :copyChannelResources build 28-Nov-2024 11:46:05 build 28-Nov-2024 11:46:05 > Task :createBuildProperties build 28-Nov-2024 11:46:05 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 28-Nov-2024 11:46:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:46:05 build 28-Nov-2024 11:46:05 > Task :buildResources build 28-Nov-2024 11:46:06 > Task :copyDocs build 28-Nov-2024 11:46:06 build 28-Nov-2024 11:46:06 > Task :convertMdFiles build 28-Nov-2024 11:46:06 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 28-Nov-2024 11:46:06 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/resources/doc_build/doc/releaseprocess.html build 28-Nov-2024 11:46:06 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 28-Nov-2024 11:46:06 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/resources/doc_build/doc/building.html build 28-Nov-2024 11:46:06 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/resources/doc_build/doc/jalview-projects.html build 28-Nov-2024 11:46:07 build 28-Nov-2024 11:46:07 > Task :releasesTemplates build 28-Nov-2024 11:46:07 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 28-Nov-2024 11:46:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:46:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:46:07 Stripping rc/test/etc for TEST build 28-Nov-2024 11:46:07 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 28-Nov-2024 11:46:07 build 28-Nov-2024 11:46:07 > Task :prepare build 28-Nov-2024 11:46:09 build 28-Nov-2024 11:46:09 > Task :compileJava build 28-Nov-2024 11:46:09 Setting target compatibility to 11 error 28-Nov-2024 11:46:14 Note: Some input files use or override a deprecated API. error 28-Nov-2024 11:46:14 Note: Recompile with -Xlint:deprecation for details. error 28-Nov-2024 11:46:14 Note: Some input files use unchecked or unsafe operations. error 28-Nov-2024 11:46:14 Note: Recompile with -Xlint:unchecked for details. build 28-Nov-2024 11:46:18 build 28-Nov-2024 11:46:18 > Task :compileTestJava build 28-Nov-2024 11:46:18 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 28-Nov-2024 11:46:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:46:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:46:18 Setting target compatibility to 11 error 28-Nov-2024 11:46:24 Note: Some input files use or override a deprecated API. error 28-Nov-2024 11:46:24 Note: Recompile with -Xlint:deprecation for details. error 28-Nov-2024 11:46:24 Note: Some input files use unchecked or unsafe operations. error 28-Nov-2024 11:46:24 Note: Recompile with -Xlint:unchecked for details. build 28-Nov-2024 11:46:25 build 28-Nov-2024 11:46:25 > Task :processTestResources build 28-Nov-2024 11:46:25 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 28-Nov-2024 11:46:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:46:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:46:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:46:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:46:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:46:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:46:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:46:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-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 28-Nov-2024 11:46:25 build 28-Nov-2024 11:46:25 > Task :testClasses build 28-Nov-2024 11:46:27 build 28-Nov-2024 11:46:27 > Task :testTask0 build 28-Nov-2024 11:46:27 Running tests WITH clover error 28-Nov-2024 11:46:31 WARNING: An illegal reflective access operation has occurred error 28-Nov-2024 11:46:31 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 28-Nov-2024 11:46:31 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 28-Nov-2024 11:46:31 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 28-Nov-2024 11:46:31 WARNING: All illegal access operations will be denied in a future release build 28-Nov-2024 11:50:22 build 28-Nov-2024 11:50:22 > Task :testTask1 build 28-Nov-2024 11:50:22 Running tests WITH clover error 28-Nov-2024 11:50:24 WARNING: An illegal reflective access operation has occurred error 28-Nov-2024 11:50:24 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 28-Nov-2024 11:50:24 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 28-Nov-2024 11:50:24 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 28-Nov-2024 11:50:24 WARNING: All illegal access operations will be denied in a future release build 28-Nov-2024 11:51:58 build 28-Nov-2024 11:51:58 > Task :testTask2 build 28-Nov-2024 11:51:58 Running tests WITH clover build 28-Nov-2024 11:52:02 build 28-Nov-2024 11:52:02 > Task :testTask3 build 28-Nov-2024 11:52:02 Running tests WITH clover error 28-Nov-2024 11:52:04 WARNING: An illegal reflective access operation has occurred error 28-Nov-2024 11:52:04 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 28-Nov-2024 11:52:04 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 28-Nov-2024 11:52:04 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 28-Nov-2024 11:52:04 WARNING: All illegal access operations will be denied in a future release build 28-Nov-2024 11:52:50 build 28-Nov-2024 11:52:50 > Task :test NO-SOURCE build 28-Nov-2024 11:52:50 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 28-Nov-2024 11:52:50 │jalview:testTask0 results: SUCCESS (1744 tests, 1744 successes, 0 failures, 0 skipped) in 3 minutes, 54.699 seconds │ build 28-Nov-2024 11:52:50 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/reports/tests/testTask0/index.html│ build 28-Nov-2024 11:52:50 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 28-Nov-2024 11:52:50 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 35.861 seconds │ build 28-Nov-2024 11:52:50 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/reports/tests/testTask1/index.html│ build 28-Nov-2024 11:52:50 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 28-Nov-2024 11:52:50 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.655 seconds │ build 28-Nov-2024 11:52:50 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/reports/tests/testTask2/index.html│ build 28-Nov-2024 11:52:50 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 28-Nov-2024 11:52:50 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 49.628 seconds │ build 28-Nov-2024 11:52:50 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/reports/tests/testTask3/index.html│ build 28-Nov-2024 11:52:50 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 28-Nov-2024 11:52:50 │OVERALL: results: SUCCESS (1819 tests, 1819 successes, 0 failures, 0 skipped) in 4 minutes, 143.843 seconds │ build 28-Nov-2024 11:52:50 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 28-Nov-2024 11:52:50 build 28-Nov-2024 11:52:50 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 28-Nov-2024 11:52:50 build 28-Nov-2024 11:52:50 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 28-Nov-2024 11:52:50 build 28-Nov-2024 11:52:50 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 28-Nov-2024 11:52:50 build 28-Nov-2024 11:52:50 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 28-Nov-2024 11:52:50 Please consult deprecation warnings for more details. build 28-Nov-2024 11:52:50 build 28-Nov-2024 11:52:50 BUILD SUCCESSFUL in 7m 49s build 28-Nov-2024 11:52:50 21 actionable tasks: 20 executed, 1 up-to-date simple 28-Nov-2024 11:52:50 Finished task 'Run tests with openclover under gradle' with result: Success simple 28-Nov-2024 11:52:50 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 28-Nov-2024 11:52:50 Bamboo Artifactory Plugin version: 2.6.2 command 28-Nov-2024 11:52:50 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4492_gradle_build_not_excluding_classes - Clover and Tests #3 (JB-GDB648-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-GDB648-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_revision_number=f1f306f9af0fb1643345831b8880aebb526a5f61\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB648-JOB1-3\nbamboo_repository_46498222_git_branch=bug/JAL-4492_gradle_build_not_excluding_classes\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_46498222_branch_name=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB648-JOB1\nbamboo_shortPlanName=bug-JAL-4492_gradle_build_not_excluding_classes\nbamboo_planRepository_name=Jalview Git\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-GDB648-JOB1-3\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_46498222_name=Jalview Git\nbamboo_shortPlanKey=GDB648\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=f1f306f9af0fb1643345831b8880aebb526a5f61\nbamboo_buildTimeStamp=2024-11-28T11:45:00.392Z\nbamboo_repository_previous_revision_number=ffe484b2223e4a07ded26429b159f02faa082bb2\nbamboo_planRepository_previousRevision=ffe484b2223e4a07ded26429b159f02faa082bb2\nbamboo_repository_git_branch=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_buildResultKey=JB-GDB648-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4492_gradle_build_not_excluding_classes - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=f1f306f9af0fb1643345831b8880aebb526a5f61\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498222_git_username=\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\nbamboo_repository_46498222_revision_number=f1f306f9af0fb1643345831b8880aebb526a5f61\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_46498222_previous_revision_number=ffe484b2223e4a07ded26429b159f02faa082bb2\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_46498222_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branch=bug/JAL-4492_gradle_build_not_excluding_classes\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=ffe484b2223e4a07ded26429b159f02faa082bb2\nbamboo_planRepository_branchDisplayName=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4492_gradle_build_not_excluding_classes\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-46302043\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=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-GDB648-JOB1\nbamboo_planKey=JB-GDB648\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4492_gradle_build_not_excluding_classes\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 28-Nov-2024 11:52:50 444 build 28-Nov-2024 11:52:59 build 28-Nov-2024 11:52:59 > Configure project : build 28-Nov-2024 11:52:59 Using properties from file './utils/channels/default/channel_gradle.properties' build 28-Nov-2024 11:52:59 JALVIEW_VERSION is set to '2.11.4.2' build 28-Nov-2024 11:52:59 HEADLESS BUILD build 28-Nov-2024 11:52:59 J2S ENABLED build 28-Nov-2024 11:52:59 Using a LOCAL profile. build 28-Nov-2024 11:53:01 eclipseDir exists build 28-Nov-2024 11:53:03 build 28-Nov-2024 11:53:03 > Task :cloverHtmlReport build 28-Nov-2024 11:53:03 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 28-Nov-2024 11:53:04 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/reports/clover' build 28-Nov-2024 11:53:40 Done. Processed 113 packages in 35960ms (318ms per package). build 28-Nov-2024 11:53:45 build 28-Nov-2024 11:53:45 > Task :cloverXmlReport build 28-Nov-2024 11:53:45 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 28-Nov-2024 11:53:46 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/reports/clover/clover.xml' build 28-Nov-2024 11:53:46 build 28-Nov-2024 11:53:46 > Task :cloverReport build 28-Nov-2024 11:53:46 build 28-Nov-2024 11:53:46 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 28-Nov-2024 11:53:46 build 28-Nov-2024 11:53:46 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 28-Nov-2024 11:53:46 build 28-Nov-2024 11:53:46 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 28-Nov-2024 11:53:46 build 28-Nov-2024 11:53:46 BUILD SUCCESSFUL in 55s build 28-Nov-2024 11:53:46 2 actionable tasks: 2 executed simple 28-Nov-2024 11:53:46 Finished task 'Clover Report' with result: Success simple 28-Nov-2024 11:53:46 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 28-Nov-2024 11:53:46 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1... simple 28-Nov-2024 11:53:46 Finished task 'TestNG Parser' with result: Success simple 28-Nov-2024 11:53:46 Running post build plugin 'NCover Results Collector' simple 28-Nov-2024 11:53:46 Running post build plugin 'Artifact Copier' simple 28-Nov-2024 11:53:46 Publishing an artifact: Clover Report (System) simple 28-Nov-2024 11:53:48 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.461 s simple 28-Nov-2024 11:53:48 Publishing an artifact: TestNG report error 28-Nov-2024 11:53:48 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB648-JOB1/build/reports/tests/test does not exist. simple 28-Nov-2024 11:53:48 The artifact hasn't been successfully published after 1.478 ms simple 28-Nov-2024 11:53:48 Running post build plugin 'Artifactory Release Management Staging' simple 28-Nov-2024 11:53:48 Running post build plugin 'Artifactory Build Info Copier' simple 28-Nov-2024 11:53:48 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 28-Nov-2024 11:53:48 Running post build plugin 'npm Cache Cleanup' simple 28-Nov-2024 11:53:48 Running post build plugin 'Clover Results Collector' simple 28-Nov-2024 11:53:48 Running post build plugin 'Docker Container Cleanup' simple 28-Nov-2024 11:53:48 Finalising the build... simple 28-Nov-2024 11:53:48 Stopping timer. simple 28-Nov-2024 11:53:48 Build JB-GDB648-JOB1-3 completed. simple 28-Nov-2024 11:53:48 Running on server: post build plugin 'NCover Results Collector' simple 28-Nov-2024 11:53:48 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 28-Nov-2024 11:53:48 Running on server: post build plugin 'Clover Delta Calculator' simple 28-Nov-2024 11:53:48 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 28-Nov-2024 11:53:48 All post build plugins have finished simple 28-Nov-2024 11:53:48 Generating build results summary... simple 28-Nov-2024 11:53:48 Saving build results to disk... simple 28-Nov-2024 11:53:48 Logging substituted variables... simple 28-Nov-2024 11:53:48 Indexing build results... simple 28-Nov-2024 11:53:48 Finished building JB-GDB648-JOB1-3.