simple 29-Oct-2024 21:36:39 Build Jalview Builds - Gradle Develop Build - releases-Release_2_11_4_Branch - Clover and Tests #3 (JB-GDB636-JOB1-3) started building on agent Default Agent simple 29-Oct-2024 21:36:39 simple 29-Oct-2024 21:36:39 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1 simple 29-Oct-2024 21:36:39 Executing build Jalview Builds - Gradle Develop Build - releases-Release_2_11_4_Branch - Clover and Tests #3 (JB-GDB636-JOB1-3) simple 29-Oct-2024 21:36:39 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 29-Oct-2024 21:36:39 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1 simple 29-Oct-2024 21:36:39 Updating source code to revision: 6d1fc3490ca522df0ad2f6f25cadcff87a91eec9 simple 29-Oct-2024 21:36:40 Fetching 'refs/heads/releases/Release_2_11_4_Branch' from 'http://source.jalview.org/git/jalview.git'. simple 29-Oct-2024 21:36:40 Checking out revision 6d1fc3490ca522df0ad2f6f25cadcff87a91eec9. simple 29-Oct-2024 21:36:40 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 29-Oct-2024 21:36:40 10a9794..6d1fc34 releases/Release_2_11_4_Branch -> origin/releases/Release_2_11_4_Branch simple 29-Oct-2024 21:36:40 * [new branch] bug/JAL-4477_unmapped_filename_characters -> origin/bug/JAL-4477_unmapped_filename_characters simple 29-Oct-2024 21:36:40 6cbc639..9fb123c develop -> origin/develop simple 29-Oct-2024 21:36:40 Already on 'releases/Release_2_11_4_Branch' simple 29-Oct-2024 21:36:40 Your branch is behind 'origin/releases/Release_2_11_4_Branch' by 4 commits, and can be fast-forwarded. simple 29-Oct-2024 21:36:40 (use "git pull" to update your local branch) simple 29-Oct-2024 21:36:40 HEAD is now at 6d1fc34 Merge branch 'develop' into releases/Release_2_11_4_Branch simple 29-Oct-2024 21:36:40 Updated source code to revision: 6d1fc3490ca522df0ad2f6f25cadcff87a91eec9 simple 29-Oct-2024 21:36:40 Finished task 'Checkout Default Repository' with result: Success simple 29-Oct-2024 21:36:40 Running pre-build action: VCS Version Collector simple 29-Oct-2024 21:36:40 Running pre-build action: Artifactory Release Staging simple 29-Oct-2024 21:36:40 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 29-Oct-2024 21:36:40 Bamboo Artifactory Plugin version: 2.6.2 command 29-Oct-2024 21:36:40 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - releases-Release_2_11_4_Branch - Clover and Tests #3 (JB-GDB636-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-GDB636-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=releases/Release_2_11_4_Branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_repository_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB636-JOB1-3\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-GDB636-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB636-JOB1\nbamboo_shortPlanName=releases-Release_2_11_4_Branch\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-GDB636-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 - releases-Release_2_11_4_Branch\nbamboo_shortPlanKey=GDB636\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498153_git_username=\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_buildTimeStamp=2024-10-29T21:34:00.838Z\nbamboo_repository_previous_revision_number=10a9794a2580ed9e589ecb708c186b28133771c4\nbamboo_planRepository_previousRevision=10a9794a2580ed9e589ecb708c186b28133771c4\nbamboo_repository_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultKey=JB-GDB636-JOB1-3\nbamboo_repository_branch_name=releases/Release_2_11_4_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - releases-Release_2_11_4_Branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\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_46498153_previous_revision_number=10a9794a2580ed9e589ecb708c186b28133771c4\nbamboo_planRepository_branch=releases/Release_2_11_4_Branch\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=10a9794a2580ed9e589ecb708c186b28133771c4\nbamboo_planRepository_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=releases/Release_2_11_4_Branch\nbamboo_repository_46498153_name=Jalview Git\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498153_git_branch=releases/Release_2_11_4_Branch\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301905\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46498153_branch_name=releases/Release_2_11_4_Branch\nbamboo_repository_46498153_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_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_repository_46498153_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\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-GDB636-JOB1\nbamboo_planKey=JB-GDB636\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=releases/Release_2_11_4_Branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 29-Oct-2024 21:36:40 444 build 29-Oct-2024 21:36:42 build 29-Oct-2024 21:36:42 > Configure project : build 29-Oct-2024 21:36:42 Using properties from file './utils/channels/default/channel_gradle.properties' build 29-Oct-2024 21:36:42 JALVIEW_VERSION is set to '2.11.4.1' build 29-Oct-2024 21:36:42 HEADLESS BUILD build 29-Oct-2024 21:36:42 J2S ENABLED build 29-Oct-2024 21:36:42 Using a LOCAL profile. build 29-Oct-2024 21:36:42 eclipseDir exists build 29-Oct-2024 21:36:42 build 29-Oct-2024 21:36:42 > Task :clean build 29-Oct-2024 21:36:42 > Task :cleanClover build 29-Oct-2024 21:36:42 > Task :cleanTest UP-TO-DATE build 29-Oct-2024 21:36:44 build 29-Oct-2024 21:36:44 > Task :cloverInstrJava build 29-Oct-2024 21:36:44 Clover: About to instrument 1103 files build 29-Oct-2024 21:36:44 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 29-Oct-2024 21:36:44 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/clover/clover.db'. build 29-Oct-2024 21:36:44 Processing files at 1.9 source level. error 29-Oct-2024 21:36:47 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 29-Oct-2024 21:36:47 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 29-Oct-2024 21:36:47 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 29-Oct-2024 21:36:47 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 29-Oct-2024 21:36:47 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 29-Oct-2024 21:36:47 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 29-Oct-2024 21:36:47 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 29-Oct-2024 21:36:54 Clover all over. Instrumented 1103 files (112 packages). build 29-Oct-2024 21:36:56 build 29-Oct-2024 21:36:56 > Task :cloverInstrTests build 29-Oct-2024 21:36:56 Clover: About to instrument test files build 29-Oct-2024 21:36:56 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 29-Oct-2024 21:36:56 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/clover/clover.db'. build 29-Oct-2024 21:36:56 Processing files at 1.9 source level. build 29-Oct-2024 21:36:59 Clover all over. Instrumented 291 files (52 packages). build 29-Oct-2024 21:36:59 1594 test methods detected. build 29-Oct-2024 21:36:59 build 29-Oct-2024 21:36:59 > Task :cloverInstr build 29-Oct-2024 21:37:01 build 29-Oct-2024 21:37:01 > Task :compileCloverJava build 29-Oct-2024 21:37:01 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 29-Oct-2024 21:37:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:01 Setting target compatibility to 11 error 29-Oct-2024 21:37:15 Note: Some input files use or override a deprecated API. error 29-Oct-2024 21:37:15 Note: Recompile with -Xlint:deprecation for details. error 29-Oct-2024 21:37:15 Note: Some input files use unchecked or unsafe operations. error 29-Oct-2024 21:37:15 Note: Recompile with -Xlint:unchecked for details. build 29-Oct-2024 21:37:19 build 29-Oct-2024 21:37:19 > Task :processCloverResources NO-SOURCE build 29-Oct-2024 21:37:19 > Task :cloverClasses build 29-Oct-2024 21:37:20 > Task :copyHelp build 29-Oct-2024 21:37:21 > Task :buildIndices build 29-Oct-2024 21:37:21 > Task :copyResources build 29-Oct-2024 21:37:21 > Task :copyChannelResources build 29-Oct-2024 21:37:21 build 29-Oct-2024 21:37:21 > Task :createBuildProperties build 29-Oct-2024 21:37:21 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 29-Oct-2024 21:37:21 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:21 build 29-Oct-2024 21:37:21 > Task :buildResources build 29-Oct-2024 21:37:21 > Task :copyDocs build 29-Oct-2024 21:37:21 build 29-Oct-2024 21:37:21 > Task :convertMdFiles build 29-Oct-2024 21:37:21 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 29-Oct-2024 21:37:21 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/resources/doc_build/doc/releaseprocess.html build 29-Oct-2024 21:37:21 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 29-Oct-2024 21:37:21 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/resources/doc_build/doc/building.html build 29-Oct-2024 21:37:21 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/resources/doc_build/doc/jalview-projects.html build 29-Oct-2024 21:37:21 build 29-Oct-2024 21:37:21 > Task :releasesTemplates build 29-Oct-2024 21:37:21 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 29-Oct-2024 21:37:21 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:21 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:21 Stripping rc/test/etc for TEST build 29-Oct-2024 21:37:21 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 29-Oct-2024 21:37:21 build 29-Oct-2024 21:37:21 > Task :prepare build 29-Oct-2024 21:37:23 build 29-Oct-2024 21:37:23 > Task :compileJava build 29-Oct-2024 21:37:23 Setting target compatibility to 11 error 29-Oct-2024 21:37:29 Note: Some input files use or override a deprecated API. error 29-Oct-2024 21:37:29 Note: Recompile with -Xlint:deprecation for details. error 29-Oct-2024 21:37:29 Note: Some input files use unchecked or unsafe operations. error 29-Oct-2024 21:37:29 Note: Recompile with -Xlint:unchecked for details. build 29-Oct-2024 21:37:31 build 29-Oct-2024 21:37:31 > Task :compileTestJava build 29-Oct-2024 21:37:31 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 29-Oct-2024 21:37:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:31 Setting target compatibility to 11 error 29-Oct-2024 21:37:36 Note: Some input files use or override a deprecated API. error 29-Oct-2024 21:37:36 Note: Recompile with -Xlint:deprecation for details. error 29-Oct-2024 21:37:36 Note: Some input files use unchecked or unsafe operations. error 29-Oct-2024 21:37:36 Note: Recompile with -Xlint:unchecked for details. build 29-Oct-2024 21:37:37 build 29-Oct-2024 21:37:37 > Task :processTestResources build 29-Oct-2024 21:37:37 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 29-Oct-2024 21:37:37 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:37 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:37 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:37 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:37 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:37 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:37 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:37 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-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 29-Oct-2024 21:37:37 build 29-Oct-2024 21:37:37 > Task :testClasses build 29-Oct-2024 21:37:39 build 29-Oct-2024 21:37:39 > Task :testTask0 build 29-Oct-2024 21:37:39 Running tests WITH clover error 29-Oct-2024 21:37:42 WARNING: An illegal reflective access operation has occurred error 29-Oct-2024 21:37:42 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 29-Oct-2024 21:37:42 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 29-Oct-2024 21:37:42 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 29-Oct-2024 21:37:42 WARNING: All illegal access operations will be denied in a future release build 29-Oct-2024 21:41:23 build 29-Oct-2024 21:41:23 > Task :testTask1 build 29-Oct-2024 21:41:23 Running tests WITH clover error 29-Oct-2024 21:41:24 WARNING: An illegal reflective access operation has occurred error 29-Oct-2024 21:41:24 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 29-Oct-2024 21:41:24 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 29-Oct-2024 21:41:24 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 29-Oct-2024 21:41:24 WARNING: All illegal access operations will be denied in a future release build 29-Oct-2024 21:42:56 build 29-Oct-2024 21:42:56 > Task :testTask2 build 29-Oct-2024 21:42:56 Running tests WITH clover build 29-Oct-2024 21:43:00 build 29-Oct-2024 21:43:00 > Task :testTask3 build 29-Oct-2024 21:43:00 Running tests WITH clover error 29-Oct-2024 21:43:01 WARNING: An illegal reflective access operation has occurred error 29-Oct-2024 21:43:01 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 29-Oct-2024 21:43:01 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 29-Oct-2024 21:43:01 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 29-Oct-2024 21:43:01 WARNING: All illegal access operations will be denied in a future release build 29-Oct-2024 21:43:46 build 29-Oct-2024 21:43:46 > Task :test NO-SOURCE build 29-Oct-2024 21:43:46 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 29-Oct-2024 21:43:46 │jalview:testTask0 results: SUCCESS (1728 tests, 1728 successes, 0 failures, 0 skipped) in 3 minutes, 43.542 seconds │ build 29-Oct-2024 21:43:46 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/reports/tests/testTask0/index.html│ build 29-Oct-2024 21:43:46 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 29-Oct-2024 21:43:46 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 33.278 seconds │ build 29-Oct-2024 21:43:46 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/reports/tests/testTask1/index.html│ build 29-Oct-2024 21:43:46 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 29-Oct-2024 21:43:46 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.552 seconds │ build 29-Oct-2024 21:43:46 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/reports/tests/testTask2/index.html│ build 29-Oct-2024 21:43:46 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 29-Oct-2024 21:43:46 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 47.673 seconds │ build 29-Oct-2024 21:43:46 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/reports/tests/testTask3/index.html│ build 29-Oct-2024 21:43:46 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 29-Oct-2024 21:43:46 │OVERALL: results: SUCCESS (1803 tests, 1803 successes, 0 failures, 0 skipped) in 4 minutes, 128.045 seconds │ build 29-Oct-2024 21:43:46 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 29-Oct-2024 21:43:46 build 29-Oct-2024 21:43:46 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 29-Oct-2024 21:43:46 build 29-Oct-2024 21:43:46 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 29-Oct-2024 21:43:46 build 29-Oct-2024 21:43:46 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 29-Oct-2024 21:43:46 build 29-Oct-2024 21:43:46 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 29-Oct-2024 21:43:46 Please consult deprecation warnings for more details. build 29-Oct-2024 21:43:46 build 29-Oct-2024 21:43:46 BUILD SUCCESSFUL in 7m 5s build 29-Oct-2024 21:43:46 21 actionable tasks: 20 executed, 1 up-to-date simple 29-Oct-2024 21:43:46 Finished task 'Run tests with openclover under gradle' with result: Success simple 29-Oct-2024 21:43:46 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 29-Oct-2024 21:43:46 Bamboo Artifactory Plugin version: 2.6.2 command 29-Oct-2024 21:43:46 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - releases-Release_2_11_4_Branch - Clover and Tests #3 (JB-GDB636-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-GDB636-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=releases/Release_2_11_4_Branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_repository_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB636-JOB1-3\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-GDB636-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB636-JOB1\nbamboo_shortPlanName=releases-Release_2_11_4_Branch\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-GDB636-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 - releases-Release_2_11_4_Branch\nbamboo_shortPlanKey=GDB636\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498153_git_username=\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\nbamboo_buildTimeStamp=2024-10-29T21:34:00.838Z\nbamboo_repository_previous_revision_number=10a9794a2580ed9e589ecb708c186b28133771c4\nbamboo_planRepository_previousRevision=10a9794a2580ed9e589ecb708c186b28133771c4\nbamboo_repository_git_branch=releases/Release_2_11_4_Branch\nbamboo_buildResultKey=JB-GDB636-JOB1-3\nbamboo_repository_branch_name=releases/Release_2_11_4_Branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - releases-Release_2_11_4_Branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\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_46498153_previous_revision_number=10a9794a2580ed9e589ecb708c186b28133771c4\nbamboo_planRepository_branch=releases/Release_2_11_4_Branch\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=10a9794a2580ed9e589ecb708c186b28133771c4\nbamboo_planRepository_branchDisplayName=releases/Release_2_11_4_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=releases/Release_2_11_4_Branch\nbamboo_repository_46498153_name=Jalview Git\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498153_git_branch=releases/Release_2_11_4_Branch\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301905\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46498153_branch_name=releases/Release_2_11_4_Branch\nbamboo_repository_46498153_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_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_repository_46498153_revision_number=6d1fc3490ca522df0ad2f6f25cadcff87a91eec9\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-GDB636-JOB1\nbamboo_planKey=JB-GDB636\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=releases/Release_2_11_4_Branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 29-Oct-2024 21:43:46 444 build 29-Oct-2024 21:44:03 build 29-Oct-2024 21:44:03 > Configure project : build 29-Oct-2024 21:44:03 Using properties from file './utils/channels/default/channel_gradle.properties' build 29-Oct-2024 21:44:03 JALVIEW_VERSION is set to '2.11.4.1' build 29-Oct-2024 21:44:03 HEADLESS BUILD build 29-Oct-2024 21:44:03 J2S ENABLED build 29-Oct-2024 21:44:04 Using a LOCAL profile. build 29-Oct-2024 21:44:05 eclipseDir exists build 29-Oct-2024 21:44:07 build 29-Oct-2024 21:44:07 > Task :cloverHtmlReport build 29-Oct-2024 21:44:07 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 29-Oct-2024 21:44:08 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/reports/clover' build 29-Oct-2024 21:44:46 Done. Processed 116 packages in 37491ms (323ms per package). build 29-Oct-2024 21:44:51 build 29-Oct-2024 21:44:51 > Task :cloverXmlReport build 29-Oct-2024 21:44:51 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 29-Oct-2024 21:44:52 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/reports/clover/clover.xml' build 29-Oct-2024 21:44:52 build 29-Oct-2024 21:44:52 > Task :cloverReport build 29-Oct-2024 21:44:52 build 29-Oct-2024 21:44:52 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 29-Oct-2024 21:44:52 build 29-Oct-2024 21:44:52 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 29-Oct-2024 21:44:52 build 29-Oct-2024 21:44:52 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 29-Oct-2024 21:44:52 build 29-Oct-2024 21:44:52 BUILD SUCCESSFUL in 1m 5s build 29-Oct-2024 21:44:52 2 actionable tasks: 2 executed simple 29-Oct-2024 21:44:52 Finished task 'Clover Report' with result: Success simple 29-Oct-2024 21:44:52 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 29-Oct-2024 21:44:52 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1... simple 29-Oct-2024 21:44:52 Finished task 'TestNG Parser' with result: Success simple 29-Oct-2024 21:44:52 Running post build plugin 'NCover Results Collector' simple 29-Oct-2024 21:44:52 Running post build plugin 'Artifact Copier' simple 29-Oct-2024 21:44:52 Publishing an artifact: Clover Report (System) simple 29-Oct-2024 21:44:54 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.408 s simple 29-Oct-2024 21:44:54 Publishing an artifact: TestNG report error 29-Oct-2024 21:44:54 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB636-JOB1/build/reports/tests/test does not exist. simple 29-Oct-2024 21:44:54 The artifact hasn't been successfully published after 1.341 ms simple 29-Oct-2024 21:44:54 Running post build plugin 'Artifactory Release Management Staging' simple 29-Oct-2024 21:44:54 Running post build plugin 'Artifactory Build Info Copier' simple 29-Oct-2024 21:44:54 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 29-Oct-2024 21:44:54 Running post build plugin 'npm Cache Cleanup' simple 29-Oct-2024 21:44:54 Running post build plugin 'Clover Results Collector' simple 29-Oct-2024 21:44:54 Running post build plugin 'Docker Container Cleanup' simple 29-Oct-2024 21:44:54 Finalising the build... simple 29-Oct-2024 21:44:54 Stopping timer. simple 29-Oct-2024 21:44:54 Build JB-GDB636-JOB1-3 completed. simple 29-Oct-2024 21:44:54 Running on server: post build plugin 'NCover Results Collector' simple 29-Oct-2024 21:44:54 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 29-Oct-2024 21:44:54 Running on server: post build plugin 'Clover Delta Calculator' simple 29-Oct-2024 21:44:54 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 29-Oct-2024 21:44:54 All post build plugins have finished simple 29-Oct-2024 21:44:54 Generating build results summary... simple 29-Oct-2024 21:44:54 Saving build results to disk... simple 29-Oct-2024 21:44:54 Logging substituted variables... simple 29-Oct-2024 21:44:54 Indexing build results... simple 29-Oct-2024 21:44:54 Finished building JB-GDB636-JOB1-3.