simple 06-Nov-2024 00:56:00 Build Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop - Clover and Tests #4 (JB-GDB639-JOB1-4) started building on agent Default Agent simple 06-Nov-2024 00:56:00 simple 06-Nov-2024 00:56:00 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1 simple 06-Nov-2024 00:56:00 Executing build Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop - Clover and Tests #4 (JB-GDB639-JOB1-4) simple 06-Nov-2024 00:56:00 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 06-Nov-2024 00:56:00 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1 simple 06-Nov-2024 00:56:00 Updating source code to revision: 5ef2e9ac9664438c3ffd47762e83a296b2b3b01c simple 06-Nov-2024 00:56:00 Fetching 'refs/heads/improvement/JAL-4485_not_finding_chimerax_on_managed_desktop' from 'http://source.jalview.org/git/jalview.git'. simple 06-Nov-2024 00:56:00 Checking out revision 5ef2e9ac9664438c3ffd47762e83a296b2b3b01c. simple 06-Nov-2024 00:56:00 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 06-Nov-2024 00:56:00 d96be07..5ef2e9a improvement/JAL-4485_not_finding_chimerax_on_managed_desktop -> origin/improvement/JAL-4485_not_finding_chimerax_on_managed_desktop simple 06-Nov-2024 00:56:01 Already on 'improvement/JAL-4485_not_finding_chimerax_on_managed_desktop' simple 06-Nov-2024 00:56:01 Your branch is behind 'origin/improvement/JAL-4485_not_finding_chimerax_on_managed_desktop' by 2 commits, and can be fast-forwarded. simple 06-Nov-2024 00:56:01 (use "git pull" to update your local branch) simple 06-Nov-2024 00:56:01 HEAD is now at 5ef2e9a JAL-4485 Fix the template path for Windows Chimera/X executable. Added more debugging for path finding. simple 06-Nov-2024 00:56:01 Updated source code to revision: 5ef2e9ac9664438c3ffd47762e83a296b2b3b01c simple 06-Nov-2024 00:56:01 Finished task 'Checkout Default Repository' with result: Success simple 06-Nov-2024 00:56:01 Running pre-build action: VCS Version Collector simple 06-Nov-2024 00:56:01 Running pre-build action: Artifactory Release Staging simple 06-Nov-2024 00:56:01 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 06-Nov-2024 00:56:01 Bamboo Artifactory Plugin version: 2.6.2 command 06-Nov-2024 00:56:01 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop - Clover and Tests #4 (JB-GDB639-JOB1-4)'\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-GDB639-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_repository_revision_number=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB639-JOB1-4\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-GDB639-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB639-JOB1\nbamboo_shortPlanName=improvement-JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=4\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-GDB639-JOB1-4\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498170_previous_revision_number=d96be07c64432e609182c3bf09c629a6163c28de\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_shortPlanKey=GDB639\nbamboo_repository_46498170_name=Jalview Git\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_buildTimeStamp=2024-11-06T00:56:00.822Z\nbamboo_repository_previous_revision_number=d96be07c64432e609182c3bf09c629a6163c28de\nbamboo_repository_46498170_git_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_planRepository_previousRevision=d96be07c64432e609182c3bf09c629a6163c28de\nbamboo_repository_git_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_buildResultKey=JB-GDB639-JOB1-4\nbamboo_repository_branch_name=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\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_46498170_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\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=d96be07c64432e609182c3bf09c629a6163c28de\nbamboo_planRepository_branchDisplayName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_repository_46498170_revision_number=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498170_branch_name=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301939\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_repository_46498170_git_username=\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-GDB639-JOB1\nbamboo_planKey=JB-GDB639\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 06-Nov-2024 00:56:01 444 build 06-Nov-2024 00:56:01 Starting a Gradle Daemon (subsequent builds will be faster) build 06-Nov-2024 00:56:09 build 06-Nov-2024 00:56:09 > Configure project : build 06-Nov-2024 00:56:09 Using properties from file './utils/channels/default/channel_gradle.properties' build 06-Nov-2024 00:56:09 JALVIEW_VERSION is set to '2.11.4.1' build 06-Nov-2024 00:56:09 HEADLESS BUILD build 06-Nov-2024 00:56:09 J2S ENABLED build 06-Nov-2024 00:56:09 Using a LOCAL profile. build 06-Nov-2024 00:56:10 eclipseDir exists build 06-Nov-2024 00:56:11 build 06-Nov-2024 00:56:11 > Task :clean build 06-Nov-2024 00:56:11 > Task :cleanClover build 06-Nov-2024 00:56:11 > Task :cleanTest UP-TO-DATE build 06-Nov-2024 00:56:13 build 06-Nov-2024 00:56:13 > Task :cloverInstrJava build 06-Nov-2024 00:56:13 Clover: About to instrument 1103 files build 06-Nov-2024 00:56:13 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Nov-2024 00:56:13 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/clover/clover.db'. build 06-Nov-2024 00:56:13 Processing files at 1.9 source level. error 06-Nov-2024 00:56:16 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-Nov-2024 00:56:16 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-Nov-2024 00:56:16 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-Nov-2024 00:56:16 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-Nov-2024 00:56:16 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-Nov-2024 00:56:16 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-Nov-2024 00:56:16 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-Nov-2024 00:56:23 Clover all over. Instrumented 1103 files (112 packages). build 06-Nov-2024 00:56:26 build 06-Nov-2024 00:56:26 > Task :cloverInstrTests build 06-Nov-2024 00:56:26 Clover: About to instrument test files build 06-Nov-2024 00:56:26 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Nov-2024 00:56:26 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/clover/clover.db'. build 06-Nov-2024 00:56:26 Processing files at 1.9 source level. build 06-Nov-2024 00:56:28 Clover all over. Instrumented 291 files (52 packages). build 06-Nov-2024 00:56:28 1594 test methods detected. build 06-Nov-2024 00:56:28 build 06-Nov-2024 00:56:28 > Task :cloverInstr build 06-Nov-2024 00:56:30 build 06-Nov-2024 00:56:30 > Task :compileCloverJava build 06-Nov-2024 00:56:30 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 06-Nov-2024 00:56:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:56:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:56:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:56:30 Setting target compatibility to 11 error 06-Nov-2024 00:56:52 Note: Some input files use or override a deprecated API. error 06-Nov-2024 00:56:52 Note: Recompile with -Xlint:deprecation for details. error 06-Nov-2024 00:56:52 Note: Some input files use unchecked or unsafe operations. error 06-Nov-2024 00:56:52 Note: Recompile with -Xlint:unchecked for details. build 06-Nov-2024 00:56:58 build 06-Nov-2024 00:56:58 > Task :processCloverResources NO-SOURCE build 06-Nov-2024 00:56:58 > Task :cloverClasses build 06-Nov-2024 00:56:58 > Task :copyHelp build 06-Nov-2024 00:56:59 > Task :buildIndices build 06-Nov-2024 00:56:59 > Task :copyResources build 06-Nov-2024 00:56:59 > Task :copyChannelResources build 06-Nov-2024 00:56:59 build 06-Nov-2024 00:56:59 > Task :createBuildProperties build 06-Nov-2024 00:56:59 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 06-Nov-2024 00:56:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:56:59 build 06-Nov-2024 00:56:59 > Task :buildResources build 06-Nov-2024 00:56:59 > Task :copyDocs build 06-Nov-2024 00:57:01 build 06-Nov-2024 00:57:01 > Task :convertMdFiles build 06-Nov-2024 00:57:01 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 06-Nov-2024 00:57:01 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/resources/doc_build/doc/releaseprocess.html build 06-Nov-2024 00:57:01 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 06-Nov-2024 00:57:01 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/resources/doc_build/doc/building.html build 06-Nov-2024 00:57:01 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/resources/doc_build/doc/jalview-projects.html build 06-Nov-2024 00:57:01 build 06-Nov-2024 00:57:01 > Task :releasesTemplates build 06-Nov-2024 00:57:01 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 06-Nov-2024 00:57:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:57:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:57:01 Stripping rc/test/etc for TEST build 06-Nov-2024 00:57:01 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 06-Nov-2024 00:57:01 build 06-Nov-2024 00:57:01 > Task :prepare build 06-Nov-2024 00:57:03 build 06-Nov-2024 00:57:03 > Task :compileJava build 06-Nov-2024 00:57:03 Setting target compatibility to 11 error 06-Nov-2024 00:57:09 Note: Some input files use or override a deprecated API. error 06-Nov-2024 00:57:09 Note: Recompile with -Xlint:deprecation for details. error 06-Nov-2024 00:57:09 Note: Some input files use unchecked or unsafe operations. error 06-Nov-2024 00:57:09 Note: Recompile with -Xlint:unchecked for details. build 06-Nov-2024 00:57:13 build 06-Nov-2024 00:57:13 > Task :compileTestJava build 06-Nov-2024 00:57:13 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 06-Nov-2024 00:57:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:57:13 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:57:13 Setting target compatibility to 11 error 06-Nov-2024 00:57:18 Note: Some input files use or override a deprecated API. error 06-Nov-2024 00:57:18 Note: Recompile with -Xlint:deprecation for details. error 06-Nov-2024 00:57:18 Note: Some input files use unchecked or unsafe operations. error 06-Nov-2024 00:57:18 Note: Recompile with -Xlint:unchecked for details. build 06-Nov-2024 00:57:19 build 06-Nov-2024 00:57:19 > Task :processTestResources build 06-Nov-2024 00:57:19 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 06-Nov-2024 00:57:19 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:57:19 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:57:19 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:57:19 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:57:19 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:57:19 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:57:19 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:57:19 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-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-Nov-2024 00:57:19 build 06-Nov-2024 00:57:19 > Task :testClasses build 06-Nov-2024 00:57:21 build 06-Nov-2024 00:57:21 > Task :testTask0 build 06-Nov-2024 00:57:21 Running tests WITH clover error 06-Nov-2024 00:57:24 WARNING: An illegal reflective access operation has occurred error 06-Nov-2024 00:57:24 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 06-Nov-2024 00:57:24 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 06-Nov-2024 00:57:24 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 06-Nov-2024 00:57:24 WARNING: All illegal access operations will be denied in a future release build 06-Nov-2024 01:01:07 build 06-Nov-2024 01:01:07 > Task :testTask1 build 06-Nov-2024 01:01:07 Running tests WITH clover error 06-Nov-2024 01:01:09 WARNING: An illegal reflective access operation has occurred error 06-Nov-2024 01:01:09 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 06-Nov-2024 01:01:09 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 06-Nov-2024 01:01:09 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 06-Nov-2024 01:01:09 WARNING: All illegal access operations will be denied in a future release build 06-Nov-2024 01:02:41 build 06-Nov-2024 01:02:41 > Task :testTask2 build 06-Nov-2024 01:02:41 Running tests WITH clover build 06-Nov-2024 01:02:45 build 06-Nov-2024 01:02:45 > Task :testTask3 build 06-Nov-2024 01:02:45 Running tests WITH clover error 06-Nov-2024 01:02:46 WARNING: An illegal reflective access operation has occurred error 06-Nov-2024 01:02:46 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 06-Nov-2024 01:02:46 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 06-Nov-2024 01:02:46 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 06-Nov-2024 01:02:46 WARNING: All illegal access operations will be denied in a future release build 06-Nov-2024 01:03:32 build 06-Nov-2024 01:03:32 > Task :test NO-SOURCE build 06-Nov-2024 01:03:32 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 06-Nov-2024 01:03:32 │jalview:testTask0 results: SUCCESS (1728 tests, 1728 successes, 0 failures, 0 skipped) in 3 minutes, 45.203 seconds │ build 06-Nov-2024 01:03:32 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/tests/testTask0/index.html│ build 06-Nov-2024 01:03:32 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Nov-2024 01:03:32 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 33.387 seconds │ build 06-Nov-2024 01:03:32 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/tests/testTask1/index.html│ build 06-Nov-2024 01:03:32 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Nov-2024 01:03:32 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.534 seconds │ build 06-Nov-2024 01:03:32 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/tests/testTask2/index.html│ build 06-Nov-2024 01:03:32 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Nov-2024 01:03:32 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 49.500 seconds │ build 06-Nov-2024 01:03:32 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/tests/testTask3/index.html│ build 06-Nov-2024 01:03:32 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 06-Nov-2024 01:03:32 │OVERALL: results: SUCCESS (1803 tests, 1803 successes, 0 failures, 0 skipped) in 4 minutes, 131.624 seconds │ build 06-Nov-2024 01:03:32 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 06-Nov-2024 01:03:32 build 06-Nov-2024 01:03:32 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 06-Nov-2024 01:03:32 build 06-Nov-2024 01:03:32 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-Nov-2024 01:03:32 build 06-Nov-2024 01:03:32 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 06-Nov-2024 01:03:32 build 06-Nov-2024 01:03:32 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 06-Nov-2024 01:03:32 Please consult deprecation warnings for more details. build 06-Nov-2024 01:03:32 build 06-Nov-2024 01:03:32 BUILD SUCCESSFUL in 7m 31s build 06-Nov-2024 01:03:32 21 actionable tasks: 20 executed, 1 up-to-date simple 06-Nov-2024 01:03:33 Finished task 'Run tests with openclover under gradle' with result: Success simple 06-Nov-2024 01:03:33 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 06-Nov-2024 01:03:33 Bamboo Artifactory Plugin version: 2.6.2 command 06-Nov-2024 01:03:33 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop - Clover and Tests #4 (JB-GDB639-JOB1-4)'\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-GDB639-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_repository_revision_number=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB639-JOB1-4\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-GDB639-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB639-JOB1\nbamboo_shortPlanName=improvement-JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=4\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-GDB639-JOB1-4\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498170_previous_revision_number=d96be07c64432e609182c3bf09c629a6163c28de\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_shortPlanKey=GDB639\nbamboo_repository_46498170_name=Jalview Git\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_buildTimeStamp=2024-11-06T00:56:00.822Z\nbamboo_repository_previous_revision_number=d96be07c64432e609182c3bf09c629a6163c28de\nbamboo_repository_46498170_git_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_planRepository_previousRevision=d96be07c64432e609182c3bf09c629a6163c28de\nbamboo_repository_git_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_buildResultKey=JB-GDB639-JOB1-4\nbamboo_repository_branch_name=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - improvement-JAL-4485_not_finding_chimerax_on_managed_desktop - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\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_46498170_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branch=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\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=d96be07c64432e609182c3bf09c629a6163c28de\nbamboo_planRepository_branchDisplayName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_repository_46498170_revision_number=5ef2e9ac9664438c3ffd47762e83a296b2b3b01c\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498170_branch_name=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301939\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_repository_46498170_git_username=\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-GDB639-JOB1\nbamboo_planKey=JB-GDB639\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=improvement/JAL-4485_not_finding_chimerax_on_managed_desktop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 06-Nov-2024 01:03:33 444 build 06-Nov-2024 01:03:38 build 06-Nov-2024 01:03:38 > Configure project : build 06-Nov-2024 01:03:38 Using properties from file './utils/channels/default/channel_gradle.properties' build 06-Nov-2024 01:03:38 JALVIEW_VERSION is set to '2.11.4.1' build 06-Nov-2024 01:03:38 HEADLESS BUILD build 06-Nov-2024 01:03:38 J2S ENABLED build 06-Nov-2024 01:03:38 Using a LOCAL profile. build 06-Nov-2024 01:03:39 eclipseDir exists build 06-Nov-2024 01:03:41 build 06-Nov-2024 01:03:41 > Task :cloverHtmlReport build 06-Nov-2024 01:03:41 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Nov-2024 01:03:43 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/clover' build 06-Nov-2024 01:04:22 Done. Processed 116 packages in 39400ms (339ms per package). build 06-Nov-2024 01:04:28 build 06-Nov-2024 01:04:28 > Task :cloverXmlReport build 06-Nov-2024 01:04:28 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 06-Nov-2024 01:04:29 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/clover/clover.xml' build 06-Nov-2024 01:04:29 build 06-Nov-2024 01:04:29 > Task :cloverReport build 06-Nov-2024 01:04:29 build 06-Nov-2024 01:04:29 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 06-Nov-2024 01:04:29 build 06-Nov-2024 01:04:29 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-Nov-2024 01:04:29 build 06-Nov-2024 01:04:29 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 06-Nov-2024 01:04:29 build 06-Nov-2024 01:04:29 BUILD SUCCESSFUL in 56s build 06-Nov-2024 01:04:29 2 actionable tasks: 2 executed simple 06-Nov-2024 01:04:29 Finished task 'Clover Report' with result: Success simple 06-Nov-2024 01:04:29 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 06-Nov-2024 01:04:29 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1... simple 06-Nov-2024 01:04:29 Finished task 'TestNG Parser' with result: Success simple 06-Nov-2024 01:04:29 Running post build plugin 'NCover Results Collector' simple 06-Nov-2024 01:04:29 Running post build plugin 'Artifact Copier' simple 06-Nov-2024 01:04:29 Publishing an artifact: Clover Report (System) simple 06-Nov-2024 01:04:31 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.432 s simple 06-Nov-2024 01:04:31 Publishing an artifact: TestNG report error 06-Nov-2024 01:04:31 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB639-JOB1/build/reports/tests/test does not exist. simple 06-Nov-2024 01:04:31 The artifact hasn't been successfully published after 1.529 ms simple 06-Nov-2024 01:04:31 Running post build plugin 'Artifactory Release Management Staging' simple 06-Nov-2024 01:04:31 Running post build plugin 'Artifactory Build Info Copier' simple 06-Nov-2024 01:04:31 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 06-Nov-2024 01:04:31 Running post build plugin 'npm Cache Cleanup' simple 06-Nov-2024 01:04:31 Running post build plugin 'Clover Results Collector' simple 06-Nov-2024 01:04:31 Running post build plugin 'Docker Container Cleanup' simple 06-Nov-2024 01:04:31 Finalising the build... simple 06-Nov-2024 01:04:31 Stopping timer. simple 06-Nov-2024 01:04:31 Build JB-GDB639-JOB1-4 completed. simple 06-Nov-2024 01:04:31 Running on server: post build plugin 'NCover Results Collector' simple 06-Nov-2024 01:04:31 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 06-Nov-2024 01:04:31 Running on server: post build plugin 'Clover Delta Calculator' simple 06-Nov-2024 01:04:31 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 06-Nov-2024 01:04:31 All post build plugins have finished simple 06-Nov-2024 01:04:31 Generating build results summary... simple 06-Nov-2024 01:04:31 Saving build results to disk... simple 06-Nov-2024 01:04:31 Logging substituted variables... simple 06-Nov-2024 01:04:31 Indexing build results... simple 06-Nov-2024 01:04:31 Finished building JB-GDB639-JOB1-4.