simple 07-Nov-2024 10:11:00 Build Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #6 (JB-GDB633-JOB1-6) started building on agent Default Agent simple 07-Nov-2024 10:11:00 simple 07-Nov-2024 10:11:00 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1 simple 07-Nov-2024 10:11:00 Executing build Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #6 (JB-GDB633-JOB1-6) simple 07-Nov-2024 10:11:00 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 07-Nov-2024 10:11:00 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1 simple 07-Nov-2024 10:11:00 Updating source code to revision: 1c79fdcc0d6c6c934767a6a04e192b262ec78de3 simple 07-Nov-2024 10:11:00 Fetching 'refs/heads/feature/JAL-4386_JAL-4435_reformat_node_labels' from 'http://source.jalview.org/git/jalview.git'. simple 07-Nov-2024 10:11:01 Checking out revision 1c79fdcc0d6c6c934767a6a04e192b262ec78de3. simple 07-Nov-2024 10:11:01 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 07-Nov-2024 10:11:01 e1ff67b..1c79fdc feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels simple 07-Nov-2024 10:11:01 * [new branch] JAL-4474_jalview.ps1_not_working -> origin/JAL-4474_jalview.ps1_not_working simple 07-Nov-2024 10:11:01 * [new branch] bug/JAL-4477_unmapped_filename_characters -> origin/bug/JAL-4477_unmapped_filename_characters simple 07-Nov-2024 10:11:01 839b67d..9fb123c develop -> origin/develop simple 07-Nov-2024 10:11:01 * [new branch] experiment/JAL-4386_experimental_string_to_colour_scheme_methods -> origin/experiment/JAL-4386_experimental_string_to_colour_scheme_methods simple 07-Nov-2024 10:11:01 * [new branch] improvement/JAL-4485_not_finding_chimerax_on_managed_desktop -> origin/improvement/JAL-4485_not_finding_chimerax_on_managed_desktop simple 07-Nov-2024 10:11:01 7edd078..6d1fc34 releases/Release_2_11_4_Branch -> origin/releases/Release_2_11_4_Branch simple 07-Nov-2024 10:11:01 * [new tag] Release_2_11_4_1 -> Release_2_11_4_1 simple 07-Nov-2024 10:11:01 Already on 'feature/JAL-4386_JAL-4435_reformat_node_labels' simple 07-Nov-2024 10:11:01 Your branch is behind 'origin/feature/JAL-4386_JAL-4435_reformat_node_labels' by 1 commit, and can be fast-forwarded. simple 07-Nov-2024 10:11:01 (use "git pull" to update your local branch) simple 07-Nov-2024 10:11:01 HEAD is now at 1c79fdc JAL-4435 Menu option and colouring for sec struct providers simple 07-Nov-2024 10:11:01 Updated source code to revision: 1c79fdcc0d6c6c934767a6a04e192b262ec78de3 simple 07-Nov-2024 10:11:01 Finished task 'Checkout Default Repository' with result: Success simple 07-Nov-2024 10:11:01 Running pre-build action: VCS Version Collector simple 07-Nov-2024 10:11:01 Running pre-build action: Artifactory Release Staging simple 07-Nov-2024 10:11:01 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 07-Nov-2024 10:11:01 Bamboo Artifactory Plugin version: 2.6.2 command 07-Nov-2024 10:11:01 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #6 (JB-GDB633-JOB1-6)'\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-GDB633-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_revision_number=1c79fdcc0d6c6c934767a6a04e192b262ec78de3\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB633-JOB1-6\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-GDB633-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB633-JOB1\nbamboo_shortPlanName=feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_46498136_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_repository_46498136_revision_number=1c79fdcc0d6c6c934767a6a04e192b262ec78de3\nbamboo_buildNumber=6\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-GDB633-JOB1-6\nbamboo_repository_46498136_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_shortPlanKey=GDB633\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1c79fdcc0d6c6c934767a6a04e192b262ec78de3\nbamboo_buildTimeStamp=2024-11-07T10:11:00.790Z\nbamboo_repository_previous_revision_number=e1ff67badd0334881d8f07bbcac4262e16e5a709\nbamboo_planRepository_previousRevision=e1ff67badd0334881d8f07bbcac4262e16e5a709\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDB633-JOB1-6\nbamboo_repository_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=1c79fdcc0d6c6c934767a6a04e192b262ec78de3\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_repository_46498136_previous_revision_number=e1ff67badd0334881d8f07bbcac4262e16e5a709\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\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=e1ff67badd0334881d8f07bbcac4262e16e5a709\nbamboo_planRepository_branchDisplayName=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_46498136_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498136_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301871\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_repository_46498136_name=Jalview Git\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-GDB633-JOB1\nbamboo_planKey=JB-GDB633\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 07-Nov-2024 10:11:01 444 build 07-Nov-2024 10:11:02 Starting a Gradle Daemon (subsequent builds will be faster) build 07-Nov-2024 10:11:12 build 07-Nov-2024 10:11:12 > Configure project : build 07-Nov-2024 10:11:12 Using properties from file './utils/channels/default/channel_gradle.properties' build 07-Nov-2024 10:11:12 JALVIEW_VERSION is set to '2.11.4.0' build 07-Nov-2024 10:11:12 HEADLESS BUILD build 07-Nov-2024 10:11:12 J2S ENABLED build 07-Nov-2024 10:11:12 Using a LOCAL profile. build 07-Nov-2024 10:11:14 eclipseDir exists build 07-Nov-2024 10:11:16 build 07-Nov-2024 10:11:16 > Task :clean build 07-Nov-2024 10:11:16 > Task :cleanClover build 07-Nov-2024 10:11:16 > Task :cleanTest UP-TO-DATE build 07-Nov-2024 10:11:18 build 07-Nov-2024 10:11:18 > Task :cloverInstrJava build 07-Nov-2024 10:11:18 Clover: About to instrument 1102 files build 07-Nov-2024 10:11:19 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 07-Nov-2024 10:11:19 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover.db'. build 07-Nov-2024 10:11:19 Processing files at 1.9 source level. error 07-Nov-2024 10:11:25 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 07-Nov-2024 10:11:25 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 07-Nov-2024 10:11:25 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 07-Nov-2024 10:11:25 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 07-Nov-2024 10:11:25 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 07-Nov-2024 10:11:25 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 07-Nov-2024 10:11:25 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 07-Nov-2024 10:11:33 Clover all over. Instrumented 1102 files (111 packages). build 07-Nov-2024 10:11:36 build 07-Nov-2024 10:11:36 > Task :cloverInstrTests build 07-Nov-2024 10:11:36 Clover: About to instrument test files build 07-Nov-2024 10:11:36 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 07-Nov-2024 10:11:36 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover.db'. build 07-Nov-2024 10:11:36 Processing files at 1.9 source level. build 07-Nov-2024 10:11:39 Clover all over. Instrumented 290 files (52 packages). build 07-Nov-2024 10:11:39 1591 test methods detected. build 07-Nov-2024 10:11:39 build 07-Nov-2024 10:11:39 > Task :cloverInstr build 07-Nov-2024 10:11:41 build 07-Nov-2024 10:11:41 > Task :compileCloverJava build 07-Nov-2024 10:11:41 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 07-Nov-2024 10:11:41 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:11:41 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:11:41 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:11:41 Setting target compatibility to 11 error 07-Nov-2024 10:12:04 Note: Some input files use or override a deprecated API. error 07-Nov-2024 10:12:04 Note: Recompile with -Xlint:deprecation for details. error 07-Nov-2024 10:12:04 Note: Some input files use unchecked or unsafe operations. error 07-Nov-2024 10:12:04 Note: Recompile with -Xlint:unchecked for details. build 07-Nov-2024 10:12:09 build 07-Nov-2024 10:12:09 > Task :processCloverResources NO-SOURCE build 07-Nov-2024 10:12:09 > Task :cloverClasses build 07-Nov-2024 10:12:11 > Task :copyHelp build 07-Nov-2024 10:12:12 > Task :buildIndices build 07-Nov-2024 10:12:12 > Task :copyResources build 07-Nov-2024 10:12:12 > Task :copyChannelResources build 07-Nov-2024 10:12:12 build 07-Nov-2024 10:12:12 > Task :createBuildProperties build 07-Nov-2024 10:12:12 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 07-Nov-2024 10:12:12 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:12:12 build 07-Nov-2024 10:12:12 > Task :buildResources build 07-Nov-2024 10:12:12 > Task :copyDocs build 07-Nov-2024 10:12:13 build 07-Nov-2024 10:12:13 > Task :convertMdFiles build 07-Nov-2024 10:12:13 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 07-Nov-2024 10:12:13 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/releaseprocess.html build 07-Nov-2024 10:12:13 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 07-Nov-2024 10:12:13 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/building.html build 07-Nov-2024 10:12:13 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/jalview-projects.html build 07-Nov-2024 10:12:14 build 07-Nov-2024 10:12:14 > Task :releasesTemplates build 07-Nov-2024 10:12:14 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 07-Nov-2024 10:12:14 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:12:14 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:12:14 Stripping rc/test/etc for TEST build 07-Nov-2024 10:12:14 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 07-Nov-2024 10:12:14 build 07-Nov-2024 10:12:14 > Task :prepare build 07-Nov-2024 10:12:16 build 07-Nov-2024 10:12:16 > Task :compileJava build 07-Nov-2024 10:12:16 Setting target compatibility to 11 error 07-Nov-2024 10:12:22 Note: Some input files use or override a deprecated API. error 07-Nov-2024 10:12:22 Note: Recompile with -Xlint:deprecation for details. error 07-Nov-2024 10:12:22 Note: Some input files use unchecked or unsafe operations. error 07-Nov-2024 10:12:22 Note: Recompile with -Xlint:unchecked for details. build 07-Nov-2024 10:12:26 build 07-Nov-2024 10:12:26 > Task :compileTestJava build 07-Nov-2024 10:12:26 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 07-Nov-2024 10:12:26 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:12:26 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:12:26 Setting target compatibility to 11 error 07-Nov-2024 10:12:31 Note: Some input files use or override a deprecated API. error 07-Nov-2024 10:12:31 Note: Recompile with -Xlint:deprecation for details. error 07-Nov-2024 10:12:31 Note: Some input files use unchecked or unsafe operations. error 07-Nov-2024 10:12:31 Note: Recompile with -Xlint:unchecked for details. build 07-Nov-2024 10:12:32 build 07-Nov-2024 10:12:32 > Task :processTestResources build 07-Nov-2024 10:12:32 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 07-Nov-2024 10:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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 07-Nov-2024 10:12:32 build 07-Nov-2024 10:12:32 > Task :testClasses build 07-Nov-2024 10:12:34 build 07-Nov-2024 10:12:34 > Task :testTask0 build 07-Nov-2024 10:12:34 Running tests WITH clover error 07-Nov-2024 10:12:37 WARNING: An illegal reflective access operation has occurred error 07-Nov-2024 10:12:37 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 07-Nov-2024 10:12:37 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 07-Nov-2024 10:12:37 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 07-Nov-2024 10:12:37 WARNING: All illegal access operations will be denied in a future release build 07-Nov-2024 10:16:28 build 07-Nov-2024 10:16:28 > Task :testTask1 build 07-Nov-2024 10:16:28 Running tests WITH clover error 07-Nov-2024 10:16:29 WARNING: An illegal reflective access operation has occurred error 07-Nov-2024 10:16:29 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 07-Nov-2024 10:16:29 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 07-Nov-2024 10:16:29 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 07-Nov-2024 10:16:29 WARNING: All illegal access operations will be denied in a future release build 07-Nov-2024 10:18:03 build 07-Nov-2024 10:18:03 > Task :testTask2 build 07-Nov-2024 10:18:03 Running tests WITH clover build 07-Nov-2024 10:18:06 build 07-Nov-2024 10:18:06 > Task :testTask3 build 07-Nov-2024 10:18:06 Running tests WITH clover error 07-Nov-2024 10:18:08 WARNING: An illegal reflective access operation has occurred error 07-Nov-2024 10:18:08 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 07-Nov-2024 10:18:08 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 07-Nov-2024 10:18:08 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 07-Nov-2024 10:18:08 WARNING: All illegal access operations will be denied in a future release build 07-Nov-2024 10:18:54 build 07-Nov-2024 10:18:54 > Task :test NO-SOURCE build 07-Nov-2024 10:18:54 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 07-Nov-2024 10:18:54 │jalview:testTask0 results: SUCCESS (1693 tests, 1693 successes, 0 failures, 0 skipped) in 3 minutes, 53.280 seconds │ build 07-Nov-2024 10:18:54 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/testTask0/index.html│ build 07-Nov-2024 10:18:54 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 07-Nov-2024 10:18:54 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 34.852 seconds │ build 07-Nov-2024 10:18:54 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/testTask1/index.html│ build 07-Nov-2024 10:18:54 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 07-Nov-2024 10:18:54 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.349 seconds │ build 07-Nov-2024 10:18:54 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/testTask2/index.html│ build 07-Nov-2024 10:18:54 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 07-Nov-2024 10:18:54 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 49.424 seconds │ build 07-Nov-2024 10:18:54 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/testTask3/index.html│ build 07-Nov-2024 10:18:54 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 07-Nov-2024 10:18:54 │OVERALL: results: SUCCESS (1768 tests, 1768 successes, 0 failures, 0 skipped) in 4 minutes, 140.905 seconds │ build 07-Nov-2024 10:18:54 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 07-Nov-2024 10:18:54 build 07-Nov-2024 10:18:54 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 07-Nov-2024 10:18:54 build 07-Nov-2024 10:18:54 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 07-Nov-2024 10:18:54 build 07-Nov-2024 10:18:54 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 07-Nov-2024 10:18:54 build 07-Nov-2024 10:18:54 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 07-Nov-2024 10:18:54 Please consult deprecation warnings for more details. build 07-Nov-2024 10:18:54 build 07-Nov-2024 10:18:54 BUILD SUCCESSFUL in 7m 52s build 07-Nov-2024 10:18:54 21 actionable tasks: 20 executed, 1 up-to-date simple 07-Nov-2024 10:18:54 Finished task 'Run tests with openclover under gradle' with result: Success simple 07-Nov-2024 10:18:54 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 07-Nov-2024 10:18:54 Bamboo Artifactory Plugin version: 2.6.2 command 07-Nov-2024 10:18:54 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #6 (JB-GDB633-JOB1-6)'\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-GDB633-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_revision_number=1c79fdcc0d6c6c934767a6a04e192b262ec78de3\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB633-JOB1-6\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-GDB633-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB633-JOB1\nbamboo_shortPlanName=feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_46498136_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_repository_46498136_revision_number=1c79fdcc0d6c6c934767a6a04e192b262ec78de3\nbamboo_buildNumber=6\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-GDB633-JOB1-6\nbamboo_repository_46498136_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_shortPlanKey=GDB633\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1c79fdcc0d6c6c934767a6a04e192b262ec78de3\nbamboo_buildTimeStamp=2024-11-07T10:11:00.790Z\nbamboo_repository_previous_revision_number=e1ff67badd0334881d8f07bbcac4262e16e5a709\nbamboo_planRepository_previousRevision=e1ff67badd0334881d8f07bbcac4262e16e5a709\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDB633-JOB1-6\nbamboo_repository_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=1c79fdcc0d6c6c934767a6a04e192b262ec78de3\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_repository_46498136_previous_revision_number=e1ff67badd0334881d8f07bbcac4262e16e5a709\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\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=e1ff67badd0334881d8f07bbcac4262e16e5a709\nbamboo_planRepository_branchDisplayName=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_46498136_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498136_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301871\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_repository_46498136_name=Jalview Git\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-GDB633-JOB1\nbamboo_planKey=JB-GDB633\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 07-Nov-2024 10:18:54 444 build 07-Nov-2024 10:19:03 build 07-Nov-2024 10:19:03 > Configure project : build 07-Nov-2024 10:19:03 Using properties from file './utils/channels/default/channel_gradle.properties' build 07-Nov-2024 10:19:03 JALVIEW_VERSION is set to '2.11.4.0' build 07-Nov-2024 10:19:03 HEADLESS BUILD build 07-Nov-2024 10:19:03 J2S ENABLED build 07-Nov-2024 10:19:03 Using a LOCAL profile. build 07-Nov-2024 10:19:04 eclipseDir exists build 07-Nov-2024 10:19:07 build 07-Nov-2024 10:19:07 > Task :cloverHtmlReport build 07-Nov-2024 10:19:07 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 07-Nov-2024 10:19:08 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/clover' build 07-Nov-2024 10:19:47 Done. Processed 115 packages in 39015ms (339ms per package). build 07-Nov-2024 10:19:52 build 07-Nov-2024 10:19:52 > Task :cloverXmlReport build 07-Nov-2024 10:19:52 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 07-Nov-2024 10:19:53 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/clover/clover.xml' build 07-Nov-2024 10:19:53 build 07-Nov-2024 10:19:53 > Task :cloverReport build 07-Nov-2024 10:19:53 build 07-Nov-2024 10:19:53 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 07-Nov-2024 10:19:53 build 07-Nov-2024 10:19:53 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 07-Nov-2024 10:19:53 build 07-Nov-2024 10:19:53 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 07-Nov-2024 10:19:53 build 07-Nov-2024 10:19:53 BUILD SUCCESSFUL in 58s build 07-Nov-2024 10:19:53 2 actionable tasks: 2 executed simple 07-Nov-2024 10:19:53 Finished task 'Clover Report' with result: Success simple 07-Nov-2024 10:19:53 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 07-Nov-2024 10:19:53 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1... simple 07-Nov-2024 10:19:53 Finished task 'TestNG Parser' with result: Success simple 07-Nov-2024 10:19:53 Running post build plugin 'NCover Results Collector' simple 07-Nov-2024 10:19:53 Running post build plugin 'Artifact Copier' simple 07-Nov-2024 10:19:53 Publishing an artifact: Clover Report (System) simple 07-Nov-2024 10:19:54 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.429 s simple 07-Nov-2024 10:19:54 Publishing an artifact: TestNG report error 07-Nov-2024 10:19:54 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/test does not exist. simple 07-Nov-2024 10:19:54 The artifact hasn't been successfully published after 1.322 ms simple 07-Nov-2024 10:19:54 Running post build plugin 'Artifactory Release Management Staging' simple 07-Nov-2024 10:19:54 Running post build plugin 'Artifactory Build Info Copier' simple 07-Nov-2024 10:19:54 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 07-Nov-2024 10:19:54 Running post build plugin 'npm Cache Cleanup' simple 07-Nov-2024 10:19:54 Running post build plugin 'Clover Results Collector' simple 07-Nov-2024 10:19:54 Running post build plugin 'Docker Container Cleanup' simple 07-Nov-2024 10:19:54 Finalising the build... simple 07-Nov-2024 10:19:54 Stopping timer. simple 07-Nov-2024 10:19:54 Build JB-GDB633-JOB1-6 completed. simple 07-Nov-2024 10:19:54 Running on server: post build plugin 'NCover Results Collector' simple 07-Nov-2024 10:19:54 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 07-Nov-2024 10:19:54 Running on server: post build plugin 'Clover Delta Calculator' simple 07-Nov-2024 10:19:54 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 07-Nov-2024 10:19:54 All post build plugins have finished simple 07-Nov-2024 10:19:54 Generating build results summary... simple 07-Nov-2024 10:19:55 Saving build results to disk... simple 07-Nov-2024 10:19:55 Logging substituted variables... simple 07-Nov-2024 10:19:55 Indexing build results... simple 07-Nov-2024 10:19:55 Finished building JB-GDB633-JOB1-6.