simple 05-Nov-2025 13:15:12 Build Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Clover and Tests #3 (JB-GDB714-JOB1-3) started building on agent Default Agent simple 05-Nov-2025 13:15:12 simple 05-Nov-2025 13:15:12 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1 simple 05-Nov-2025 13:15:12 Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Clover and Tests #3 (JB-GDB714-JOB1-3) simple 05-Nov-2025 13:15:12 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 05-Nov-2025 13:15:12 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1 simple 05-Nov-2025 13:15:12 Updating source code to revision: 0d10b35174aa38a4a48c5965e683dabe47dcd553 simple 05-Nov-2025 13:15:12 Fetching 'refs/heads/bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 05-Nov-2025 13:15:12 Checking out revision 0d10b35174aa38a4a48c5965e683dabe47dcd553. simple 05-Nov-2025 13:15:13 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 05-Nov-2025 13:15:13 01b48f0..0d10b35 bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection -> origin/bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection simple 05-Nov-2025 13:15:13 * [new branch] bug/JAL-4594_ss_consensus_overlap_other_annot -> origin/bug/JAL-4594_ss_consensus_overlap_other_annot simple 05-Nov-2025 13:15:13 0ef8e14..12f0a1a bug/JAL-4603_Export_files_missing_part_of_sequence -> origin/bug/JAL-4603_Export_files_missing_part_of_sequence simple 05-Nov-2025 13:15:13 * [new branch] bug/JAL-4603_export_svg_files_missing_part_of_sequence -> origin/bug/JAL-4603_export_svg_files_missing_part_of_sequence simple 05-Nov-2025 13:15:13 * [new branch] bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 -> origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 simple 05-Nov-2025 13:15:13 5883ea0..aca2c5f development/Release_2_12_Branch -> origin/development/Release_2_12_Branch simple 05-Nov-2025 13:15:13 * [new branch] feature/JAL-4521_Allow_PCA_tree_for_one_seq_mul_ss -> origin/feature/JAL-4521_Allow_PCA_tree_for_one_seq_mul_ss simple 05-Nov-2025 13:15:13 * [new branch] feature/JAL-835_hhsuite_a3m_support -> origin/feature/JAL-835_hhsuite_a3m_support simple 05-Nov-2025 13:15:13 * [new branch] improvement/JAL-4607_install4j_dark_mode_background_colour -> origin/improvement/JAL-4607_install4j_dark_mode_background_colour simple 05-Nov-2025 13:15:13 * [new branch] improvement/JAL-4620_faster_sim_matrices -> origin/improvement/JAL-4620_faster_sim_matrices simple 05-Nov-2025 13:15:13 Already on 'bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' simple 05-Nov-2025 13:15:13 Your branch is behind 'origin/bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' by 1 commit, and can be fast-forwarded. simple 05-Nov-2025 13:15:13 (use "git pull" to update your local branch) simple 05-Nov-2025 13:15:13 HEAD is now at 0d10b35 JAL-4604 Fixed Console logger being initiated too early and log level in props file not being set. This was causing jalview.util.Log4jTest.testLog4j to fail. Neatened the args in that test to use '--' to prevent mixed argstyle warning. simple 05-Nov-2025 13:15:13 Updated source code to revision: 0d10b35174aa38a4a48c5965e683dabe47dcd553 simple 05-Nov-2025 13:15:13 Finished task 'Checkout Default Repository' with result: Success simple 05-Nov-2025 13:15:13 Running pre-build action: VCS Version Collector simple 05-Nov-2025 13:15:13 Running pre-build action: Artifactory Release Staging simple 05-Nov-2025 13:15:13 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 05-Nov-2025 13:15:13 Bamboo Artifactory Plugin version: 2.6.2 command 05-Nov-2025 13:15:13 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Clover and Tests #3 (JB-GDB714-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-GDB714-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_repository_revision_number=0d10b35174aa38a4a48c5965e683dabe47dcd553\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB714-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-GDB714-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB714-JOB1\nbamboo_shortPlanName=bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_repository_46498506_name=Jalview Gitlab\nbamboo_planRepository_name=Jalview Gitlab\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-GDB714-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_shortPlanKey=GDB714\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=0d10b35174aa38a4a48c5965e683dabe47dcd553\nbamboo_buildTimeStamp=2025-11-05T13:15:12.595Z\nbamboo_repository_previous_revision_number=01b48f04818d683d5d0f90d7833ae0c6d4191a8c\nbamboo_planRepository_previousRevision=01b48f04818d683d5d0f90d7833ae0c6d4191a8c\nbamboo_repository_46498506_revision_number=0d10b35174aa38a4a48c5965e683dabe47dcd553\nbamboo_repository_git_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_buildResultKey=JB-GDB714-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_repository_46498506_previous_revision_number=01b48f04818d683d5d0f90d7833ae0c6d4191a8c\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=0d10b35174aa38a4a48c5965e683dabe47dcd553\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_46498506_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\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=01b48f04818d683d5d0f90d7833ae0c6d4191a8c\nbamboo_planRepository_branchDisplayName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498506_branch_name=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_repository_46498506_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302583\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=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1\nbamboo_planKey=JB-GDB714\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498506_git_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 05-Nov-2025 13:15:13 444 build 05-Nov-2025 13:15:14 Starting a Gradle Daemon (subsequent builds will be faster) build 05-Nov-2025 13:15:22 build 05-Nov-2025 13:15:22 > Configure project : build 05-Nov-2025 13:15:22 Using properties from file './utils/channels/default/channel_gradle.properties' build 05-Nov-2025 13:15:22 JALVIEW_VERSION is set to '2.11.5.1' build 05-Nov-2025 13:15:22 HEADLESS BUILD build 05-Nov-2025 13:15:22 J2S ENABLED build 05-Nov-2025 13:15:23 Using a LOCAL profile. build 05-Nov-2025 13:15:24 eclipseDir exists build 05-Nov-2025 13:15:25 build 05-Nov-2025 13:15:25 > Task :clean build 05-Nov-2025 13:15:25 > Task :cleanClover build 05-Nov-2025 13:15:25 > Task :cleanTest UP-TO-DATE build 05-Nov-2025 13:15:27 build 05-Nov-2025 13:15:27 > Task :cloverInstrJava build 05-Nov-2025 13:15:27 Clover: About to instrument 1106 files build 05-Nov-2025 13:15:27 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 05-Nov-2025 13:15:27 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/clover/clover.db'. build 05-Nov-2025 13:15:27 Processing files at 1.9 source level. error 05-Nov-2025 13:15:32 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 05-Nov-2025 13:15:32 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 05-Nov-2025 13:15:32 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 05-Nov-2025 13:15:32 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 05-Nov-2025 13:15:32 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 05-Nov-2025 13:15:32 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 05-Nov-2025 13:15:32 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 05-Nov-2025 13:15:39 Clover all over. Instrumented 1106 files (112 packages). build 05-Nov-2025 13:15:42 build 05-Nov-2025 13:15:42 > Task :cloverInstrTests build 05-Nov-2025 13:15:42 Clover: About to instrument test files build 05-Nov-2025 13:15:42 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 05-Nov-2025 13:15:42 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/clover/clover.db'. build 05-Nov-2025 13:15:42 Processing files at 1.9 source level. build 05-Nov-2025 13:15:45 Clover all over. Instrumented 293 files (52 packages). build 05-Nov-2025 13:15:45 1618 test methods detected. build 05-Nov-2025 13:15:45 build 05-Nov-2025 13:15:45 > Task :cloverInstr build 05-Nov-2025 13:15:47 build 05-Nov-2025 13:15:47 > Task :compileCloverJava build 05-Nov-2025 13:15:47 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 05-Nov-2025 13:15:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:15:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:15:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:15:47 Setting target compatibility to 11 error 05-Nov-2025 13:16:13 Note: Some input files use or override a deprecated API. error 05-Nov-2025 13:16:13 Note: Recompile with -Xlint:deprecation for details. error 05-Nov-2025 13:16:13 Note: Some input files use unchecked or unsafe operations. error 05-Nov-2025 13:16:13 Note: Recompile with -Xlint:unchecked for details. build 05-Nov-2025 13:16:21 build 05-Nov-2025 13:16:21 > Task :processCloverResources NO-SOURCE build 05-Nov-2025 13:16:21 > Task :cloverClasses build 05-Nov-2025 13:16:21 > Task :copyHelp build 05-Nov-2025 13:16:23 > Task :buildIndices build 05-Nov-2025 13:16:23 > Task :copyResources build 05-Nov-2025 13:16:23 > Task :copyChannelResources build 05-Nov-2025 13:16:23 build 05-Nov-2025 13:16:23 > Task :createBuildProperties build 05-Nov-2025 13:16:23 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 05-Nov-2025 13:16:23 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:16:23 build 05-Nov-2025 13:16:23 > Task :buildResources build 05-Nov-2025 13:16:23 > Task :copyDocs build 05-Nov-2025 13:16:23 build 05-Nov-2025 13:16:23 > Task :convertMdFiles build 05-Nov-2025 13:16:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 05-Nov-2025 13:16:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/resources/doc_build/doc/releaseprocess.html build 05-Nov-2025 13:16:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 05-Nov-2025 13:16:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/resources/doc_build/doc/building.html build 05-Nov-2025 13:16:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/resources/doc_build/doc/jalview-projects.html build 05-Nov-2025 13:16:24 build 05-Nov-2025 13:16:24 > Task :releasesTemplates build 05-Nov-2025 13:16:24 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 05-Nov-2025 13:16:24 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:16:24 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:16:24 Stripping rc/test/etc for TEST build 05-Nov-2025 13:16:24 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 05-Nov-2025 13:16:24 build 05-Nov-2025 13:16:24 > Task :prepare build 05-Nov-2025 13:16:26 build 05-Nov-2025 13:16:26 > Task :compileJava build 05-Nov-2025 13:16:26 Setting target compatibility to 11 error 05-Nov-2025 13:16:33 Note: Some input files use or override a deprecated API. error 05-Nov-2025 13:16:33 Note: Recompile with -Xlint:deprecation for details. error 05-Nov-2025 13:16:33 Note: Some input files use unchecked or unsafe operations. error 05-Nov-2025 13:16:33 Note: Recompile with -Xlint:unchecked for details. build 05-Nov-2025 13:16:37 build 05-Nov-2025 13:16:37 > Task :compileTestJava build 05-Nov-2025 13:16:37 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 05-Nov-2025 13:16:37 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:16:37 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:16:37 Setting target compatibility to 11 error 05-Nov-2025 13:16:43 Note: Some input files use or override a deprecated API. error 05-Nov-2025 13:16:43 Note: Recompile with -Xlint:deprecation for details. error 05-Nov-2025 13:16:43 Note: Some input files use unchecked or unsafe operations. error 05-Nov-2025 13:16:43 Note: Recompile with -Xlint:unchecked for details. build 05-Nov-2025 13:16:44 build 05-Nov-2025 13:16:44 > Task :processTestResources build 05-Nov-2025 13:16:44 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 05-Nov-2025 13:16:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:16:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:16:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:16:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:16:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:16:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:16:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:16:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-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 05-Nov-2025 13:16:44 build 05-Nov-2025 13:16:44 > Task :testClasses build 05-Nov-2025 13:16:46 build 05-Nov-2025 13:16:46 > Task :testTask0 build 05-Nov-2025 13:16:46 Running tests WITH clover error 05-Nov-2025 13:16:49 WARNING: An illegal reflective access operation has occurred error 05-Nov-2025 13:16:49 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 05-Nov-2025 13:16:49 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 05-Nov-2025 13:16:49 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 05-Nov-2025 13:16:49 WARNING: All illegal access operations will be denied in a future release build 05-Nov-2025 13:21:35 build 05-Nov-2025 13:21:35 > Task :testTask1 build 05-Nov-2025 13:21:35 Running tests WITH clover error 05-Nov-2025 13:21:37 WARNING: An illegal reflective access operation has occurred error 05-Nov-2025 13:21:37 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 05-Nov-2025 13:21:37 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 05-Nov-2025 13:21:37 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 05-Nov-2025 13:21:37 WARNING: All illegal access operations will be denied in a future release build 05-Nov-2025 13:24:19 build 05-Nov-2025 13:24:19 > Task :testTask2 build 05-Nov-2025 13:24:19 Running tests WITH clover build 05-Nov-2025 13:24:23 build 05-Nov-2025 13:24:23 > Task :testTask3 build 05-Nov-2025 13:24:23 Running tests WITH clover error 05-Nov-2025 13:24:26 WARNING: An illegal reflective access operation has occurred error 05-Nov-2025 13:24:26 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 05-Nov-2025 13:24:26 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 05-Nov-2025 13:24:26 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 05-Nov-2025 13:24:26 WARNING: All illegal access operations will be denied in a future release build 05-Nov-2025 13:25:24 build 05-Nov-2025 13:25:24 > Task :test NO-SOURCE build 05-Nov-2025 13:25:24 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 05-Nov-2025 13:25:24 │jalview:testTask0 results: SUCCESS (1819 tests, 1819 successes, 0 failures, 0 skipped) in 4 minutes, 47.538 seconds │ build 05-Nov-2025 13:25:24 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/tests/testTask0/index.html│ build 05-Nov-2025 13:25:24 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 05-Nov-2025 13:25:24 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 43.887 seconds │ build 05-Nov-2025 13:25:24 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/tests/testTask1/index.html│ build 05-Nov-2025 13:25:24 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 05-Nov-2025 13:25:24 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.351 seconds │ build 05-Nov-2025 13:25:24 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/tests/testTask2/index.html│ build 05-Nov-2025 13:25:24 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 05-Nov-2025 13:25:24 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 2.536 seconds │ build 05-Nov-2025 13:25:24 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/tests/testTask3/index.html│ build 05-Nov-2025 13:25:24 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 05-Nov-2025 13:25:24 │OVERALL: results: SUCCESS (1907 tests, 1907 successes, 0 failures, 0 skipped) in 7 minutes, 98.312 seconds │ build 05-Nov-2025 13:25:24 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 05-Nov-2025 13:25:24 build 05-Nov-2025 13:25:24 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 05-Nov-2025 13:25:24 build 05-Nov-2025 13:25:24 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 05-Nov-2025 13:25:24 build 05-Nov-2025 13:25:24 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 05-Nov-2025 13:25:24 build 05-Nov-2025 13:25:24 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 05-Nov-2025 13:25:24 Please consult deprecation warnings for more details. build 05-Nov-2025 13:25:24 build 05-Nov-2025 13:25:24 BUILD SUCCESSFUL in 10m 10s build 05-Nov-2025 13:25:24 21 actionable tasks: 20 executed, 1 up-to-date simple 05-Nov-2025 13:25:25 Finished task 'Run tests with openclover under gradle' with result: Success simple 05-Nov-2025 13:25:25 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 05-Nov-2025 13:25:25 Bamboo Artifactory Plugin version: 2.6.2 command 05-Nov-2025 13:25:25 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Clover and Tests #3 (JB-GDB714-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-GDB714-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_repository_revision_number=0d10b35174aa38a4a48c5965e683dabe47dcd553\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB714-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-GDB714-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB714-JOB1\nbamboo_shortPlanName=bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_repository_46498506_name=Jalview Gitlab\nbamboo_planRepository_name=Jalview Gitlab\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-GDB714-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_shortPlanKey=GDB714\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=0d10b35174aa38a4a48c5965e683dabe47dcd553\nbamboo_buildTimeStamp=2025-11-05T13:15:12.595Z\nbamboo_repository_previous_revision_number=01b48f04818d683d5d0f90d7833ae0c6d4191a8c\nbamboo_planRepository_previousRevision=01b48f04818d683d5d0f90d7833ae0c6d4191a8c\nbamboo_repository_46498506_revision_number=0d10b35174aa38a4a48c5965e683dabe47dcd553\nbamboo_repository_git_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_buildResultKey=JB-GDB714-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_repository_46498506_previous_revision_number=01b48f04818d683d5d0f90d7833ae0c6d4191a8c\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=0d10b35174aa38a4a48c5965e683dabe47dcd553\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\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/\nbamboo_repository_46498506_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\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=01b48f04818d683d5d0f90d7833ae0c6d4191a8c\nbamboo_planRepository_branchDisplayName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498506_branch_name=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_repository_46498506_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302583\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=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1\nbamboo_planKey=JB-GDB714\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498506_git_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 05-Nov-2025 13:25:25 444 build 05-Nov-2025 13:25:32 build 05-Nov-2025 13:25:32 > Configure project : build 05-Nov-2025 13:25:32 Using properties from file './utils/channels/default/channel_gradle.properties' build 05-Nov-2025 13:25:32 JALVIEW_VERSION is set to '2.11.5.1' build 05-Nov-2025 13:25:32 HEADLESS BUILD build 05-Nov-2025 13:25:32 J2S ENABLED build 05-Nov-2025 13:25:33 Using a LOCAL profile. build 05-Nov-2025 13:25:34 eclipseDir exists build 05-Nov-2025 13:25:36 build 05-Nov-2025 13:25:36 > Task :cloverHtmlReport build 05-Nov-2025 13:25:36 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 05-Nov-2025 13:25:38 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/clover' build 05-Nov-2025 13:26:32 Done. Processed 116 packages in 54118ms (466ms per package). build 05-Nov-2025 13:26:39 build 05-Nov-2025 13:26:39 > Task :cloverXmlReport build 05-Nov-2025 13:26:39 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 05-Nov-2025 13:26:40 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/clover/clover.xml' build 05-Nov-2025 13:26:40 build 05-Nov-2025 13:26:40 > Task :cloverReport build 05-Nov-2025 13:26:40 build 05-Nov-2025 13:26:40 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 05-Nov-2025 13:26:40 build 05-Nov-2025 13:26:40 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 05-Nov-2025 13:26:40 build 05-Nov-2025 13:26:40 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 05-Nov-2025 13:26:40 build 05-Nov-2025 13:26:40 BUILD SUCCESSFUL in 1m 15s build 05-Nov-2025 13:26:40 2 actionable tasks: 2 executed simple 05-Nov-2025 13:26:41 Finished task 'Clover Report' with result: Success simple 05-Nov-2025 13:26:41 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 05-Nov-2025 13:26:41 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1... simple 05-Nov-2025 13:26:41 Finished task 'TestNG Parser' with result: Success simple 05-Nov-2025 13:26:41 Running post build plugin 'NCover Results Collector' simple 05-Nov-2025 13:26:41 Running post build plugin 'Artifact Copier' simple 05-Nov-2025 13:26:41 Publishing an artifact: Clover Report (System) simple 05-Nov-2025 13:26:46 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 5.261 s simple 05-Nov-2025 13:26:46 Publishing an artifact: TestNG report error 05-Nov-2025 13:26:46 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB714-JOB1/build/reports/tests/test does not exist. simple 05-Nov-2025 13:26:46 The artifact hasn't been successfully published after 4.602 ms simple 05-Nov-2025 13:26:46 Running post build plugin 'Artifactory Release Management Staging' simple 05-Nov-2025 13:26:46 Running post build plugin 'Artifactory Build Info Copier' simple 05-Nov-2025 13:26:46 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 05-Nov-2025 13:26:46 Running post build plugin 'npm Cache Cleanup' simple 05-Nov-2025 13:26:46 Running post build plugin 'Clover Results Collector' simple 05-Nov-2025 13:26:46 Running post build plugin 'Docker Container Cleanup' simple 05-Nov-2025 13:26:46 Finalising the build... simple 05-Nov-2025 13:26:46 Stopping timer. simple 05-Nov-2025 13:26:46 Build JB-GDB714-JOB1-3 completed. simple 05-Nov-2025 13:26:46 Running on server: post build plugin 'NCover Results Collector' simple 05-Nov-2025 13:26:46 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 05-Nov-2025 13:26:46 Running on server: post build plugin 'Clover Delta Calculator' simple 05-Nov-2025 13:26:46 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 05-Nov-2025 13:26:46 All post build plugins have finished simple 05-Nov-2025 13:26:46 Generating build results summary... simple 05-Nov-2025 13:26:47 Saving build results to disk... simple 05-Nov-2025 13:26:47 Logging substituted variables... simple 05-Nov-2025 13:26:47 Indexing build results... simple 05-Nov-2025 13:26:47 Finished building JB-GDB714-JOB1-3.