simple 13-Nov-2024 16:20:48 Build Jalview Builds - Gradle Develop Build - Clover and Tests #697 (JB-GDB-JOB1-697) started building on agent Default Agent simple 13-Nov-2024 16:20:48 simple 13-Nov-2024 16:20:48 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1 simple 13-Nov-2024 16:20:48 Executing build Jalview Builds - Gradle Develop Build - Clover and Tests #697 (JB-GDB-JOB1-697) simple 13-Nov-2024 16:20:48 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 13-Nov-2024 16:20:48 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1 simple 13-Nov-2024 16:20:48 Updating source code to revision: a3bb626cf79d42346add84b85a593d20253e723a simple 13-Nov-2024 16:20:50 Fetching 'refs/heads/develop' from 'http://source.jalview.org/git/jalview.git'. simple 13-Nov-2024 16:20:50 Checking out revision a3bb626cf79d42346add84b85a593d20253e723a. simple 13-Nov-2024 16:20:51 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 13-Nov-2024 16:20:51 416aad3..a3bb626 develop -> origin/develop simple 13-Nov-2024 16:20:51 d7c3dc7..a8875a0 bug/JAL-4477_unmapped_filename_characters -> origin/bug/JAL-4477_unmapped_filename_characters simple 13-Nov-2024 16:20:51 * [new branch] experiment/JAL-4386_JAL-4435_with_HSB_colours -> origin/experiment/JAL-4386_JAL-4435_with_HSB_colours simple 13-Nov-2024 16:20:51 * [new branch] patch/JAL-4077_jmolsaveloadwindows -> origin/patch/JAL-4077_jmolsaveloadwindows simple 13-Nov-2024 16:20:52 Already on 'develop' simple 13-Nov-2024 16:20:52 Your branch is behind 'origin/develop' by 3 commits, and can be fast-forwarded. simple 13-Nov-2024 16:20:52 (use "git pull" to update your local branch) simple 13-Nov-2024 16:20:52 HEAD is now at a3bb626 JAL-4482 JAL-4490 release notes simple 13-Nov-2024 16:20:52 Updated source code to revision: a3bb626cf79d42346add84b85a593d20253e723a simple 13-Nov-2024 16:20:52 Finished task 'Checkout Default Repository' with result: Success simple 13-Nov-2024 16:20:52 Running pre-build action: VCS Version Collector simple 13-Nov-2024 16:20:52 Running pre-build action: Artifactory Release Staging simple 13-Nov-2024 16:20:52 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 13-Nov-2024 16:20:52 Bamboo Artifactory Plugin version: 2.6.2 command 13-Nov-2024 16:20:52 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - Clover and Tests #697 (JB-GDB-JOB1-697)'\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-GDB-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=a3bb626cf79d42346add84b85a593d20253e723a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB-JOB1-697\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-GDB-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB-JOB1\nbamboo_shortPlanName=Gradle Develop Build\nbamboo_repository_8060939_revision_number=a3bb626cf79d42346add84b85a593d20253e723a\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_8060939_git_username=\nLOGNAME=bamboo\nbamboo_buildNumber=697\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-GDB-JOB1-697\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build\nbamboo_shortPlanKey=GDB\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a3bb626cf79d42346add84b85a593d20253e723a\nbamboo_buildTimeStamp=2024-11-13T16:11:46.580Z\nbamboo_repository_previous_revision_number=416aad339a728afd5ca4c2a558b6a395dd53a3ac\nbamboo_repository_8060939_branch_name=develop\nbamboo_planRepository_previousRevision=416aad339a728afd5ca4c2a558b6a395dd53a3ac\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-GDB-JOB1-697\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - Clover and Tests\nbamboo_repository_8060939_name=Jalview Git\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=a3bb626cf79d42346add84b85a593d20253e723a\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_8060939_git_branch=develop\nbamboo_planRepository_branch=develop\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=416aad339a728afd5ca4c2a558b6a395dd53a3ac\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-7864341\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_8060939_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_repository_8060939_previous_revision_number=416aad339a728afd5ca4c2a558b6a395dd53a3ac\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1\nbamboo_planKey=JB-GDB\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 13-Nov-2024 16:20:52 444 build 13-Nov-2024 16:20:54 build 13-Nov-2024 16:20:54 > Configure project : build 13-Nov-2024 16:20:54 Using properties from file './utils/channels/default/channel_gradle.properties' build 13-Nov-2024 16:20:54 JALVIEW_VERSION is set to '2.11.4.2' build 13-Nov-2024 16:20:54 HEADLESS BUILD build 13-Nov-2024 16:20:54 J2S ENABLED build 13-Nov-2024 16:20:54 Using a LOCAL profile. build 13-Nov-2024 16:20:54 eclipseDir exists build 13-Nov-2024 16:20:55 build 13-Nov-2024 16:20:55 > Task :clean build 13-Nov-2024 16:20:55 > Task :cleanClover build 13-Nov-2024 16:20:55 > Task :cleanTest UP-TO-DATE build 13-Nov-2024 16:20:57 build 13-Nov-2024 16:20:57 > Task :cloverInstrJava build 13-Nov-2024 16:20:57 Clover: About to instrument 1103 files build 13-Nov-2024 16:20:59 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 13-Nov-2024 16:20:59 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover.db'. build 13-Nov-2024 16:20:59 Processing files at 1.9 source level. error 13-Nov-2024 16:21:06 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 13-Nov-2024 16:21:06 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 13-Nov-2024 16:21:06 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 13-Nov-2024 16:21:06 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 13-Nov-2024 16:21:06 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 13-Nov-2024 16:21:06 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 13-Nov-2024 16:21:06 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 13-Nov-2024 16:21:16 Clover all over. Instrumented 1103 files (112 packages). build 13-Nov-2024 16:21:18 build 13-Nov-2024 16:21:18 > Task :cloverInstrTests build 13-Nov-2024 16:21:18 Clover: About to instrument test files build 13-Nov-2024 16:21:18 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 13-Nov-2024 16:21:18 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover.db'. build 13-Nov-2024 16:21:18 Processing files at 1.9 source level. build 13-Nov-2024 16:21:24 Clover all over. Instrumented 291 files (52 packages). build 13-Nov-2024 16:21:24 1595 test methods detected. build 13-Nov-2024 16:21:24 build 13-Nov-2024 16:21:24 > Task :cloverInstr build 13-Nov-2024 16:21:26 build 13-Nov-2024 16:21:26 > Task :compileCloverJava build 13-Nov-2024 16:21:26 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 13-Nov-2024 16:21:26 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:21:26 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:21:26 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:21:26 Setting target compatibility to 11 error 13-Nov-2024 16:21:42 Note: Some input files use or override a deprecated API. error 13-Nov-2024 16:21:42 Note: Recompile with -Xlint:deprecation for details. error 13-Nov-2024 16:21:42 Note: Some input files use unchecked or unsafe operations. error 13-Nov-2024 16:21:42 Note: Recompile with -Xlint:unchecked for details. build 13-Nov-2024 16:21:46 build 13-Nov-2024 16:21:46 > Task :processCloverResources NO-SOURCE build 13-Nov-2024 16:21:46 > Task :cloverClasses build 13-Nov-2024 16:21:48 > Task :copyHelp build 13-Nov-2024 16:21:49 > Task :buildIndices build 13-Nov-2024 16:21:50 > Task :copyResources build 13-Nov-2024 16:21:50 > Task :copyChannelResources build 13-Nov-2024 16:21:50 build 13-Nov-2024 16:21:50 > Task :createBuildProperties build 13-Nov-2024 16:21:50 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 13-Nov-2024 16:21:50 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:21:50 build 13-Nov-2024 16:21:50 > Task :buildResources build 13-Nov-2024 16:21:51 > Task :copyDocs build 13-Nov-2024 16:21:51 build 13-Nov-2024 16:21:51 > Task :convertMdFiles build 13-Nov-2024 16:21:51 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 13-Nov-2024 16:21:51 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/releaseprocess.html build 13-Nov-2024 16:21:51 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 13-Nov-2024 16:21:51 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/building.html build 13-Nov-2024 16:21:51 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/resources/doc_build/doc/jalview-projects.html build 13-Nov-2024 16:21:51 build 13-Nov-2024 16:21:51 > Task :releasesTemplates build 13-Nov-2024 16:21:51 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 13-Nov-2024 16:21:51 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:21:51 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:21:51 Stripping rc/test/etc for TEST build 13-Nov-2024 16:21:51 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 13-Nov-2024 16:21:51 build 13-Nov-2024 16:21:51 > Task :prepare build 13-Nov-2024 16:21:53 build 13-Nov-2024 16:21:53 > Task :compileJava build 13-Nov-2024 16:21:53 Setting target compatibility to 11 error 13-Nov-2024 16:21:59 Note: Some input files use or override a deprecated API. error 13-Nov-2024 16:21:59 Note: Recompile with -Xlint:deprecation for details. error 13-Nov-2024 16:21:59 Note: Some input files use unchecked or unsafe operations. error 13-Nov-2024 16:21:59 Note: Recompile with -Xlint:unchecked for details. build 13-Nov-2024 16:22:01 build 13-Nov-2024 16:22:01 > Task :compileTestJava build 13-Nov-2024 16:22:01 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 13-Nov-2024 16:22:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:22:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:22:01 Setting target compatibility to 11 error 13-Nov-2024 16:22:06 Note: Some input files use or override a deprecated API. error 13-Nov-2024 16:22:06 Note: Recompile with -Xlint:deprecation for details. error 13-Nov-2024 16:22:06 Note: Some input files use unchecked or unsafe operations. error 13-Nov-2024 16:22:06 Note: Recompile with -Xlint:unchecked for details. build 13-Nov-2024 16:22:07 build 13-Nov-2024 16:22:07 > Task :processTestResources build 13-Nov-2024 16:22:07 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 13-Nov-2024 16:22:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:22:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:22:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:22:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:22:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:22:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:22:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:22:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-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 13-Nov-2024 16:22:07 build 13-Nov-2024 16:22:07 > Task :testClasses build 13-Nov-2024 16:22:09 build 13-Nov-2024 16:22:09 > Task :testTask0 build 13-Nov-2024 16:22:09 Running tests WITH clover error 13-Nov-2024 16:22:12 WARNING: An illegal reflective access operation has occurred error 13-Nov-2024 16:22:12 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 13-Nov-2024 16:22:12 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 13-Nov-2024 16:22:12 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 13-Nov-2024 16:22:12 WARNING: All illegal access operations will be denied in a future release build 13-Nov-2024 16:25:54 build 13-Nov-2024 16:25:54 > Task :testTask1 build 13-Nov-2024 16:25:54 Running tests WITH clover error 13-Nov-2024 16:25:56 WARNING: An illegal reflective access operation has occurred error 13-Nov-2024 16:25:56 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 13-Nov-2024 16:25:56 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 13-Nov-2024 16:25:56 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 13-Nov-2024 16:25:56 WARNING: All illegal access operations will be denied in a future release build 13-Nov-2024 16:27:30 build 13-Nov-2024 16:27:30 > Task :testTask2 build 13-Nov-2024 16:27:30 Running tests WITH clover build 13-Nov-2024 16:27:33 build 13-Nov-2024 16:27:33 > Task :testTask3 build 13-Nov-2024 16:27:33 Running tests WITH clover error 13-Nov-2024 16:27:35 WARNING: An illegal reflective access operation has occurred error 13-Nov-2024 16:27:35 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 13-Nov-2024 16:27:35 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 13-Nov-2024 16:27:35 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 13-Nov-2024 16:27:35 WARNING: All illegal access operations will be denied in a future release build 13-Nov-2024 16:28:18 build 13-Nov-2024 16:28:18 > Task :test NO-SOURCE build 13-Nov-2024 16:28:18 ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 13-Nov-2024 16:28:18 │jalview:testTask0 results: SUCCESS (1735 tests, 1735 successes, 0 failures, 0 skipped) in 3 minutes, 44.581 seconds│ build 13-Nov-2024 16:28:18 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask0/index.html│ build 13-Nov-2024 16:28:18 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 13-Nov-2024 16:28:18 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 35.088 seconds │ build 13-Nov-2024 16:28:18 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask1/index.html│ build 13-Nov-2024 16:28:18 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 13-Nov-2024 16:28:18 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.633 seconds │ build 13-Nov-2024 16:28:18 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask2/index.html│ build 13-Nov-2024 16:28:18 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 13-Nov-2024 16:28:18 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 47.051 seconds │ build 13-Nov-2024 16:28:18 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/testTask3/index.html│ build 13-Nov-2024 16:28:18 ├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 13-Nov-2024 16:28:18 │OVERALL: results: SUCCESS (1810 tests, 1810 successes, 0 failures, 0 skipped) in 4 minutes, 130.353 seconds │ build 13-Nov-2024 16:28:18 └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 13-Nov-2024 16:28:18 build 13-Nov-2024 16:28:18 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 13-Nov-2024 16:28:18 build 13-Nov-2024 16:28:18 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 13-Nov-2024 16:28:18 build 13-Nov-2024 16:28:18 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 13-Nov-2024 16:28:18 build 13-Nov-2024 16:28:18 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 13-Nov-2024 16:28:18 Please consult deprecation warnings for more details. build 13-Nov-2024 16:28:18 build 13-Nov-2024 16:28:18 BUILD SUCCESSFUL in 7m 26s build 13-Nov-2024 16:28:18 21 actionable tasks: 20 executed, 1 up-to-date simple 13-Nov-2024 16:28:19 Finished task 'Run tests with openclover under gradle' with result: Success simple 13-Nov-2024 16:28:19 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 13-Nov-2024 16:28:19 Bamboo Artifactory Plugin version: 2.6.2 command 13-Nov-2024 16:28:19 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - Clover and Tests #697 (JB-GDB-JOB1-697)'\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-GDB-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=a3bb626cf79d42346add84b85a593d20253e723a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB-JOB1-697\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-GDB-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB-JOB1\nbamboo_shortPlanName=Gradle Develop Build\nbamboo_repository_8060939_revision_number=a3bb626cf79d42346add84b85a593d20253e723a\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_8060939_git_username=\nLOGNAME=bamboo\nbamboo_buildNumber=697\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-GDB-JOB1-697\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build\nbamboo_shortPlanKey=GDB\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a3bb626cf79d42346add84b85a593d20253e723a\nbamboo_buildTimeStamp=2024-11-13T16:11:46.580Z\nbamboo_repository_previous_revision_number=416aad339a728afd5ca4c2a558b6a395dd53a3ac\nbamboo_repository_8060939_branch_name=develop\nbamboo_planRepository_previousRevision=416aad339a728afd5ca4c2a558b6a395dd53a3ac\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-GDB-JOB1-697\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - Clover and Tests\nbamboo_repository_8060939_name=Jalview Git\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=a3bb626cf79d42346add84b85a593d20253e723a\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_8060939_git_branch=develop\nbamboo_planRepository_branch=develop\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=416aad339a728afd5ca4c2a558b6a395dd53a3ac\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-7864341\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_8060939_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_repository_8060939_previous_revision_number=416aad339a728afd5ca4c2a558b6a395dd53a3ac\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1\nbamboo_planKey=JB-GDB\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 13-Nov-2024 16:28:19 444 build 13-Nov-2024 16:28:27 build 13-Nov-2024 16:28:27 > Configure project : build 13-Nov-2024 16:28:27 Using properties from file './utils/channels/default/channel_gradle.properties' build 13-Nov-2024 16:28:27 JALVIEW_VERSION is set to '2.11.4.2' build 13-Nov-2024 16:28:28 HEADLESS BUILD build 13-Nov-2024 16:28:28 J2S ENABLED build 13-Nov-2024 16:28:28 Using a LOCAL profile. build 13-Nov-2024 16:28:29 eclipseDir exists build 13-Nov-2024 16:28:31 build 13-Nov-2024 16:28:31 > Task :cloverHtmlReport build 13-Nov-2024 16:28:31 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 13-Nov-2024 16:28:33 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/clover' build 13-Nov-2024 16:29:12 Done. Processed 116 packages in 39354ms (339ms per package). build 13-Nov-2024 16:29:18 build 13-Nov-2024 16:29:18 > Task :cloverXmlReport build 13-Nov-2024 16:29:18 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 13-Nov-2024 16:29:18 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/clover/clover.xml' build 13-Nov-2024 16:29:18 build 13-Nov-2024 16:29:18 > Task :cloverReport build 13-Nov-2024 16:29:19 build 13-Nov-2024 16:29:19 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 13-Nov-2024 16:29:19 build 13-Nov-2024 16:29:19 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 13-Nov-2024 16:29:19 build 13-Nov-2024 16:29:19 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 13-Nov-2024 16:29:19 build 13-Nov-2024 16:29:19 BUILD SUCCESSFUL in 59s build 13-Nov-2024 16:29:19 2 actionable tasks: 2 executed simple 13-Nov-2024 16:29:19 Finished task 'Clover Report' with result: Success simple 13-Nov-2024 16:29:19 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 13-Nov-2024 16:29:19 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1... simple 13-Nov-2024 16:29:19 Finished task 'TestNG Parser' with result: Success simple 13-Nov-2024 16:29:19 Running post build plugin 'NCover Results Collector' simple 13-Nov-2024 16:29:19 Running post build plugin 'Artifact Copier' simple 13-Nov-2024 16:29:19 Publishing an artifact: Clover Report (System) simple 13-Nov-2024 16:29:20 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.420 s simple 13-Nov-2024 16:29:20 Publishing an artifact: TestNG report error 13-Nov-2024 16:29:20 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB-JOB1/build/reports/tests/test does not exist. simple 13-Nov-2024 16:29:20 The artifact hasn't been successfully published after 1.298 ms simple 13-Nov-2024 16:29:20 Running post build plugin 'Artifactory Release Management Staging' simple 13-Nov-2024 16:29:20 Running post build plugin 'Artifactory Build Info Copier' simple 13-Nov-2024 16:29:20 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 13-Nov-2024 16:29:20 Running post build plugin 'npm Cache Cleanup' simple 13-Nov-2024 16:29:20 Running post build plugin 'Clover Results Collector' simple 13-Nov-2024 16:29:20 Running post build plugin 'Docker Container Cleanup' simple 13-Nov-2024 16:29:20 Finalising the build... simple 13-Nov-2024 16:29:20 Stopping timer. simple 13-Nov-2024 16:29:20 Build JB-GDB-JOB1-697 completed. simple 13-Nov-2024 16:29:20 Running on server: post build plugin 'NCover Results Collector' simple 13-Nov-2024 16:29:20 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 13-Nov-2024 16:29:20 Running on server: post build plugin 'Clover Delta Calculator' simple 13-Nov-2024 16:29:20 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 13-Nov-2024 16:29:20 All post build plugins have finished simple 13-Nov-2024 16:29:20 Generating build results summary... simple 13-Nov-2024 16:29:21 Saving build results to disk... simple 13-Nov-2024 16:29:21 Logging substituted variables... simple 13-Nov-2024 16:29:21 Indexing build results... simple 13-Nov-2024 16:29:21 Finished building JB-GDB-JOB1-697.