simple 04-Oct-2024 17:10:01 Build Jalview Builds - Gradle Develop Build - patch-fix_JAL-4470_JAL-4471_for_2_11_4_1 - Clover and Tests #2 (JB-GDB630-JOB1-2) started building on agent Default Agent simple 04-Oct-2024 17:10:01 simple 04-Oct-2024 17:10:01 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1 simple 04-Oct-2024 17:10:01 Executing build Jalview Builds - Gradle Develop Build - patch-fix_JAL-4470_JAL-4471_for_2_11_4_1 - Clover and Tests #2 (JB-GDB630-JOB1-2) simple 04-Oct-2024 17:10:01 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 04-Oct-2024 17:10:01 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1 simple 04-Oct-2024 17:10:01 Updating source code to revision: d5180397f74424e44495cffe9c822873fc974441 simple 04-Oct-2024 17:10:01 Fetching 'refs/heads/patch/fix_JAL-4470_JAL-4471_for_2_11_4_1' from 'http://source.jalview.org/git/jalview.git'. simple 04-Oct-2024 17:10:01 Checking out revision d5180397f74424e44495cffe9c822873fc974441. simple 04-Oct-2024 17:10:01 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 04-Oct-2024 17:10:01 c1b0c7c..d518039 patch/fix_JAL-4470_JAL-4471_for_2_11_4_1 -> origin/patch/fix_JAL-4470_JAL-4471_for_2_11_4_1 simple 04-Oct-2024 17:10:02 Already on 'patch/fix_JAL-4470_JAL-4471_for_2_11_4_1' simple 04-Oct-2024 17:10:02 Your branch is behind 'origin/patch/fix_JAL-4470_JAL-4471_for_2_11_4_1' by 1 commit, and can be fast-forwarded. simple 04-Oct-2024 17:10:02 (use "git pull" to update your local branch) simple 04-Oct-2024 17:10:02 HEAD is now at d518039 JAL-4473 whatsNew 2.11.4.1 simple 04-Oct-2024 17:10:02 Updated source code to revision: d5180397f74424e44495cffe9c822873fc974441 simple 04-Oct-2024 17:10:02 Finished task 'Checkout Default Repository' with result: Success simple 04-Oct-2024 17:10:02 Running pre-build action: VCS Version Collector simple 04-Oct-2024 17:10:02 Running pre-build action: Artifactory Release Staging simple 04-Oct-2024 17:10:02 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 04-Oct-2024 17:10:02 Bamboo Artifactory Plugin version: 2.6.2 command 04-Oct-2024 17:10:02 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-fix_JAL-4470_JAL-4471_for_2_11_4_1 - Clover and Tests #2 (JB-GDB630-JOB1-2)'\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-GDB630-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_repository_revision_number=d5180397f74424e44495cffe9c822873fc974441\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB630-JOB1-2\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-GDB630-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB630-JOB1\nbamboo_shortPlanName=patch-fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=2\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-GDB630-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_repository_46498119_git_username=\nbamboo_shortPlanKey=GDB630\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=d5180397f74424e44495cffe9c822873fc974441\nbamboo_buildTimeStamp=2024-10-04T17:10:01.034+01:00\nbamboo_repository_previous_revision_number=c1b0c7cf530b405353da3d42c227af7e22edb461\nbamboo_planRepository_previousRevision=c1b0c7cf530b405353da3d42c227af7e22edb461\nbamboo_repository_46498119_git_branch=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_repository_46498119_name=Jalview Git\nbamboo_repository_git_branch=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_buildResultKey=JB-GDB630-JOB1-2\nbamboo_repository_branch_name=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_repository_46498119_revision_number=d5180397f74424e44495cffe9c822873fc974441\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-fix_JAL-4470_JAL-4471_for_2_11_4_1 - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=d5180397f74424e44495cffe9c822873fc974441\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/\nbamboo_repository_46498119_branch_name=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\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=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\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=c1b0c7cf530b405353da3d42c227af7e22edb461\nbamboo_planRepository_branchDisplayName=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\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-46301837\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46498119_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_46498119_previous_revision_number=c1b0c7cf530b405353da3d42c227af7e22edb461\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-GDB630-JOB1\nbamboo_planKey=JB-GDB630\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 04-Oct-2024 17:10:02 444 build 04-Oct-2024 17:10:04 build 04-Oct-2024 17:10:04 > Configure project : build 04-Oct-2024 17:10:04 Using properties from file './utils/channels/default/channel_gradle.properties' build 04-Oct-2024 17:10:04 JALVIEW_VERSION is set to '2.11.4.1' build 04-Oct-2024 17:10:04 HEADLESS BUILD build 04-Oct-2024 17:10:04 J2S ENABLED build 04-Oct-2024 17:10:04 Using a LOCAL profile. build 04-Oct-2024 17:10:04 eclipseDir exists build 04-Oct-2024 17:10:04 build 04-Oct-2024 17:10:04 > Task :clean build 04-Oct-2024 17:10:04 > Task :cleanClover build 04-Oct-2024 17:10:04 > Task :cleanTest UP-TO-DATE build 04-Oct-2024 17:10:06 build 04-Oct-2024 17:10:06 > Task :cloverInstrJava build 04-Oct-2024 17:10:06 Clover: About to instrument 1103 files build 04-Oct-2024 17:10:06 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 04-Oct-2024 17:10:06 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/clover/clover.db'. build 04-Oct-2024 17:10:06 Processing files at 1.9 source level. error 04-Oct-2024 17:10:09 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 04-Oct-2024 17:10:09 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 04-Oct-2024 17:10:09 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 04-Oct-2024 17:10:09 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 04-Oct-2024 17:10:09 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 04-Oct-2024 17:10:09 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 04-Oct-2024 17:10:09 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 04-Oct-2024 17:10:16 Clover all over. Instrumented 1103 files (112 packages). build 04-Oct-2024 17:10:18 build 04-Oct-2024 17:10:18 > Task :cloverInstrTests build 04-Oct-2024 17:10:18 Clover: About to instrument test files build 04-Oct-2024 17:10:18 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 04-Oct-2024 17:10:18 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/clover/clover.db'. build 04-Oct-2024 17:10:18 Processing files at 1.9 source level. build 04-Oct-2024 17:10:21 Clover all over. Instrumented 291 files (52 packages). build 04-Oct-2024 17:10:21 1594 test methods detected. build 04-Oct-2024 17:10:21 build 04-Oct-2024 17:10:21 > Task :cloverInstr build 04-Oct-2024 17:10:23 build 04-Oct-2024 17:10:23 > Task :compileCloverJava build 04-Oct-2024 17:10:23 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 04-Oct-2024 17:10:23 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:10:23 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:10:23 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:10:23 Setting target compatibility to 11 error 04-Oct-2024 17:10:36 Note: Some input files use or override a deprecated API. error 04-Oct-2024 17:10:36 Note: Recompile with -Xlint:deprecation for details. error 04-Oct-2024 17:10:36 Note: Some input files use unchecked or unsafe operations. error 04-Oct-2024 17:10:36 Note: Recompile with -Xlint:unchecked for details. build 04-Oct-2024 17:10:44 build 04-Oct-2024 17:10:44 > Task :processCloverResources NO-SOURCE build 04-Oct-2024 17:10:44 > Task :cloverClasses build 04-Oct-2024 17:10:44 > Task :copyHelp build 04-Oct-2024 17:10:45 > Task :buildIndices build 04-Oct-2024 17:10:45 > Task :copyResources build 04-Oct-2024 17:10:45 > Task :copyChannelResources build 04-Oct-2024 17:10:45 build 04-Oct-2024 17:10:45 > Task :createBuildProperties build 04-Oct-2024 17:10:45 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 04-Oct-2024 17:10:45 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:10:45 build 04-Oct-2024 17:10:45 > Task :buildResources build 04-Oct-2024 17:10:45 > Task :copyDocs build 04-Oct-2024 17:10:45 build 04-Oct-2024 17:10:45 > Task :convertMdFiles build 04-Oct-2024 17:10:45 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 04-Oct-2024 17:10:45 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/resources/doc_build/doc/releaseprocess.html build 04-Oct-2024 17:10:45 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 04-Oct-2024 17:10:45 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/resources/doc_build/doc/building.html build 04-Oct-2024 17:10:45 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/resources/doc_build/doc/jalview-projects.html build 04-Oct-2024 17:10:45 build 04-Oct-2024 17:10:45 > Task :releasesTemplates build 04-Oct-2024 17:10:45 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 04-Oct-2024 17:10:45 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:10:45 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:10:45 Stripping rc/test/etc for TEST build 04-Oct-2024 17:10:45 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 04-Oct-2024 17:10:45 build 04-Oct-2024 17:10:45 > Task :prepare build 04-Oct-2024 17:10:47 build 04-Oct-2024 17:10:47 > Task :compileJava build 04-Oct-2024 17:10:47 Setting target compatibility to 11 error 04-Oct-2024 17:10:52 Note: Some input files use or override a deprecated API. error 04-Oct-2024 17:10:52 Note: Recompile with -Xlint:deprecation for details. error 04-Oct-2024 17:10:52 Note: Some input files use unchecked or unsafe operations. error 04-Oct-2024 17:10:52 Note: Recompile with -Xlint:unchecked for details. build 04-Oct-2024 17:10:55 build 04-Oct-2024 17:10:55 > Task :compileTestJava build 04-Oct-2024 17:10:55 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 04-Oct-2024 17:10:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:10:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:10:55 Setting target compatibility to 11 error 04-Oct-2024 17:10:59 Note: Some input files use or override a deprecated API. error 04-Oct-2024 17:10:59 Note: Recompile with -Xlint:deprecation for details. error 04-Oct-2024 17:10:59 Note: Some input files use unchecked or unsafe operations. error 04-Oct-2024 17:10:59 Note: Recompile with -Xlint:unchecked for details. build 04-Oct-2024 17:11:01 build 04-Oct-2024 17:11:01 > Task :processTestResources build 04-Oct-2024 17:11:01 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 04-Oct-2024 17:11:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:11:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:11:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:11:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:11:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:11:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:11:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:11:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-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 04-Oct-2024 17:11:01 build 04-Oct-2024 17:11:01 > Task :testClasses build 04-Oct-2024 17:11:03 build 04-Oct-2024 17:11:03 > Task :testTask0 build 04-Oct-2024 17:11:03 Running tests WITH clover error 04-Oct-2024 17:11:05 WARNING: An illegal reflective access operation has occurred error 04-Oct-2024 17:11:05 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 04-Oct-2024 17:11:05 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 04-Oct-2024 17:11:05 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 04-Oct-2024 17:11:05 WARNING: All illegal access operations will be denied in a future release build 04-Oct-2024 17:14:51 build 04-Oct-2024 17:14:51 > Task :testTask1 build 04-Oct-2024 17:14:51 Running tests WITH clover error 04-Oct-2024 17:14:53 WARNING: An illegal reflective access operation has occurred error 04-Oct-2024 17:14:53 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 04-Oct-2024 17:14:53 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 04-Oct-2024 17:14:53 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 04-Oct-2024 17:14:53 WARNING: All illegal access operations will be denied in a future release build 04-Oct-2024 17:16:25 build 04-Oct-2024 17:16:25 > Task :testTask2 build 04-Oct-2024 17:16:25 Running tests WITH clover build 04-Oct-2024 17:16:29 build 04-Oct-2024 17:16:29 > Task :testTask3 build 04-Oct-2024 17:16:29 Running tests WITH clover error 04-Oct-2024 17:16:30 WARNING: An illegal reflective access operation has occurred error 04-Oct-2024 17:16:30 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 04-Oct-2024 17:16:30 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 04-Oct-2024 17:16:30 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 04-Oct-2024 17:16:30 WARNING: All illegal access operations will be denied in a future release build 04-Oct-2024 17:17:15 build 04-Oct-2024 17:17:15 > Task :test NO-SOURCE build 04-Oct-2024 17:17:15 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 04-Oct-2024 17:17:15 │jalview:testTask0 results: SUCCESS (1728 tests, 1728 successes, 0 failures, 0 skipped) in 3 minutes, 48.429 seconds │ build 04-Oct-2024 17:17:15 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/reports/tests/testTask0/index.html│ build 04-Oct-2024 17:17:15 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 04-Oct-2024 17:17:15 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 33.865 seconds │ build 04-Oct-2024 17:17:15 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/reports/tests/testTask1/index.html│ build 04-Oct-2024 17:17:15 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 04-Oct-2024 17:17:15 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.382 seconds │ build 04-Oct-2024 17:17:15 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/reports/tests/testTask2/index.html│ build 04-Oct-2024 17:17:15 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 04-Oct-2024 17:17:15 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 48.119 seconds │ build 04-Oct-2024 17:17:15 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/reports/tests/testTask3/index.html│ build 04-Oct-2024 17:17:15 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 04-Oct-2024 17:17:15 │OVERALL: results: SUCCESS (1803 tests, 1803 successes, 0 failures, 0 skipped) in 4 minutes, 133.795 seconds │ build 04-Oct-2024 17:17:15 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 04-Oct-2024 17:17:15 build 04-Oct-2024 17:17:15 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 04-Oct-2024 17:17:15 build 04-Oct-2024 17:17:15 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 04-Oct-2024 17:17:15 build 04-Oct-2024 17:17:15 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 04-Oct-2024 17:17:15 build 04-Oct-2024 17:17:15 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 04-Oct-2024 17:17:15 Please consult deprecation warnings for more details. build 04-Oct-2024 17:17:15 build 04-Oct-2024 17:17:15 BUILD SUCCESSFUL in 7m 12s build 04-Oct-2024 17:17:15 21 actionable tasks: 20 executed, 1 up-to-date simple 04-Oct-2024 17:17:15 Finished task 'Run tests with openclover under gradle' with result: Success simple 04-Oct-2024 17:17:15 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 04-Oct-2024 17:17:15 Bamboo Artifactory Plugin version: 2.6.2 command 04-Oct-2024 17:17:15 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-fix_JAL-4470_JAL-4471_for_2_11_4_1 - Clover and Tests #2 (JB-GDB630-JOB1-2)'\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-GDB630-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_repository_revision_number=d5180397f74424e44495cffe9c822873fc974441\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB630-JOB1-2\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-GDB630-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB630-JOB1\nbamboo_shortPlanName=patch-fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=2\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-GDB630-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_repository_46498119_git_username=\nbamboo_shortPlanKey=GDB630\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=d5180397f74424e44495cffe9c822873fc974441\nbamboo_buildTimeStamp=2024-10-04T17:10:01.034+01:00\nbamboo_repository_previous_revision_number=c1b0c7cf530b405353da3d42c227af7e22edb461\nbamboo_planRepository_previousRevision=c1b0c7cf530b405353da3d42c227af7e22edb461\nbamboo_repository_46498119_git_branch=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_repository_46498119_name=Jalview Git\nbamboo_repository_git_branch=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_buildResultKey=JB-GDB630-JOB1-2\nbamboo_repository_branch_name=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_repository_46498119_revision_number=d5180397f74424e44495cffe9c822873fc974441\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-fix_JAL-4470_JAL-4471_for_2_11_4_1 - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=d5180397f74424e44495cffe9c822873fc974441\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/\nbamboo_repository_46498119_branch_name=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\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=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\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=c1b0c7cf530b405353da3d42c227af7e22edb461\nbamboo_planRepository_branchDisplayName=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\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-46301837\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46498119_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_46498119_previous_revision_number=c1b0c7cf530b405353da3d42c227af7e22edb461\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-GDB630-JOB1\nbamboo_planKey=JB-GDB630\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/fix_JAL-4470_JAL-4471_for_2_11_4_1\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 04-Oct-2024 17:17:15 444 build 04-Oct-2024 17:17:27 build 04-Oct-2024 17:17:27 > Configure project : build 04-Oct-2024 17:17:27 Using properties from file './utils/channels/default/channel_gradle.properties' build 04-Oct-2024 17:17:27 JALVIEW_VERSION is set to '2.11.4.1' build 04-Oct-2024 17:17:27 HEADLESS BUILD build 04-Oct-2024 17:17:27 J2S ENABLED build 04-Oct-2024 17:17:27 Using a LOCAL profile. build 04-Oct-2024 17:17:29 eclipseDir exists build 04-Oct-2024 17:17:31 build 04-Oct-2024 17:17:31 > Task :cloverHtmlReport build 04-Oct-2024 17:17:31 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 04-Oct-2024 17:17:32 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/reports/clover' build 04-Oct-2024 17:18:08 Done. Processed 116 packages in 35977ms (310ms per package). build 04-Oct-2024 17:18:13 build 04-Oct-2024 17:18:13 > Task :cloverXmlReport build 04-Oct-2024 17:18:13 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 04-Oct-2024 17:18:14 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/reports/clover/clover.xml' build 04-Oct-2024 17:18:14 build 04-Oct-2024 17:18:14 > Task :cloverReport build 04-Oct-2024 17:18:14 build 04-Oct-2024 17:18:14 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 04-Oct-2024 17:18:14 build 04-Oct-2024 17:18:14 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 04-Oct-2024 17:18:14 build 04-Oct-2024 17:18:14 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 04-Oct-2024 17:18:14 build 04-Oct-2024 17:18:14 BUILD SUCCESSFUL in 58s build 04-Oct-2024 17:18:14 2 actionable tasks: 2 executed simple 04-Oct-2024 17:18:14 Finished task 'Clover Report' with result: Success simple 04-Oct-2024 17:18:14 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 04-Oct-2024 17:18:14 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1... simple 04-Oct-2024 17:18:14 Finished task 'TestNG Parser' with result: Success simple 04-Oct-2024 17:18:14 Running post build plugin 'NCover Results Collector' simple 04-Oct-2024 17:18:14 Running post build plugin 'Artifact Copier' simple 04-Oct-2024 17:18:14 Publishing an artifact: Clover Report (System) simple 04-Oct-2024 17:18:15 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.401 s simple 04-Oct-2024 17:18:15 Publishing an artifact: TestNG report error 04-Oct-2024 17:18:15 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB630-JOB1/build/reports/tests/test does not exist. simple 04-Oct-2024 17:18:15 The artifact hasn't been successfully published after 1.335 ms simple 04-Oct-2024 17:18:15 Running post build plugin 'Artifactory Release Management Staging' simple 04-Oct-2024 17:18:15 Running post build plugin 'Artifactory Build Info Copier' simple 04-Oct-2024 17:18:15 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 04-Oct-2024 17:18:15 Running post build plugin 'npm Cache Cleanup' simple 04-Oct-2024 17:18:15 Running post build plugin 'Clover Results Collector' simple 04-Oct-2024 17:18:15 Running post build plugin 'Docker Container Cleanup' simple 04-Oct-2024 17:18:15 Finalising the build... simple 04-Oct-2024 17:18:15 Stopping timer. simple 04-Oct-2024 17:18:15 Build JB-GDB630-JOB1-2 completed. simple 04-Oct-2024 17:18:15 Running on server: post build plugin 'NCover Results Collector' simple 04-Oct-2024 17:18:15 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 04-Oct-2024 17:18:15 Running on server: post build plugin 'Clover Delta Calculator' simple 04-Oct-2024 17:18:15 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 04-Oct-2024 17:18:15 All post build plugins have finished simple 04-Oct-2024 17:18:15 Generating build results summary... simple 04-Oct-2024 17:18:16 Saving build results to disk... simple 04-Oct-2024 17:18:16 Logging substituted variables... simple 04-Oct-2024 17:18:16 Indexing build results... simple 04-Oct-2024 17:18:16 Finished building JB-GDB630-JOB1-2.