simple 04-Dec-2024 16:36:11 Build Jalview Builds - Gradle Develop Build - patch-JAL-4333_translatecodonexception - Clover and Tests #1 (JB-GDB649-JOB1-1) started building on agent Default Agent simple 04-Dec-2024 16:36:11 simple 04-Dec-2024 16:36:11 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1 simple 04-Dec-2024 16:36:11 Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4333_translatecodonexception - Clover and Tests #1 (JB-GDB649-JOB1-1) simple 04-Dec-2024 16:36:11 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 04-Dec-2024 16:36:11 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1 simple 04-Dec-2024 16:36:11 Updating source code to revision: 3f848bf2699737ea0daea99f4b5d2b68e09da06b simple 04-Dec-2024 16:36:11 Fetching 'refs/heads/patch/JAL-4333_translatecodonexception' from 'http://source.jalview.org/git/jalview.git'. simple 04-Dec-2024 16:36:13 Checking out revision 3f848bf2699737ea0daea99f4b5d2b68e09da06b. simple 04-Dec-2024 16:36:13 Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/.git'. simple 04-Dec-2024 16:36:13 Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1'... simple 04-Dec-2024 16:36:13 done. simple 04-Dec-2024 16:36:24 Branch patch/JAL-4333_translatecodonexception set up to track remote branch patch/JAL-4333_translatecodonexception from origin. simple 04-Dec-2024 16:36:24 Switched to a new branch 'patch/JAL-4333_translatecodonexception' simple 04-Dec-2024 16:36:25 Updated source code to revision: 3f848bf2699737ea0daea99f4b5d2b68e09da06b simple 04-Dec-2024 16:36:25 Finished task 'Checkout Default Repository' with result: Success simple 04-Dec-2024 16:36:25 Running pre-build action: VCS Version Collector simple 04-Dec-2024 16:36:25 Running pre-build action: Artifactory Release Staging simple 04-Dec-2024 16:36:25 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 04-Dec-2024 16:36:25 Bamboo Artifactory Plugin version: 2.6.2 command 04-Dec-2024 16:36:25 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4333_translatecodonexception - Clover and Tests #1 (JB-GDB649-JOB1-1)'\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-GDB649-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4333_translatecodonexception\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4333_translatecodonexception\nbamboo_repository_revision_number=3f848bf2699737ea0daea99f4b5d2b68e09da06b\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB649-JOB1-1\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-GDB649-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB649-JOB1\nbamboo_shortPlanName=patch-JAL-4333_translatecodonexception\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_46498227_git_username=\nLOGNAME=bamboo\nbamboo_buildNumber=1\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-GDB649-JOB1-1\nbamboo_repository_46498227_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4333_translatecodonexception\nbamboo_shortPlanKey=GDB649\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=3f848bf2699737ea0daea99f4b5d2b68e09da06b\nbamboo_buildTimeStamp=2024-12-04T16:36:11.143Z\nbamboo_repository_46498227_branch_name=patch/JAL-4333_translatecodonexception\nbamboo_repository_git_branch=patch/JAL-4333_translatecodonexception\nbamboo_buildResultKey=JB-GDB649-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4333_translatecodonexception\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4333_translatecodonexception - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=3f848bf2699737ea0daea99f4b5d2b68e09da06b\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498227_name=Jalview Git\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_planRepository_branch=patch/JAL-4333_translatecodonexception\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46498227_git_branch=patch/JAL-4333_translatecodonexception\nbamboo_planRepository_branchDisplayName=patch/JAL-4333_translatecodonexception\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4333_translatecodonexception\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-46302053\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_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-GDB649-JOB1\nbamboo_planKey=JB-GDB649\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498227_revision_number=3f848bf2699737ea0daea99f4b5d2b68e09da06b\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4333_translatecodonexception\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 04-Dec-2024 16:36:25 444 build 04-Dec-2024 16:36:29 Starting a Gradle Daemon (subsequent builds will be faster) build 04-Dec-2024 16:36:42 build 04-Dec-2024 16:36:42 > Configure project : build 04-Dec-2024 16:36:42 Using properties from file './utils/channels/default/channel_gradle.properties' build 04-Dec-2024 16:36:42 JALVIEW_VERSION is set to '2.11.4.2' build 04-Dec-2024 16:36:42 HEADLESS BUILD build 04-Dec-2024 16:36:42 J2S ENABLED build 04-Dec-2024 16:36:43 Using a LOCAL profile. build 04-Dec-2024 16:36:44 eclipseDir exists build 04-Dec-2024 16:36:44 build 04-Dec-2024 16:36:44 > Task :clean build 04-Dec-2024 16:36:44 > Task :cleanClover build 04-Dec-2024 16:36:44 > Task :cleanTest UP-TO-DATE build 04-Dec-2024 16:36:47 build 04-Dec-2024 16:36:47 > Task :cloverInstrJava build 04-Dec-2024 16:36:47 Clover: About to instrument 1103 files build 04-Dec-2024 16:36:47 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 04-Dec-2024 16:36:47 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/clover/clover.db'. build 04-Dec-2024 16:36:47 Processing files at 1.9 source level. error 04-Dec-2024 16:36:52 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-Dec-2024 16:36:52 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-Dec-2024 16:36:52 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-Dec-2024 16:36:52 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-Dec-2024 16:36:52 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-Dec-2024 16:36:52 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-Dec-2024 16:36:52 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-Dec-2024 16:36:58 Clover all over. Instrumented 1103 files (112 packages). build 04-Dec-2024 16:37:01 build 04-Dec-2024 16:37:01 > Task :cloverInstrTests build 04-Dec-2024 16:37:01 Clover: About to instrument test files build 04-Dec-2024 16:37:01 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 04-Dec-2024 16:37:01 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/clover/clover.db'. build 04-Dec-2024 16:37:01 Processing files at 1.9 source level. build 04-Dec-2024 16:37:04 Clover all over. Instrumented 291 files (52 packages). build 04-Dec-2024 16:37:04 1597 test methods detected. build 04-Dec-2024 16:37:04 build 04-Dec-2024 16:37:04 > Task :cloverInstr build 04-Dec-2024 16:37:08 build 04-Dec-2024 16:37:08 > Task :compileCloverJava build 04-Dec-2024 16:37:08 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 04-Dec-2024 16:37:08 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:08 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:08 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:08 Setting target compatibility to 11 error 04-Dec-2024 16:37:31 Note: Some input files use or override a deprecated API. error 04-Dec-2024 16:37:31 Note: Recompile with -Xlint:deprecation for details. error 04-Dec-2024 16:37:31 Note: Some input files use unchecked or unsafe operations. error 04-Dec-2024 16:37:31 Note: Recompile with -Xlint:unchecked for details. build 04-Dec-2024 16:37:38 build 04-Dec-2024 16:37:38 > Task :processCloverResources NO-SOURCE build 04-Dec-2024 16:37:38 > Task :cloverClasses build 04-Dec-2024 16:37:38 > Task :copyHelp build 04-Dec-2024 16:37:40 > Task :buildIndices build 04-Dec-2024 16:37:40 > Task :copyResources build 04-Dec-2024 16:37:40 > Task :copyChannelResources build 04-Dec-2024 16:37:40 build 04-Dec-2024 16:37:40 > Task :createBuildProperties build 04-Dec-2024 16:37:40 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 04-Dec-2024 16:37:40 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:40 build 04-Dec-2024 16:37:40 > Task :buildResources build 04-Dec-2024 16:37:40 > Task :copyDocs build 04-Dec-2024 16:37:40 build 04-Dec-2024 16:37:40 > Task :convertMdFiles build 04-Dec-2024 16:37:40 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 04-Dec-2024 16:37:40 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/resources/doc_build/doc/releaseprocess.html build 04-Dec-2024 16:37:40 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 04-Dec-2024 16:37:40 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/resources/doc_build/doc/building.html build 04-Dec-2024 16:37:40 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/resources/doc_build/doc/jalview-projects.html build 04-Dec-2024 16:37:41 build 04-Dec-2024 16:37:41 > Task :releasesTemplates build 04-Dec-2024 16:37:41 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 04-Dec-2024 16:37:41 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:41 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:41 Stripping rc/test/etc for TEST build 04-Dec-2024 16:37:41 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 04-Dec-2024 16:37:41 build 04-Dec-2024 16:37:41 > Task :prepare build 04-Dec-2024 16:37:43 build 04-Dec-2024 16:37:43 > Task :compileJava build 04-Dec-2024 16:37:43 Setting target compatibility to 11 error 04-Dec-2024 16:37:49 Note: Some input files use or override a deprecated API. error 04-Dec-2024 16:37:49 Note: Recompile with -Xlint:deprecation for details. error 04-Dec-2024 16:37:49 Note: Some input files use unchecked or unsafe operations. error 04-Dec-2024 16:37:49 Note: Recompile with -Xlint:unchecked for details. build 04-Dec-2024 16:37:53 build 04-Dec-2024 16:37:53 > Task :compileTestJava build 04-Dec-2024 16:37:53 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 04-Dec-2024 16:37:53 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:53 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:53 Setting target compatibility to 11 error 04-Dec-2024 16:37:58 Note: Some input files use or override a deprecated API. error 04-Dec-2024 16:37:58 Note: Recompile with -Xlint:deprecation for details. error 04-Dec-2024 16:37:58 Note: Some input files use unchecked or unsafe operations. error 04-Dec-2024 16:37:58 Note: Recompile with -Xlint:unchecked for details. build 04-Dec-2024 16:37:59 build 04-Dec-2024 16:37:59 > Task :processTestResources build 04-Dec-2024 16:37:59 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 04-Dec-2024 16:37:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-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-Dec-2024 16:37:59 build 04-Dec-2024 16:37:59 > Task :testClasses build 04-Dec-2024 16:38:01 build 04-Dec-2024 16:38:01 > Task :testTask0 build 04-Dec-2024 16:38:01 Running tests WITH clover error 04-Dec-2024 16:38:05 WARNING: An illegal reflective access operation has occurred error 04-Dec-2024 16:38:05 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 04-Dec-2024 16:38:05 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 04-Dec-2024 16:38:05 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 04-Dec-2024 16:38:05 WARNING: All illegal access operations will be denied in a future release build 04-Dec-2024 16:41:53 build 04-Dec-2024 16:41:53 > Task :testTask1 build 04-Dec-2024 16:41:53 Running tests WITH clover error 04-Dec-2024 16:41:54 WARNING: An illegal reflective access operation has occurred error 04-Dec-2024 16:41:54 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 04-Dec-2024 16:41:54 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 04-Dec-2024 16:41:54 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 04-Dec-2024 16:41:54 WARNING: All illegal access operations will be denied in a future release build 04-Dec-2024 16:43:30 build 04-Dec-2024 16:43:30 > Task :testTask2 build 04-Dec-2024 16:43:30 Running tests WITH clover build 04-Dec-2024 16:43:34 build 04-Dec-2024 16:43:34 > Task :testTask3 build 04-Dec-2024 16:43:34 Running tests WITH clover error 04-Dec-2024 16:43:35 WARNING: An illegal reflective access operation has occurred error 04-Dec-2024 16:43:35 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 04-Dec-2024 16:43:35 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 04-Dec-2024 16:43:35 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 04-Dec-2024 16:43:35 WARNING: All illegal access operations will be denied in a future release build 04-Dec-2024 16:44:21 build 04-Dec-2024 16:44:21 > Task :test NO-SOURCE build 04-Dec-2024 16:44:21 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 04-Dec-2024 16:44:21 │jalview:testTask0 results: SUCCESS (1746 tests, 1746 successes, 0 failures, 0 skipped) in 3 minutes, 50.949 seconds │ build 04-Dec-2024 16:44:21 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/reports/tests/testTask0/index.html│ build 04-Dec-2024 16:44:21 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 04-Dec-2024 16:44:21 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 37.405 seconds │ build 04-Dec-2024 16:44:21 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/reports/tests/testTask1/index.html│ build 04-Dec-2024 16:44:21 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 04-Dec-2024 16:44:21 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.550 seconds │ build 04-Dec-2024 16:44:21 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/reports/tests/testTask2/index.html│ build 04-Dec-2024 16:44:21 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 04-Dec-2024 16:44:21 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 49.397 seconds │ build 04-Dec-2024 16:44:21 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/reports/tests/testTask3/index.html│ build 04-Dec-2024 16:44:21 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 04-Dec-2024 16:44:21 │OVERALL: results: SUCCESS (1821 tests, 1821 successes, 0 failures, 0 skipped) in 4 minutes, 141.301 seconds │ build 04-Dec-2024 16:44:21 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 04-Dec-2024 16:44:21 build 04-Dec-2024 16:44:21 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 04-Dec-2024 16:44:21 build 04-Dec-2024 16:44:21 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-Dec-2024 16:44:21 build 04-Dec-2024 16:44:21 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 04-Dec-2024 16:44:21 build 04-Dec-2024 16:44:21 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 04-Dec-2024 16:44:21 Please consult deprecation warnings for more details. build 04-Dec-2024 16:44:21 build 04-Dec-2024 16:44:21 BUILD SUCCESSFUL in 7m 56s build 04-Dec-2024 16:44:21 21 actionable tasks: 20 executed, 1 up-to-date simple 04-Dec-2024 16:44:22 Finished task 'Run tests with openclover under gradle' with result: Success simple 04-Dec-2024 16:44:22 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 04-Dec-2024 16:44:22 Bamboo Artifactory Plugin version: 2.6.2 command 04-Dec-2024 16:44:22 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4333_translatecodonexception - Clover and Tests #1 (JB-GDB649-JOB1-1)'\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-GDB649-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4333_translatecodonexception\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4333_translatecodonexception\nbamboo_repository_revision_number=3f848bf2699737ea0daea99f4b5d2b68e09da06b\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB649-JOB1-1\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-GDB649-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB649-JOB1\nbamboo_shortPlanName=patch-JAL-4333_translatecodonexception\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_46498227_git_username=\nLOGNAME=bamboo\nbamboo_buildNumber=1\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-GDB649-JOB1-1\nbamboo_repository_46498227_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4333_translatecodonexception\nbamboo_shortPlanKey=GDB649\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=3f848bf2699737ea0daea99f4b5d2b68e09da06b\nbamboo_buildTimeStamp=2024-12-04T16:36:11.143Z\nbamboo_repository_46498227_branch_name=patch/JAL-4333_translatecodonexception\nbamboo_repository_git_branch=patch/JAL-4333_translatecodonexception\nbamboo_buildResultKey=JB-GDB649-JOB1-1\nbamboo_repository_branch_name=patch/JAL-4333_translatecodonexception\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4333_translatecodonexception - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=3f848bf2699737ea0daea99f4b5d2b68e09da06b\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498227_name=Jalview Git\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_planRepository_branch=patch/JAL-4333_translatecodonexception\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_repository_46498227_git_branch=patch/JAL-4333_translatecodonexception\nbamboo_planRepository_branchDisplayName=patch/JAL-4333_translatecodonexception\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4333_translatecodonexception\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-46302053\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_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-GDB649-JOB1\nbamboo_planKey=JB-GDB649\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498227_revision_number=3f848bf2699737ea0daea99f4b5d2b68e09da06b\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4333_translatecodonexception\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 04-Dec-2024 16:44:22 444 build 04-Dec-2024 16:44:31 build 04-Dec-2024 16:44:31 > Configure project : build 04-Dec-2024 16:44:31 Using properties from file './utils/channels/default/channel_gradle.properties' build 04-Dec-2024 16:44:31 JALVIEW_VERSION is set to '2.11.4.2' build 04-Dec-2024 16:44:31 HEADLESS BUILD build 04-Dec-2024 16:44:31 J2S ENABLED build 04-Dec-2024 16:44:31 Using a LOCAL profile. build 04-Dec-2024 16:44:33 eclipseDir exists build 04-Dec-2024 16:44:35 build 04-Dec-2024 16:44:35 > Task :cloverHtmlReport build 04-Dec-2024 16:44:35 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 04-Dec-2024 16:44:36 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/reports/clover' build 04-Dec-2024 16:45:15 Done. Processed 116 packages in 38663ms (333ms per package). build 04-Dec-2024 16:45:19 build 04-Dec-2024 16:45:19 > Task :cloverXmlReport build 04-Dec-2024 16:45:19 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 04-Dec-2024 16:45:20 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/reports/clover/clover.xml' build 04-Dec-2024 16:45:20 build 04-Dec-2024 16:45:20 > Task :cloverReport build 04-Dec-2024 16:45:20 build 04-Dec-2024 16:45:20 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 04-Dec-2024 16:45:20 build 04-Dec-2024 16:45:20 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-Dec-2024 16:45:20 build 04-Dec-2024 16:45:20 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 04-Dec-2024 16:45:20 build 04-Dec-2024 16:45:20 BUILD SUCCESSFUL in 58s build 04-Dec-2024 16:45:20 2 actionable tasks: 2 executed simple 04-Dec-2024 16:45:22 Finished task 'Clover Report' with result: Success simple 04-Dec-2024 16:45:22 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 04-Dec-2024 16:45:22 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1... simple 04-Dec-2024 16:45:22 Finished task 'TestNG Parser' with result: Success simple 04-Dec-2024 16:45:22 Running post build plugin 'NCover Results Collector' simple 04-Dec-2024 16:45:22 Running post build plugin 'Artifact Copier' simple 04-Dec-2024 16:45:22 Publishing an artifact: Clover Report (System) simple 04-Dec-2024 16:45:24 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.423 s simple 04-Dec-2024 16:45:24 Publishing an artifact: TestNG report error 04-Dec-2024 16:45:24 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB649-JOB1/build/reports/tests/test does not exist. simple 04-Dec-2024 16:45:24 The artifact hasn't been successfully published after 1.430 ms simple 04-Dec-2024 16:45:24 Running post build plugin 'Artifactory Release Management Staging' simple 04-Dec-2024 16:45:24 Running post build plugin 'Artifactory Build Info Copier' simple 04-Dec-2024 16:45:24 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 04-Dec-2024 16:45:24 Running post build plugin 'npm Cache Cleanup' simple 04-Dec-2024 16:45:24 Running post build plugin 'Clover Results Collector' simple 04-Dec-2024 16:45:24 Running post build plugin 'Docker Container Cleanup' simple 04-Dec-2024 16:45:24 Finalising the build... simple 04-Dec-2024 16:45:24 Stopping timer. simple 04-Dec-2024 16:45:24 Build JB-GDB649-JOB1-1 completed. simple 04-Dec-2024 16:45:24 Running on server: post build plugin 'NCover Results Collector' simple 04-Dec-2024 16:45:24 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 04-Dec-2024 16:45:24 Running on server: post build plugin 'Clover Delta Calculator' simple 04-Dec-2024 16:45:24 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 04-Dec-2024 16:45:24 All post build plugins have finished simple 04-Dec-2024 16:45:24 Generating build results summary... simple 04-Dec-2024 16:45:24 Saving build results to disk... simple 04-Dec-2024 16:45:24 Logging substituted variables... simple 04-Dec-2024 16:45:24 Indexing build results... simple 04-Dec-2024 16:45:24 Finished building JB-GDB649-JOB1-1.