simple 11-Nov-2024 17:27:01 Build Jalview Builds - Gradle Develop Build - bug-JAL-4477_unmapped_filename_characters - Clover and Tests #6 (JB-GDB637-JOB1-6) started building on agent Default Agent simple 11-Nov-2024 17:27:01 simple 11-Nov-2024 17:27:01 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1 simple 11-Nov-2024 17:27:01 Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4477_unmapped_filename_characters - Clover and Tests #6 (JB-GDB637-JOB1-6) simple 11-Nov-2024 17:27:01 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 11-Nov-2024 17:27:01 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1 simple 11-Nov-2024 17:27:01 Updating source code to revision: a8875a08d16716161d51d26824b551ddc79fca9b simple 11-Nov-2024 17:27:01 Fetching 'refs/heads/bug/JAL-4477_unmapped_filename_characters' from 'http://source.jalview.org/git/jalview.git'. simple 11-Nov-2024 17:27:01 Checking out revision a8875a08d16716161d51d26824b551ddc79fca9b. simple 11-Nov-2024 17:27:02 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 11-Nov-2024 17:27:02 d7c3dc7..a8875a0 bug/JAL-4477_unmapped_filename_characters -> origin/bug/JAL-4477_unmapped_filename_characters simple 11-Nov-2024 17:27:02 67eb1f5..416aad3 develop -> origin/develop simple 11-Nov-2024 17:27:02 Your branch is behind 'origin/bug/JAL-4477_unmapped_filename_characters' by 1 commit, and can be fast-forwarded. simple 11-Nov-2024 17:27:02 (use "git pull" to update your local branch) simple 11-Nov-2024 17:27:02 Already on 'bug/JAL-4477_unmapped_filename_characters' simple 11-Nov-2024 17:27:02 HEAD is now at a8875a0 JAL-4477 missing import ? not sure how I missed this ! simple 11-Nov-2024 17:27:02 Updated source code to revision: a8875a08d16716161d51d26824b551ddc79fca9b simple 11-Nov-2024 17:27:02 Finished task 'Checkout Default Repository' with result: Success simple 11-Nov-2024 17:27:02 Running pre-build action: VCS Version Collector simple 11-Nov-2024 17:27:02 Running pre-build action: Artifactory Release Staging simple 11-Nov-2024 17:27:02 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 11-Nov-2024 17:27:02 Bamboo Artifactory Plugin version: 2.6.2 command 11-Nov-2024 17:27:02 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4477_unmapped_filename_characters - Clover and Tests #6 (JB-GDB637-JOB1-6)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4477_unmapped_filename_characters\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4477_unmapped_filename_characters\nbamboo_repository_revision_number=a8875a08d16716161d51d26824b551ddc79fca9b\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB637-JOB1-6\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB637-JOB1\nbamboo_repository_46498157_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_shortPlanName=bug-JAL-4477_unmapped_filename_characters\nbamboo_repository_46498157_revision_number=a8875a08d16716161d51d26824b551ddc79fca9b\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=6\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB637-JOB1-6\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4477_unmapped_filename_characters\nbamboo_shortPlanKey=GDB637\nbamboo_repository_46498157_git_branch=bug/JAL-4477_unmapped_filename_characters\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498157_previous_revision_number=d7c3dc79c05b6bcfb728e455ed8148650d00d551\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a8875a08d16716161d51d26824b551ddc79fca9b\nbamboo_buildTimeStamp=2024-11-11T17:27:01.674Z\nbamboo_repository_previous_revision_number=d7c3dc79c05b6bcfb728e455ed8148650d00d551\nbamboo_planRepository_previousRevision=d7c3dc79c05b6bcfb728e455ed8148650d00d551\nbamboo_repository_git_branch=bug/JAL-4477_unmapped_filename_characters\nbamboo_buildResultKey=JB-GDB637-JOB1-6\nbamboo_repository_branch_name=bug/JAL-4477_unmapped_filename_characters\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4477_unmapped_filename_characters - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498157_git_username=\nbamboo_planRepository_1_revision=a8875a08d16716161d51d26824b551ddc79fca9b\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_repository_46498157_name=Jalview Git\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46498157_branch_name=bug/JAL-4477_unmapped_filename_characters\nbamboo_planRepository_branch=bug/JAL-4477_unmapped_filename_characters\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=d7c3dc79c05b6bcfb728e455ed8148650d00d551\nbamboo_planRepository_branchDisplayName=bug/JAL-4477_unmapped_filename_characters\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4477_unmapped_filename_characters\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-46301913\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-GDB637-JOB1\nbamboo_planKey=JB-GDB637\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4477_unmapped_filename_characters\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 11-Nov-2024 17:27:02 444 build 11-Nov-2024 17:27:03 build 11-Nov-2024 17:27:03 > Configure project : build 11-Nov-2024 17:27:03 Using properties from file './utils/channels/default/channel_gradle.properties' build 11-Nov-2024 17:27:03 JALVIEW_VERSION is set to '2.11.4.2' build 11-Nov-2024 17:27:03 HEADLESS BUILD build 11-Nov-2024 17:27:03 J2S ENABLED build 11-Nov-2024 17:27:03 Using a LOCAL profile. build 11-Nov-2024 17:27:03 eclipseDir exists build 11-Nov-2024 17:27:03 build 11-Nov-2024 17:27:03 > Task :clean build 11-Nov-2024 17:27:03 > Task :cleanClover build 11-Nov-2024 17:27:03 > Task :cleanTest UP-TO-DATE build 11-Nov-2024 17:27:05 build 11-Nov-2024 17:27:05 > Task :cloverInstrJava build 11-Nov-2024 17:27:05 Clover: About to instrument 1103 files build 11-Nov-2024 17:27:05 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 11-Nov-2024 17:27:05 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/clover/clover.db'. build 11-Nov-2024 17:27:05 Processing files at 1.9 source level. error 11-Nov-2024 17:27:08 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 11-Nov-2024 17:27:08 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 11-Nov-2024 17:27:08 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 11-Nov-2024 17:27:08 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 11-Nov-2024 17:27:08 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 11-Nov-2024 17:27:08 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 11-Nov-2024 17:27:08 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 11-Nov-2024 17:27:15 Clover all over. Instrumented 1103 files (112 packages). build 11-Nov-2024 17:27:18 build 11-Nov-2024 17:27:18 > Task :cloverInstrTests build 11-Nov-2024 17:27:18 Clover: About to instrument test files build 11-Nov-2024 17:27:18 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 11-Nov-2024 17:27:18 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/clover/clover.db'. build 11-Nov-2024 17:27:18 Processing files at 1.9 source level. build 11-Nov-2024 17:27:20 Clover all over. Instrumented 291 files (52 packages). build 11-Nov-2024 17:27:20 1595 test methods detected. build 11-Nov-2024 17:27:20 build 11-Nov-2024 17:27:20 > Task :cloverInstr build 11-Nov-2024 17:27:22 build 11-Nov-2024 17:27:22 > Task :compileCloverJava build 11-Nov-2024 17:27:22 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 11-Nov-2024 17:27:22 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:22 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:22 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:22 Setting target compatibility to 11 error 11-Nov-2024 17:27:36 Note: Some input files use or override a deprecated API. error 11-Nov-2024 17:27:36 Note: Recompile with -Xlint:deprecation for details. error 11-Nov-2024 17:27:36 Note: Some input files use unchecked or unsafe operations. error 11-Nov-2024 17:27:36 Note: Recompile with -Xlint:unchecked for details. build 11-Nov-2024 17:27:40 build 11-Nov-2024 17:27:40 > Task :processCloverResources NO-SOURCE build 11-Nov-2024 17:27:40 > Task :cloverClasses build 11-Nov-2024 17:27:40 > Task :copyHelp build 11-Nov-2024 17:27:41 > Task :buildIndices build 11-Nov-2024 17:27:41 > Task :copyResources build 11-Nov-2024 17:27:41 > Task :copyChannelResources build 11-Nov-2024 17:27:41 build 11-Nov-2024 17:27:41 > Task :createBuildProperties build 11-Nov-2024 17:27:41 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 11-Nov-2024 17:27:41 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:41 build 11-Nov-2024 17:27:41 > Task :buildResources build 11-Nov-2024 17:27:41 > Task :copyDocs build 11-Nov-2024 17:27:41 build 11-Nov-2024 17:27:41 > Task :convertMdFiles build 11-Nov-2024 17:27:41 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 11-Nov-2024 17:27:41 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/resources/doc_build/doc/releaseprocess.html build 11-Nov-2024 17:27:41 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 11-Nov-2024 17:27:41 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/resources/doc_build/doc/building.html build 11-Nov-2024 17:27:41 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/resources/doc_build/doc/jalview-projects.html build 11-Nov-2024 17:27:41 build 11-Nov-2024 17:27:41 > Task :releasesTemplates build 11-Nov-2024 17:27:41 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 11-Nov-2024 17:27:41 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:41 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:41 Stripping rc/test/etc for TEST build 11-Nov-2024 17:27:41 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 11-Nov-2024 17:27:41 build 11-Nov-2024 17:27:41 > Task :prepare build 11-Nov-2024 17:27:43 build 11-Nov-2024 17:27:43 > Task :compileJava build 11-Nov-2024 17:27:43 Setting target compatibility to 11 error 11-Nov-2024 17:27:49 Note: Some input files use or override a deprecated API. error 11-Nov-2024 17:27:49 Note: Recompile with -Xlint:deprecation for details. error 11-Nov-2024 17:27:49 Note: Some input files use unchecked or unsafe operations. error 11-Nov-2024 17:27:49 Note: Recompile with -Xlint:unchecked for details. build 11-Nov-2024 17:27:51 build 11-Nov-2024 17:27:51 > Task :compileTestJava build 11-Nov-2024 17:27:51 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 11-Nov-2024 17:27:51 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:51 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:51 Setting target compatibility to 11 error 11-Nov-2024 17:27:56 Note: Some input files use or override a deprecated API. error 11-Nov-2024 17:27:56 Note: Recompile with -Xlint:deprecation for details. error 11-Nov-2024 17:27:56 Note: Some input files use unchecked or unsafe operations. error 11-Nov-2024 17:27:56 Note: Recompile with -Xlint:unchecked for details. build 11-Nov-2024 17:27:57 build 11-Nov-2024 17:27:57 > Task :processTestResources build 11-Nov-2024 17:27:57 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 11-Nov-2024 17:27:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-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 11-Nov-2024 17:27:57 build 11-Nov-2024 17:27:57 > Task :testClasses build 11-Nov-2024 17:27:59 build 11-Nov-2024 17:27:59 > Task :testTask0 build 11-Nov-2024 17:27:59 Running tests WITH clover error 11-Nov-2024 17:28:02 WARNING: An illegal reflective access operation has occurred error 11-Nov-2024 17:28:02 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 11-Nov-2024 17:28:02 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 11-Nov-2024 17:28:02 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 11-Nov-2024 17:28:02 WARNING: All illegal access operations will be denied in a future release build 11-Nov-2024 17:28:12 build 11-Nov-2024 17:28:12 jalview.bin.HiDPISettingTest1.setUp FAILED build 11-Nov-2024 17:28:12 java.lang.NullPointerException: Null action build 11-Nov-2024 17:28:12 at java.base/java.security.AccessController.doPrivileged(Native Method) build 11-Nov-2024 17:28:12 at java.desktop/javax.swing.plaf.basic.BasicLookAndFeel.uninitialize(BasicLookAndFeel.java:203) build 11-Nov-2024 17:28:12 at com.formdev.flatlaf.FlatLaf.uninitialize(FlatLaf.java:371) build 11-Nov-2024 17:28:12 at java.desktop/javax.swing.UIManager.setLookAndFeel(UIManager.java:580) build 11-Nov-2024 17:28:12 at java.desktop/javax.swing.UIManager.setLookAndFeel(UIManager.java:633) build 11-Nov-2024 17:28:12 at jalview.bin.Jalview.setFlatLookAndFeel(Jalview.java:1507) build 11-Nov-2024 17:28:12 at jalview.bin.Jalview.setLinuxLookAndFeel(Jalview.java:1601) build 11-Nov-2024 17:28:12 at jalview.bin.Jalview.setLookAndFeel(Jalview.java:1376) build 11-Nov-2024 17:28:12 at jalview.bin.Jalview.doMain(Jalview.java:652) build 11-Nov-2024 17:28:12 at jalview.bin.Jalview.main(Jalview.java:259) build 11-Nov-2024 17:28:12 at jalview.bin.HiDPISettingTest1.setUp(HiDPISettingTest1.java:63) error 11-Nov-2024 17:31:48 error 11-Nov-2024 17:31:48 1736 tests completed, 1 failed, 1 skipped build 11-Nov-2024 17:31:48 There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/tests/testTask0/index.html build 11-Nov-2024 17:31:50 build 11-Nov-2024 17:31:50 > Task :testTask1 build 11-Nov-2024 17:31:50 Running tests WITH clover error 11-Nov-2024 17:31:51 WARNING: An illegal reflective access operation has occurred error 11-Nov-2024 17:31:51 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 11-Nov-2024 17:31:51 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 11-Nov-2024 17:31:51 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 11-Nov-2024 17:31:51 WARNING: All illegal access operations will be denied in a future release build 11-Nov-2024 17:33:26 build 11-Nov-2024 17:33:26 > Task :testTask2 build 11-Nov-2024 17:33:26 Running tests WITH clover build 11-Nov-2024 17:33:29 build 11-Nov-2024 17:33:29 > Task :testTask3 build 11-Nov-2024 17:33:29 Running tests WITH clover error 11-Nov-2024 17:33:31 WARNING: An illegal reflective access operation has occurred error 11-Nov-2024 17:33:31 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName error 11-Nov-2024 17:33:31 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 11-Nov-2024 17:33:31 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 11-Nov-2024 17:33:31 WARNING: All illegal access operations will be denied in a future release build 11-Nov-2024 17:34:16 build 11-Nov-2024 17:34:16 > Task :test NO-SOURCE build 11-Nov-2024 17:34:16 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 11-Nov-2024 17:34:16 │jalview:testTask0 results: FAILURE (1736 tests, 1734 successes, 1 failures, 1 skipped) in 3 minutes, 50.479 seconds │ build 11-Nov-2024 17:34:16 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/tests/testTask0/index.html│ build 11-Nov-2024 17:34:16 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Nov-2024 17:34:16 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 35.830 seconds │ build 11-Nov-2024 17:34:16 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/tests/testTask1/index.html│ error 11-Nov-2024 17:34:16 error 11-Nov-2024 17:34:16 FAILURE: Build failed with an exception. error 11-Nov-2024 17:34:16 error 11-Nov-2024 17:34:16 * Where: error 11-Nov-2024 17:34:16 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build.gradle' line: 1966 error 11-Nov-2024 17:34:16 error 11-Nov-2024 17:34:16 * What went wrong: error 11-Nov-2024 17:34:16 Failed tests! error 11-Nov-2024 17:34:16 error 11-Nov-2024 17:34:16 * Try: error 11-Nov-2024 17:34:16 > Run with --stacktrace option to get the stack trace. error 11-Nov-2024 17:34:16 > Run with --info or --debug option to get more log output. error 11-Nov-2024 17:34:16 > Run with --scan to get full insights. error 11-Nov-2024 17:34:16 error 11-Nov-2024 17:34:16 * Get more help at https://help.gradle.org error 11-Nov-2024 17:34:16 error 11-Nov-2024 17:34:16 BUILD FAILED in 7m 14s build 11-Nov-2024 17:34:16 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Nov-2024 17:34:16 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.341 seconds │ build 11-Nov-2024 17:34:16 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/tests/testTask2/index.html│ build 11-Nov-2024 17:34:16 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Nov-2024 17:34:16 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 48.991 seconds │ build 11-Nov-2024 17:34:16 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/tests/testTask3/index.html│ build 11-Nov-2024 17:34:16 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 11-Nov-2024 17:34:16 │OVERALL: results: FAILURE (1811 tests, 1809 successes, 1 failures, 1 skipped) in 4 minutes, 138.641 seconds │ build 11-Nov-2024 17:34:16 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 11-Nov-2024 17:34:16 build 11-Nov-2024 17:34:16 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 11-Nov-2024 17:34:16 build 11-Nov-2024 17:34:16 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 11-Nov-2024 17:34:16 build 11-Nov-2024 17:34:16 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 11-Nov-2024 17:34:16 build 11-Nov-2024 17:34:16 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 11-Nov-2024 17:34:16 Please consult deprecation warnings for more details. build 11-Nov-2024 17:34:16 21 actionable tasks: 20 executed, 1 up-to-date simple 11-Nov-2024 17:34:17 simple 11-Nov-2024 17:34:17 Failing task since return code of [/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test] was 1 while expected 0 simple 11-Nov-2024 17:34:17 Finished task 'Run tests with openclover under gradle' with result: Failed simple 11-Nov-2024 17:34:17 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 11-Nov-2024 17:34:17 Bamboo Artifactory Plugin version: 2.6.2 command 11-Nov-2024 17:34:17 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4477_unmapped_filename_characters - Clover and Tests #6 (JB-GDB637-JOB1-6)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4477_unmapped_filename_characters\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4477_unmapped_filename_characters\nbamboo_repository_revision_number=a8875a08d16716161d51d26824b551ddc79fca9b\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB637-JOB1-6\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB637-JOB1\nbamboo_repository_46498157_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_shortPlanName=bug-JAL-4477_unmapped_filename_characters\nbamboo_repository_46498157_revision_number=a8875a08d16716161d51d26824b551ddc79fca9b\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=6\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB637-JOB1-6\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4477_unmapped_filename_characters\nbamboo_shortPlanKey=GDB637\nbamboo_repository_46498157_git_branch=bug/JAL-4477_unmapped_filename_characters\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498157_previous_revision_number=d7c3dc79c05b6bcfb728e455ed8148650d00d551\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a8875a08d16716161d51d26824b551ddc79fca9b\nbamboo_buildTimeStamp=2024-11-11T17:27:01.674Z\nbamboo_repository_previous_revision_number=d7c3dc79c05b6bcfb728e455ed8148650d00d551\nbamboo_planRepository_previousRevision=d7c3dc79c05b6bcfb728e455ed8148650d00d551\nbamboo_repository_git_branch=bug/JAL-4477_unmapped_filename_characters\nbamboo_buildResultKey=JB-GDB637-JOB1-6\nbamboo_repository_branch_name=bug/JAL-4477_unmapped_filename_characters\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4477_unmapped_filename_characters - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498157_git_username=\nbamboo_planRepository_1_revision=a8875a08d16716161d51d26824b551ddc79fca9b\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=true\nbamboo_repository_46498157_name=Jalview Git\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46498157_branch_name=bug/JAL-4477_unmapped_filename_characters\nbamboo_planRepository_branch=bug/JAL-4477_unmapped_filename_characters\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=d7c3dc79c05b6bcfb728e455ed8148650d00d551\nbamboo_planRepository_branchDisplayName=bug/JAL-4477_unmapped_filename_characters\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4477_unmapped_filename_characters\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-46301913\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-GDB637-JOB1\nbamboo_planKey=JB-GDB637\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4477_unmapped_filename_characters\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 11-Nov-2024 17:34:17 444 build 11-Nov-2024 17:34:29 build 11-Nov-2024 17:34:29 > Configure project : build 11-Nov-2024 17:34:29 Using properties from file './utils/channels/default/channel_gradle.properties' build 11-Nov-2024 17:34:29 JALVIEW_VERSION is set to '2.11.4.2' build 11-Nov-2024 17:34:29 HEADLESS BUILD build 11-Nov-2024 17:34:29 J2S ENABLED build 11-Nov-2024 17:34:30 Using a LOCAL profile. build 11-Nov-2024 17:34:31 eclipseDir exists build 11-Nov-2024 17:34:33 build 11-Nov-2024 17:34:33 > Task :cloverHtmlReport build 11-Nov-2024 17:34:33 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 11-Nov-2024 17:34:35 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/clover' build 11-Nov-2024 17:35:14 Done. Processed 116 packages in 39041ms (336ms per package). build 11-Nov-2024 17:35:20 build 11-Nov-2024 17:35:20 > Task :cloverXmlReport build 11-Nov-2024 17:35:20 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 11-Nov-2024 17:35:21 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/clover/clover.xml' build 11-Nov-2024 17:35:21 build 11-Nov-2024 17:35:21 > Task :cloverReport build 11-Nov-2024 17:35:21 build 11-Nov-2024 17:35:21 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 11-Nov-2024 17:35:21 build 11-Nov-2024 17:35:21 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 11-Nov-2024 17:35:21 build 11-Nov-2024 17:35:21 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 11-Nov-2024 17:35:21 build 11-Nov-2024 17:35:21 BUILD SUCCESSFUL in 1m 4s build 11-Nov-2024 17:35:21 2 actionable tasks: 2 executed simple 11-Nov-2024 17:35:21 Finished task 'Clover Report' with result: Success simple 11-Nov-2024 17:35:21 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 11-Nov-2024 17:35:21 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1... simple 11-Nov-2024 17:35:21 Failing task since 1 failing test cases were found. simple 11-Nov-2024 17:35:21 Finished task 'TestNG Parser' with result: Failed simple 11-Nov-2024 17:35:21 Running post build plugin 'NCover Results Collector' simple 11-Nov-2024 17:35:21 Running post build plugin 'Artifact Copier' simple 11-Nov-2024 17:35:21 Publishing an artifact: Clover Report (System) simple 11-Nov-2024 17:35:23 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.426 s simple 11-Nov-2024 17:35:23 Publishing an artifact: TestNG report error 11-Nov-2024 17:35:23 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/tests/test does not exist. simple 11-Nov-2024 17:35:23 The artifact hasn't been successfully published after 1.284 ms simple 11-Nov-2024 17:35:23 Running post build plugin 'Artifactory Release Management Staging' simple 11-Nov-2024 17:35:23 Running post build plugin 'Artifactory Build Info Copier' simple 11-Nov-2024 17:35:23 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 11-Nov-2024 17:35:23 Running post build plugin 'npm Cache Cleanup' simple 11-Nov-2024 17:35:23 Running post build plugin 'Clover Results Collector' simple 11-Nov-2024 17:35:23 Running post build plugin 'Docker Container Cleanup' simple 11-Nov-2024 17:35:23 Finalising the build... simple 11-Nov-2024 17:35:23 Stopping timer. simple 11-Nov-2024 17:35:23 Build JB-GDB637-JOB1-6 completed. simple 11-Nov-2024 17:35:23 Running on server: post build plugin 'NCover Results Collector' simple 11-Nov-2024 17:35:23 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 11-Nov-2024 17:35:23 Running on server: post build plugin 'Clover Delta Calculator' simple 11-Nov-2024 17:35:23 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 11-Nov-2024 17:35:23 All post build plugins have finished simple 11-Nov-2024 17:35:23 Generating build results summary... simple 11-Nov-2024 17:35:23 Saving build results to disk... simple 11-Nov-2024 17:35:23 Logging substituted variables... simple 11-Nov-2024 17:35:23 Indexing build results... simple 11-Nov-2024 17:35:23 Finished building JB-GDB637-JOB1-6.