simple 21-Nov-2024 12:06:03 Build Jalview Builds - Gradle Develop Build - bug-JAL-4477_unmapped_filename_characters - Clover and Tests #7 (JB-GDB637-JOB1-7) started building on agent Default Agent simple 21-Nov-2024 12:06:03 simple 21-Nov-2024 12:06:03 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1 simple 21-Nov-2024 12:06:03 Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4477_unmapped_filename_characters - Clover and Tests #7 (JB-GDB637-JOB1-7) simple 21-Nov-2024 12:06:03 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 21-Nov-2024 12:06:03 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1 simple 21-Nov-2024 12:06:03 Updating source code to revision: 72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9 simple 21-Nov-2024 12:06:03 Fetching 'refs/heads/bug/JAL-4477_unmapped_filename_characters' from 'http://source.jalview.org/git/jalview.git'. simple 21-Nov-2024 12:06:03 Checking out revision 72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9. simple 21-Nov-2024 12:06:03 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 21-Nov-2024 12:06:03 a8875a0..72a0f1e bug/JAL-4477_unmapped_filename_characters -> origin/bug/JAL-4477_unmapped_filename_characters simple 21-Nov-2024 12:06:03 416aad3..544bd63 develop -> origin/develop simple 21-Nov-2024 12:06:03 * [new branch] experiment/JAL-4386_JAL-4435_with_HSB_colours -> origin/experiment/JAL-4386_JAL-4435_with_HSB_colours simple 21-Nov-2024 12:06:03 * [new branch] features/JAL-3914_modelqualityscores_v2115 -> origin/features/JAL-3914_modelqualityscores_v2115 simple 21-Nov-2024 12:06:03 * [new branch] patch/JAL-4077_jmolsaveloadwindows -> origin/patch/JAL-4077_jmolsaveloadwindows simple 21-Nov-2024 12:06:03 * [new branch] spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure -> origin/spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure simple 21-Nov-2024 12:06:03 Already on 'bug/JAL-4477_unmapped_filename_characters' simple 21-Nov-2024 12:06:03 Your branch is behind 'origin/bug/JAL-4477_unmapped_filename_characters' by 3 commits, and can be fast-forwarded. simple 21-Nov-2024 12:06:03 (use "git pull" to update your local branch) simple 21-Nov-2024 12:06:03 HEAD is now at 72a0f1e JAL-4491 Allow getdown to download missing cert-chain certificates if not in the cacerts bundle (Jalview already does this). Recompile. simple 21-Nov-2024 12:06:03 Updated source code to revision: 72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9 simple 21-Nov-2024 12:06:03 Finished task 'Checkout Default Repository' with result: Success simple 21-Nov-2024 12:06:03 Running pre-build action: VCS Version Collector simple 21-Nov-2024 12:06:03 Running pre-build action: Artifactory Release Staging simple 21-Nov-2024 12:06:03 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 21-Nov-2024 12:06:03 Bamboo Artifactory Plugin version: 2.6.2 command 21-Nov-2024 12:06:03 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4477_unmapped_filename_characters - Clover and Tests #7 (JB-GDB637-JOB1-7)'\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=72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB637-JOB1-7\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=72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=7\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-JOB1-7\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=a8875a08d16716161d51d26824b551ddc79fca9b\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9\nbamboo_buildTimeStamp=2024-11-21T12:06:03.163Z\nbamboo_repository_previous_revision_number=a8875a08d16716161d51d26824b551ddc79fca9b\nbamboo_planRepository_previousRevision=a8875a08d16716161d51d26824b551ddc79fca9b\nbamboo_repository_git_branch=bug/JAL-4477_unmapped_filename_characters\nbamboo_buildResultKey=JB-GDB637-JOB1-7\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=72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9\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=a8875a08d16716161d51d26824b551ddc79fca9b\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 21-Nov-2024 12:06:03 444 build 21-Nov-2024 12:06:06 Starting a Gradle Daemon (subsequent builds will be faster) build 21-Nov-2024 12:06:20 build 21-Nov-2024 12:06:20 > Configure project : build 21-Nov-2024 12:06:20 Using properties from file './utils/channels/default/channel_gradle.properties' build 21-Nov-2024 12:06:20 JALVIEW_VERSION is set to '2.11.4.2' build 21-Nov-2024 12:06:20 HEADLESS BUILD build 21-Nov-2024 12:06:20 J2S ENABLED build 21-Nov-2024 12:06:20 Using a LOCAL profile. build 21-Nov-2024 12:06:22 eclipseDir exists build 21-Nov-2024 12:06:23 build 21-Nov-2024 12:06:23 > Task :clean build 21-Nov-2024 12:06:23 > Task :cleanClover build 21-Nov-2024 12:06:23 > Task :cleanTest UP-TO-DATE build 21-Nov-2024 12:06:25 build 21-Nov-2024 12:06:25 > Task :cloverInstrJava build 21-Nov-2024 12:06:25 Clover: About to instrument 1103 files build 21-Nov-2024 12:06:26 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 21-Nov-2024 12:06:26 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/clover/clover.db'. build 21-Nov-2024 12:06:26 Processing files at 1.9 source level. error 21-Nov-2024 12:06:31 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 21-Nov-2024 12:06:31 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 21-Nov-2024 12:06:31 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 21-Nov-2024 12:06:31 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 21-Nov-2024 12:06:31 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 21-Nov-2024 12:06:31 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 21-Nov-2024 12:06:31 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 21-Nov-2024 12:06:39 Clover all over. Instrumented 1103 files (112 packages). build 21-Nov-2024 12:06:41 build 21-Nov-2024 12:06:41 > Task :cloverInstrTests build 21-Nov-2024 12:06:41 Clover: About to instrument test files build 21-Nov-2024 12:06:41 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 21-Nov-2024 12:06:41 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/clover/clover.db'. build 21-Nov-2024 12:06:41 Processing files at 1.9 source level. build 21-Nov-2024 12:06:45 Clover all over. Instrumented 291 files (52 packages). build 21-Nov-2024 12:06:45 1595 test methods detected. build 21-Nov-2024 12:06:45 build 21-Nov-2024 12:06:45 > Task :cloverInstr build 21-Nov-2024 12:06:47 build 21-Nov-2024 12:06:47 > Task :compileCloverJava build 21-Nov-2024 12:06:47 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 21-Nov-2024 12:06:47 - 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 21-Nov-2024 12:06:47 - 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 21-Nov-2024 12:06:47 - 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 21-Nov-2024 12:06:47 Setting target compatibility to 11 error 21-Nov-2024 12:07:12 Note: Some input files use or override a deprecated API. error 21-Nov-2024 12:07:12 Note: Recompile with -Xlint:deprecation for details. error 21-Nov-2024 12:07:12 Note: Some input files use unchecked or unsafe operations. error 21-Nov-2024 12:07:12 Note: Recompile with -Xlint:unchecked for details. build 21-Nov-2024 12:07:19 build 21-Nov-2024 12:07:19 > Task :processCloverResources NO-SOURCE build 21-Nov-2024 12:07:19 > Task :cloverClasses build 21-Nov-2024 12:07:20 > Task :copyHelp build 21-Nov-2024 12:07:21 > Task :buildIndices build 21-Nov-2024 12:07:21 > Task :copyResources build 21-Nov-2024 12:07:21 > Task :copyChannelResources build 21-Nov-2024 12:07:21 build 21-Nov-2024 12:07:21 > Task :createBuildProperties build 21-Nov-2024 12:07:21 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 21-Nov-2024 12:07:21 - 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 21-Nov-2024 12:07:21 build 21-Nov-2024 12:07:21 > Task :buildResources build 21-Nov-2024 12:07:21 > Task :copyDocs build 21-Nov-2024 12:07:22 build 21-Nov-2024 12:07:22 > Task :convertMdFiles build 21-Nov-2024 12:07:22 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 21-Nov-2024 12:07:22 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/resources/doc_build/doc/releaseprocess.html build 21-Nov-2024 12:07:22 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 21-Nov-2024 12:07:22 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/resources/doc_build/doc/building.html build 21-Nov-2024 12:07:22 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/resources/doc_build/doc/jalview-projects.html build 21-Nov-2024 12:07:22 build 21-Nov-2024 12:07:22 > Task :releasesTemplates build 21-Nov-2024 12:07:22 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 21-Nov-2024 12:07:22 - 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 21-Nov-2024 12:07:22 - 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 21-Nov-2024 12:07:22 Stripping rc/test/etc for TEST build 21-Nov-2024 12:07:22 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 21-Nov-2024 12:07:22 build 21-Nov-2024 12:07:22 > Task :prepare build 21-Nov-2024 12:07:25 build 21-Nov-2024 12:07:25 > Task :compileJava build 21-Nov-2024 12:07:25 Setting target compatibility to 11 error 21-Nov-2024 12:07:31 Note: Some input files use or override a deprecated API. error 21-Nov-2024 12:07:31 Note: Recompile with -Xlint:deprecation for details. error 21-Nov-2024 12:07:31 Note: Some input files use unchecked or unsafe operations. error 21-Nov-2024 12:07:31 Note: Recompile with -Xlint:unchecked for details. build 21-Nov-2024 12:07:35 build 21-Nov-2024 12:07:35 > Task :compileTestJava build 21-Nov-2024 12:07:35 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 21-Nov-2024 12:07:35 - 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 21-Nov-2024 12:07:35 - 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 21-Nov-2024 12:07:35 Setting target compatibility to 11 error 21-Nov-2024 12:07:40 Note: Some input files use or override a deprecated API. error 21-Nov-2024 12:07:40 Note: Recompile with -Xlint:deprecation for details. error 21-Nov-2024 12:07:40 Note: Some input files use unchecked or unsafe operations. error 21-Nov-2024 12:07:40 Note: Recompile with -Xlint:unchecked for details. build 21-Nov-2024 12:07:41 build 21-Nov-2024 12:07:41 > Task :processTestResources build 21-Nov-2024 12:07:41 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 21-Nov-2024 12:07:41 - 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 ':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 21-Nov-2024 12:07:41 - 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 21-Nov-2024 12:07:41 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/resources/help_build'. 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 21-Nov-2024 12:07:41 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/resources/help_build'. 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 21-Nov-2024 12:07:41 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/resources/help_build'. 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 21-Nov-2024 12:07:41 - 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 ':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 21-Nov-2024 12:07:41 - 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 ':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 21-Nov-2024 12:07:41 - 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 ':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 21-Nov-2024 12:07:41 build 21-Nov-2024 12:07:41 > Task :testClasses build 21-Nov-2024 12:07:43 build 21-Nov-2024 12:07:43 > Task :testTask0 build 21-Nov-2024 12:07:43 Running tests WITH clover error 21-Nov-2024 12:07:47 WARNING: An illegal reflective access operation has occurred error 21-Nov-2024 12:07:47 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 21-Nov-2024 12:07:47 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 21-Nov-2024 12:07:47 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 21-Nov-2024 12:07:47 WARNING: All illegal access operations will be denied in a future release build 21-Nov-2024 12:11:36 build 21-Nov-2024 12:11:36 > Task :testTask1 build 21-Nov-2024 12:11:36 Running tests WITH clover error 21-Nov-2024 12:11:37 WARNING: An illegal reflective access operation has occurred error 21-Nov-2024 12:11:37 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 21-Nov-2024 12:11:37 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 21-Nov-2024 12:11:37 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 21-Nov-2024 12:11:37 WARNING: All illegal access operations will be denied in a future release build 21-Nov-2024 12:13:09 build 21-Nov-2024 12:13:09 > Task :testTask2 build 21-Nov-2024 12:13:09 Running tests WITH clover build 21-Nov-2024 12:13:13 build 21-Nov-2024 12:13:13 > Task :testTask3 build 21-Nov-2024 12:13:13 Running tests WITH clover error 21-Nov-2024 12:13:14 WARNING: An illegal reflective access operation has occurred error 21-Nov-2024 12:13:14 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 21-Nov-2024 12:13:14 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 21-Nov-2024 12:13:14 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 21-Nov-2024 12:13:14 WARNING: All illegal access operations will be denied in a future release build 21-Nov-2024 12:14:00 build 21-Nov-2024 12:14:00 > Task :test NO-SOURCE build 21-Nov-2024 12:14:00 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 21-Nov-2024 12:14:00 │jalview:testTask0 results: SUCCESS (1735 tests, 1735 successes, 0 failures, 0 skipped) in 3 minutes, 51.927 seconds │ build 21-Nov-2024 12:14:00 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/tests/testTask0/index.html│ build 21-Nov-2024 12:14:00 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 21-Nov-2024 12:14:00 │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 33.136 seconds │ build 21-Nov-2024 12:14:00 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/tests/testTask1/index.html│ build 21-Nov-2024 12:14:00 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 21-Nov-2024 12:14:00 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.538 seconds │ build 21-Nov-2024 12:14:00 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/tests/testTask2/index.html│ build 21-Nov-2024 12:14:00 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 21-Nov-2024 12:14:00 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 49.147 seconds │ build 21-Nov-2024 12:14:00 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/tests/testTask3/index.html│ build 21-Nov-2024 12:14:00 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 21-Nov-2024 12:14:00 │OVERALL: results: SUCCESS (1810 tests, 1810 successes, 0 failures, 0 skipped) in 4 minutes, 137.748 seconds │ build 21-Nov-2024 12:14:00 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 21-Nov-2024 12:14:00 build 21-Nov-2024 12:14:00 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 21-Nov-2024 12:14:00 build 21-Nov-2024 12:14:00 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 21-Nov-2024 12:14:00 build 21-Nov-2024 12:14:00 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 21-Nov-2024 12:14:00 build 21-Nov-2024 12:14:00 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 21-Nov-2024 12:14:00 Please consult deprecation warnings for more details. build 21-Nov-2024 12:14:00 build 21-Nov-2024 12:14:00 BUILD SUCCESSFUL in 7m 56s build 21-Nov-2024 12:14:00 21 actionable tasks: 20 executed, 1 up-to-date simple 21-Nov-2024 12:14:01 Finished task 'Run tests with openclover under gradle' with result: Success simple 21-Nov-2024 12:14:01 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 21-Nov-2024 12:14:01 Bamboo Artifactory Plugin version: 2.6.2 command 21-Nov-2024 12:14:01 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4477_unmapped_filename_characters - Clover and Tests #7 (JB-GDB637-JOB1-7)'\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=72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB637-JOB1-7\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=72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=7\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-JOB1-7\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=a8875a08d16716161d51d26824b551ddc79fca9b\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9\nbamboo_buildTimeStamp=2024-11-21T12:06:03.163Z\nbamboo_repository_previous_revision_number=a8875a08d16716161d51d26824b551ddc79fca9b\nbamboo_planRepository_previousRevision=a8875a08d16716161d51d26824b551ddc79fca9b\nbamboo_repository_git_branch=bug/JAL-4477_unmapped_filename_characters\nbamboo_buildResultKey=JB-GDB637-JOB1-7\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=72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_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=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=a8875a08d16716161d51d26824b551ddc79fca9b\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 21-Nov-2024 12:14:01 444 build 21-Nov-2024 12:14:06 build 21-Nov-2024 12:14:06 > Configure project : build 21-Nov-2024 12:14:06 Using properties from file './utils/channels/default/channel_gradle.properties' build 21-Nov-2024 12:14:06 JALVIEW_VERSION is set to '2.11.4.2' build 21-Nov-2024 12:14:06 HEADLESS BUILD build 21-Nov-2024 12:14:06 J2S ENABLED build 21-Nov-2024 12:14:06 Using a LOCAL profile. build 21-Nov-2024 12:14:07 eclipseDir exists build 21-Nov-2024 12:14:09 build 21-Nov-2024 12:14:09 > Task :cloverHtmlReport build 21-Nov-2024 12:14:09 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 21-Nov-2024 12:14:11 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/clover' build 21-Nov-2024 12:14:48 Done. Processed 116 packages in 36730ms (316ms per package). build 21-Nov-2024 12:14:53 build 21-Nov-2024 12:14:53 > Task :cloverXmlReport build 21-Nov-2024 12:14:53 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 21-Nov-2024 12:14:54 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1/build/reports/clover/clover.xml' build 21-Nov-2024 12:14:54 build 21-Nov-2024 12:14:54 > Task :cloverReport build 21-Nov-2024 12:14:54 build 21-Nov-2024 12:14:54 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 21-Nov-2024 12:14:54 build 21-Nov-2024 12:14:54 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 21-Nov-2024 12:14:54 build 21-Nov-2024 12:14:54 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 21-Nov-2024 12:14:54 build 21-Nov-2024 12:14:54 BUILD SUCCESSFUL in 53s build 21-Nov-2024 12:14:54 2 actionable tasks: 2 executed simple 21-Nov-2024 12:14:56 Finished task 'Clover Report' with result: Success simple 21-Nov-2024 12:14:56 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' simple 21-Nov-2024 12:14:56 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB637-JOB1... simple 21-Nov-2024 12:14:56 Finished task 'TestNG Parser' with result: Success simple 21-Nov-2024 12:14:56 Running post build plugin 'NCover Results Collector' simple 21-Nov-2024 12:14:56 Running post build plugin 'Artifact Copier' simple 21-Nov-2024 12:14:56 Publishing an artifact: Clover Report (System) simple 21-Nov-2024 12:14:58 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.405 s simple 21-Nov-2024 12:14:58 Publishing an artifact: TestNG report error 21-Nov-2024 12:14:58 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 21-Nov-2024 12:14:58 The artifact hasn't been successfully published after 1.430 ms simple 21-Nov-2024 12:14:58 Running post build plugin 'Artifactory Release Management Staging' simple 21-Nov-2024 12:14:58 Running post build plugin 'Artifactory Build Info Copier' simple 21-Nov-2024 12:14:58 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 21-Nov-2024 12:14:58 Running post build plugin 'npm Cache Cleanup' simple 21-Nov-2024 12:14:58 Running post build plugin 'Clover Results Collector' simple 21-Nov-2024 12:14:58 Running post build plugin 'Docker Container Cleanup' simple 21-Nov-2024 12:14:58 Finalising the build... simple 21-Nov-2024 12:14:58 Stopping timer. simple 21-Nov-2024 12:14:58 Build JB-GDB637-JOB1-7 completed. simple 21-Nov-2024 12:14:58 Running on server: post build plugin 'NCover Results Collector' simple 21-Nov-2024 12:14:58 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 21-Nov-2024 12:14:58 Running on server: post build plugin 'Clover Delta Calculator' simple 21-Nov-2024 12:14:58 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 21-Nov-2024 12:14:58 All post build plugins have finished simple 21-Nov-2024 12:14:58 Generating build results summary... simple 21-Nov-2024 12:14:58 Saving build results to disk... simple 21-Nov-2024 12:14:58 Logging substituted variables... simple 21-Nov-2024 12:14:58 Indexing build results... simple 21-Nov-2024 12:14:58 Finished building JB-GDB637-JOB1-7.