simple	07-Nov-2024 13:01:00	Build Jalview Builds - Gradle Develop Build - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Clover and Tests #2 (JB-GDB640-JOB1-2) started building on agent Default Agent
simple	07-Nov-2024 13:01:00	
simple	07-Nov-2024 13:01:00	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1
simple	07-Nov-2024 13:01:00	Executing build Jalview Builds - Gradle Develop Build - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Clover and Tests #2 (JB-GDB640-JOB1-2)
simple	07-Nov-2024 13:01:00	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	07-Nov-2024 13:01:00	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1
simple	07-Nov-2024 13:01:00	Updating source code to revision: cfb973824e06936f2f3b2c4cf9605bd687896cf4
simple	07-Nov-2024 13:01:00	Fetching 'refs/heads/experiment/JAL-4386_experimental_string_to_colour_scheme_methods' from 'http://source.jalview.org/git/jalview.git'.
simple	07-Nov-2024 13:01:00	Checking out revision cfb973824e06936f2f3b2c4cf9605bd687896cf4.
simple	07-Nov-2024 13:01:00	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164
simple	07-Nov-2024 13:01:00	   503c832..cfb9738  experiment/JAL-4386_experimental_string_to_colour_scheme_methods -> origin/experiment/JAL-4386_experimental_string_to_colour_scheme_methods
simple	07-Nov-2024 13:01:00	   e1ff67b..1c79fdc  feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels
simple	07-Nov-2024 13:01:02	Already on 'experiment/JAL-4386_experimental_string_to_colour_scheme_methods'
simple	07-Nov-2024 13:01:02	Your branch is behind 'origin/experiment/JAL-4386_experimental_string_to_colour_scheme_methods' by 4 commits, and can be fast-forwarded.
simple	07-Nov-2024 13:01:02	  (use "git pull" to update your local branch)
simple	07-Nov-2024 13:01:02	HEAD is now at cfb9738 JAL-4386 Fixed to the colour scheme ranges and application to the normal calculated tree
simple	07-Nov-2024 13:01:02	Updated source code to revision: cfb973824e06936f2f3b2c4cf9605bd687896cf4
simple	07-Nov-2024 13:01:02	Finished task 'Checkout Default Repository' with result: Success
simple	07-Nov-2024 13:01:02	Running pre-build action: VCS Version Collector
simple	07-Nov-2024 13:01:02	Running pre-build action: Artifactory Release Staging
simple	07-Nov-2024 13:01:02	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	07-Nov-2024 13:01:02	Bamboo Artifactory Plugin version: 2.6.2
command	07-Nov-2024 13:01:02	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Clover and Tests #2 (JB-GDB640-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_repository_revision_number=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB640-JOB1-2\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB640-JOB1\nbamboo_shortPlanName=experiment-JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB640-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - experiment-JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_shortPlanKey=GDB640\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nbamboo_buildTimeStamp=2024-11-07T13:01:00.512Z\nbamboo_repository_previous_revision_number=503c83212e9779b412c999dc1d64d4e6c5e41cae\nbamboo_planRepository_previousRevision=503c83212e9779b412c999dc1d64d4e6c5e41cae\nbamboo_repository_git_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_buildResultKey=JB-GDB640-JOB1-2\nbamboo_repository_branch_name=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\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=503c83212e9779b412c999dc1d64d4e6c5e41cae\nbamboo_repository_46498174_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branchDisplayName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498174_revision_number=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301947\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46498174_branch_name=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_46498174_git_username=\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-GDB640-JOB1\nbamboo_planKey=JB-GDB640\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_46498174_previous_revision_number=503c83212e9779b412c999dc1d64d4e6c5e41cae\nbamboo_planRepository_username=\nbamboo_repository_46498174_git_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_repository_46498174_name=Jalview Git\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	07-Nov-2024 13:01:02	444
build	07-Nov-2024 13:01:03	
build	07-Nov-2024 13:01:03	> Configure project :
build	07-Nov-2024 13:01:03	Using properties from file './utils/channels/default/channel_gradle.properties'
build	07-Nov-2024 13:01:03	JALVIEW_VERSION is set to '2.11.4.1'
build	07-Nov-2024 13:01:03	HEADLESS BUILD
build	07-Nov-2024 13:01:03	J2S ENABLED
build	07-Nov-2024 13:01:03	Using a LOCAL profile.
build	07-Nov-2024 13:01:03	eclipseDir exists
build	07-Nov-2024 13:01:04	
build	07-Nov-2024 13:01:04	> Task :clean
build	07-Nov-2024 13:01:04	> Task :cleanClover
build	07-Nov-2024 13:01:04	> Task :cleanTest UP-TO-DATE
build	07-Nov-2024 13:01:06	
build	07-Nov-2024 13:01:06	> Task :cloverInstrJava
build	07-Nov-2024 13:01:06	Clover: About to instrument 1103 files
build	07-Nov-2024 13:01:06	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	07-Nov-2024 13:01:06	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/clover/clover.db'.
build	07-Nov-2024 13:01:06	Processing files at 1.9 source level.
error	07-Nov-2024 13:01:09	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	07-Nov-2024 13:01:09	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	07-Nov-2024 13:01:09	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	07-Nov-2024 13:01:09	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	07-Nov-2024 13:01:09	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	07-Nov-2024 13:01:09	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	07-Nov-2024 13:01:09	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
build	07-Nov-2024 13:01:16	Clover all over. Instrumented 1103 files (112 packages).
build	07-Nov-2024 13:01:19	
build	07-Nov-2024 13:01:19	> Task :cloverInstrTests
build	07-Nov-2024 13:01:19	Clover: About to instrument test files
build	07-Nov-2024 13:01:19	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	07-Nov-2024 13:01:19	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/clover/clover.db'.
build	07-Nov-2024 13:01:19	Processing files at 1.9 source level.
build	07-Nov-2024 13:01:22	Clover all over. Instrumented 291 files (52 packages).
build	07-Nov-2024 13:01:22	1594 test methods detected.
build	07-Nov-2024 13:01:22	
build	07-Nov-2024 13:01:22	> Task :cloverInstr
build	07-Nov-2024 13:01:24	
build	07-Nov-2024 13:01:24	> Task :compileCloverJava
build	07-Nov-2024 13:01:24	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	07-Nov-2024 13:01:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:24	Setting target compatibility to 11
error	07-Nov-2024 13:01:38	Note: Some input files use or override a deprecated API.
error	07-Nov-2024 13:01:38	Note: Recompile with -Xlint:deprecation for details.
error	07-Nov-2024 13:01:38	Note: Some input files use unchecked or unsafe operations.
error	07-Nov-2024 13:01:38	Note: Recompile with -Xlint:unchecked for details.
build	07-Nov-2024 13:01:42	
build	07-Nov-2024 13:01:42	> Task :processCloverResources NO-SOURCE
build	07-Nov-2024 13:01:42	> Task :cloverClasses
build	07-Nov-2024 13:01:42	> Task :copyHelp
build	07-Nov-2024 13:01:43	> Task :buildIndices
build	07-Nov-2024 13:01:43	> Task :copyResources
build	07-Nov-2024 13:01:43	> Task :copyChannelResources
build	07-Nov-2024 13:01:43	
build	07-Nov-2024 13:01:43	> Task :createBuildProperties
build	07-Nov-2024 13:01:43	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	07-Nov-2024 13:01:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:43	
build	07-Nov-2024 13:01:43	> Task :buildResources
build	07-Nov-2024 13:01:43	> Task :copyDocs
build	07-Nov-2024 13:01:43	
build	07-Nov-2024 13:01:43	> Task :convertMdFiles
build	07-Nov-2024 13:01:43	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	07-Nov-2024 13:01:43	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	07-Nov-2024 13:01:43	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	07-Nov-2024 13:01:43	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/resources/doc_build/doc/building.html
build	07-Nov-2024 13:01:43	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	07-Nov-2024 13:01:43	
build	07-Nov-2024 13:01:43	> Task :releasesTemplates
build	07-Nov-2024 13:01:43	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	07-Nov-2024 13:01:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:43	Stripping rc/test/etc for TEST
build	07-Nov-2024 13:01:43	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	07-Nov-2024 13:01:43	
build	07-Nov-2024 13:01:43	> Task :prepare
build	07-Nov-2024 13:01:45	
build	07-Nov-2024 13:01:45	> Task :compileJava
build	07-Nov-2024 13:01:45	Setting target compatibility to 11
error	07-Nov-2024 13:01:50	Note: Some input files use or override a deprecated API.
error	07-Nov-2024 13:01:50	Note: Recompile with -Xlint:deprecation for details.
error	07-Nov-2024 13:01:50	Note: Some input files use unchecked or unsafe operations.
error	07-Nov-2024 13:01:50	Note: Recompile with -Xlint:unchecked for details.
build	07-Nov-2024 13:01:53	
build	07-Nov-2024 13:01:53	> Task :compileTestJava
build	07-Nov-2024 13:01:53	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	07-Nov-2024 13:01:53	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:53	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:53	Setting target compatibility to 11
error	07-Nov-2024 13:01:58	Note: Some input files use or override a deprecated API.
error	07-Nov-2024 13:01:58	Note: Recompile with -Xlint:deprecation for details.
error	07-Nov-2024 13:01:58	Note: Some input files use unchecked or unsafe operations.
error	07-Nov-2024 13:01:58	Note: Recompile with -Xlint:unchecked for details.
build	07-Nov-2024 13:01:59	
build	07-Nov-2024 13:01:59	> Task :processTestResources
build	07-Nov-2024 13:01:59	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	07-Nov-2024 13:01:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-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	07-Nov-2024 13:01:59	
build	07-Nov-2024 13:01:59	> Task :testClasses
build	07-Nov-2024 13:02:01	
build	07-Nov-2024 13:02:01	> Task :testTask0
build	07-Nov-2024 13:02:01	Running tests WITH clover
error	07-Nov-2024 13:02:03	WARNING: An illegal reflective access operation has occurred
error	07-Nov-2024 13:02:03	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	07-Nov-2024 13:02:03	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	07-Nov-2024 13:02:03	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	07-Nov-2024 13:02:03	WARNING: All illegal access operations will be denied in a future release
build	07-Nov-2024 13:06:00	
build	07-Nov-2024 13:06:00	> Task :testTask1
build	07-Nov-2024 13:06:00	Running tests WITH clover
error	07-Nov-2024 13:06:01	WARNING: An illegal reflective access operation has occurred
error	07-Nov-2024 13:06:01	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	07-Nov-2024 13:06:01	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	07-Nov-2024 13:06:01	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	07-Nov-2024 13:06:01	WARNING: All illegal access operations will be denied in a future release
build	07-Nov-2024 13:07:36	
build	07-Nov-2024 13:07:36	> Task :testTask2
build	07-Nov-2024 13:07:36	Running tests WITH clover
build	07-Nov-2024 13:07:40	
build	07-Nov-2024 13:07:40	> Task :testTask3
build	07-Nov-2024 13:07:40	Running tests WITH clover
error	07-Nov-2024 13:07:41	WARNING: An illegal reflective access operation has occurred
error	07-Nov-2024 13:07:41	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	07-Nov-2024 13:07:41	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	07-Nov-2024 13:07:41	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	07-Nov-2024 13:07:41	WARNING: All illegal access operations will be denied in a future release
build	07-Nov-2024 13:08:28	
build	07-Nov-2024 13:08:28	> Task :test NO-SOURCE
build	07-Nov-2024 13:08:28	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	07-Nov-2024 13:08:28	│jalview:testTask0 results: SUCCESS (1728 tests, 1728 successes, 0 failures, 0 skipped) in 3 minutes, 58.407 seconds   │
build	07-Nov-2024 13:08:28	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/reports/tests/testTask0/index.html│
build	07-Nov-2024 13:08:28	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	07-Nov-2024 13:08:28	│jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 36.544 seconds       │
build	07-Nov-2024 13:08:28	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/reports/tests/testTask1/index.html│
build	07-Nov-2024 13:08:28	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	07-Nov-2024 13:08:28	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.542 seconds                     │
build	07-Nov-2024 13:08:28	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/reports/tests/testTask2/index.html│
build	07-Nov-2024 13:08:28	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	07-Nov-2024 13:08:28	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 50.396 seconds                  │
build	07-Nov-2024 13:08:28	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/reports/tests/testTask3/index.html│
build	07-Nov-2024 13:08:28	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	07-Nov-2024 13:08:28	│OVERALL: results: SUCCESS (1803 tests, 1803 successes, 0 failures, 0 skipped) in 4 minutes, 148.889 seconds           │
build	07-Nov-2024 13:08:28	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	07-Nov-2024 13:08:28	
build	07-Nov-2024 13:08:28	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	07-Nov-2024 13:08:28	
build	07-Nov-2024 13:08:28	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	07-Nov-2024 13:08:28	
build	07-Nov-2024 13:08:28	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	07-Nov-2024 13:08:28	
build	07-Nov-2024 13:08:28	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	07-Nov-2024 13:08:28	Please consult deprecation warnings for more details.
build	07-Nov-2024 13:08:28	
build	07-Nov-2024 13:08:28	BUILD SUCCESSFUL in 7m 26s
build	07-Nov-2024 13:08:28	21 actionable tasks: 20 executed, 1 up-to-date
simple	07-Nov-2024 13:08:29	Finished task 'Run tests with openclover under gradle' with result: Success
simple	07-Nov-2024 13:08:29	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	07-Nov-2024 13:08:29	Bamboo Artifactory Plugin version: 2.6.2
command	07-Nov-2024 13:08:29	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Clover and Tests #2 (JB-GDB640-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_repository_revision_number=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB640-JOB1-2\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB640-JOB1\nbamboo_shortPlanName=experiment-JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB640-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - experiment-JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_shortPlanKey=GDB640\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nbamboo_buildTimeStamp=2024-11-07T13:01:00.512Z\nbamboo_repository_previous_revision_number=503c83212e9779b412c999dc1d64d4e6c5e41cae\nbamboo_planRepository_previousRevision=503c83212e9779b412c999dc1d64d4e6c5e41cae\nbamboo_repository_git_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_buildResultKey=JB-GDB640-JOB1-2\nbamboo_repository_branch_name=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\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=503c83212e9779b412c999dc1d64d4e6c5e41cae\nbamboo_repository_46498174_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branchDisplayName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498174_revision_number=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301947\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46498174_branch_name=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_46498174_git_username=\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-GDB640-JOB1\nbamboo_planKey=JB-GDB640\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_46498174_previous_revision_number=503c83212e9779b412c999dc1d64d4e6c5e41cae\nbamboo_planRepository_username=\nbamboo_repository_46498174_git_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_repository_46498174_name=Jalview Git\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	07-Nov-2024 13:08:29	444
build	07-Nov-2024 13:08:37	
build	07-Nov-2024 13:08:37	> Configure project :
build	07-Nov-2024 13:08:37	Using properties from file './utils/channels/default/channel_gradle.properties'
build	07-Nov-2024 13:08:37	JALVIEW_VERSION is set to '2.11.4.1'
build	07-Nov-2024 13:08:37	HEADLESS BUILD
build	07-Nov-2024 13:08:37	J2S ENABLED
build	07-Nov-2024 13:08:37	Using a LOCAL profile.
build	07-Nov-2024 13:08:38	eclipseDir exists
build	07-Nov-2024 13:08:40	
build	07-Nov-2024 13:08:40	> Task :cloverHtmlReport
build	07-Nov-2024 13:08:40	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	07-Nov-2024 13:08:41	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/reports/clover'
build	07-Nov-2024 13:09:19	Done. Processed 116 packages in 37979ms (327ms per package).
build	07-Nov-2024 13:09:24	
build	07-Nov-2024 13:09:24	> Task :cloverXmlReport
build	07-Nov-2024 13:09:24	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	07-Nov-2024 13:09:24	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/reports/clover/clover.xml'
build	07-Nov-2024 13:09:25	
build	07-Nov-2024 13:09:25	> Task :cloverReport
build	07-Nov-2024 13:09:25	
build	07-Nov-2024 13:09:25	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	07-Nov-2024 13:09:25	
build	07-Nov-2024 13:09:25	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	07-Nov-2024 13:09:25	
build	07-Nov-2024 13:09:25	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	07-Nov-2024 13:09:25	
build	07-Nov-2024 13:09:25	BUILD SUCCESSFUL in 55s
build	07-Nov-2024 13:09:25	2 actionable tasks: 2 executed
simple	07-Nov-2024 13:09:25	Finished task 'Clover Report' with result: Success
simple	07-Nov-2024 13:09:25	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	07-Nov-2024 13:09:25	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1...
simple	07-Nov-2024 13:09:25	Finished task 'TestNG Parser' with result: Success
simple	07-Nov-2024 13:09:25	Running post build plugin 'NCover Results Collector'
simple	07-Nov-2024 13:09:25	Running post build plugin 'Artifact Copier'
simple	07-Nov-2024 13:09:25	Publishing an artifact: Clover Report (System)
simple	07-Nov-2024 13:09:26	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.479 s
simple	07-Nov-2024 13:09:26	Publishing an artifact: TestNG report
error	07-Nov-2024 13:09:26	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB640-JOB1/build/reports/tests/test does not exist.
simple	07-Nov-2024 13:09:26	The artifact hasn't been successfully published after 1.355 ms
simple	07-Nov-2024 13:09:26	Running post build plugin 'Artifactory Release Management Staging'
simple	07-Nov-2024 13:09:26	Running post build plugin 'Artifactory Build Info Copier'
simple	07-Nov-2024 13:09:26	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	07-Nov-2024 13:09:26	Running post build plugin 'npm Cache Cleanup'
simple	07-Nov-2024 13:09:26	Running post build plugin 'Clover Results Collector'
simple	07-Nov-2024 13:09:26	Running post build plugin 'Docker Container Cleanup'
simple	07-Nov-2024 13:09:26	Finalising the build...
simple	07-Nov-2024 13:09:26	Stopping timer.
simple	07-Nov-2024 13:09:26	Build JB-GDB640-JOB1-2 completed.
simple	07-Nov-2024 13:09:26	Running on server: post build plugin 'NCover Results Collector'
simple	07-Nov-2024 13:09:26	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	07-Nov-2024 13:09:26	Running on server: post build plugin 'Clover Delta Calculator'
simple	07-Nov-2024 13:09:26	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	07-Nov-2024 13:09:26	All post build plugins have finished
simple	07-Nov-2024 13:09:26	Generating build results summary...
simple	07-Nov-2024 13:09:27	Saving build results to disk...
simple	07-Nov-2024 13:09:27	Logging substituted variables...
simple	07-Nov-2024 13:09:27	Indexing build results...
simple	07-Nov-2024 13:09:27	Finished building JB-GDB640-JOB1-2.