simple	26-Jul-2024 12:17:32	Build Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_calculate_tree_using_secondary_structure_annotation - Default Job #9 (JB-GDL0-JOB1-9) started building on agent Default Agent
simple	26-Jul-2024 12:17:32	
simple	26-Jul-2024 12:17:32	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1
simple	26-Jul-2024 12:17:32	Executing build Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_calculate_tree_using_secondary_structure_annotation - Default Job #9 (JB-GDL0-JOB1-9)
simple	26-Jul-2024 12:17:32	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	26-Jul-2024 12:17:32	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1
simple	26-Jul-2024 12:17:32	Updating source code to revision: a16e52efe8a069302d4aaa8230ed0dc2e592bcf4
simple	26-Jul-2024 12:17:32	Fetching 'refs/heads/feature/JAL-4386_calculate_tree_using_secondary_structure_annotation' from 'http://source.jalview.org/git/jalview.git'.
simple	26-Jul-2024 12:17:32	Checking out revision a16e52efe8a069302d4aaa8230ed0dc2e592bcf4.
simple	26-Jul-2024 12:17:33	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164
simple	26-Jul-2024 12:17:33	   a8367f0..a16e52e  feature/JAL-4386_calculate_tree_using_secondary_structure_annotation -> origin/feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
simple	26-Jul-2024 12:17:33	   c99eae6..e707f26  develop    -> origin/develop
simple	26-Jul-2024 12:17:33	   79a7d13..3ba3e6e  feature/JAL-3631_allow_jalview_to_work_from_user-space_directory -> origin/feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
simple	26-Jul-2024 12:17:33	 * [new branch]      jims/JAL-4386_from_renia -> origin/jims/JAL-4386_from_renia
simple	26-Jul-2024 12:17:33	 * [new branch]      spike/JAL-4386_develop_trial_merge -> origin/spike/JAL-4386_develop_trial_merge
simple	26-Jul-2024 12:17:33	   3bb6983..a92d9ee  spike/JAL-4386_generate_multiple_leaves_for_ss_sources -> origin/spike/JAL-4386_generate_multiple_leaves_for_ss_sources
simple	26-Jul-2024 12:17:33	Already on 'feature/JAL-4386_calculate_tree_using_secondary_structure_annotation'
simple	26-Jul-2024 12:17:33	Your branch is behind 'origin/feature/JAL-4386_calculate_tree_using_secondary_structure_annotation' by 233 commits, and can be fast-forwarded.
simple	26-Jul-2024 12:17:33	  (use "git pull" to update your local branch)
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simple	26-Jul-2024 12:17:37	Checking out files: 100% (218/218), done.
simple	26-Jul-2024 12:17:37	HEAD is now at a16e52e JAL-4386 i8n secondary structure score model
simple	26-Jul-2024 12:17:37	Updated source code to revision: a16e52efe8a069302d4aaa8230ed0dc2e592bcf4
simple	26-Jul-2024 12:17:37	Finished task 'Checkout Default Repository' with result: Success
simple	26-Jul-2024 12:17:37	Running pre-build action: VCS Version Collector
simple	26-Jul-2024 12:17:37	Running pre-build action: Artifactory Release Staging
command	26-Jul-2024 12:17:37	Substituting variable: ${bamboo.planKey} with JB-GDL0
simple	26-Jul-2024 12:17:37	Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	26-Jul-2024 12:17:37	Bamboo Artifactory Plugin version: 2.6.2
command	26-Jul-2024 12:17:37	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_calculate_tree_using_secondary_structure_annotation - Default Job #9 (JB-GDL0-JOB1-9)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL0 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_dependency_parent_0=JB-GDB580-26\nbamboo_repository_46497930_git_branch=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_46497930_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_repository_revision_number=a16e52efe8a069302d4aaa8230ed0dc2e592bcf4\nbamboo_repository_46497930_revision_number=a16e52efe8a069302d4aaa8230ed0dc2e592bcf4\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL0-JOB1-9\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-GDL0-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL0-JOB1\nbamboo_shortPlanName=feature-JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=9\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL0-JOB1-9\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_shortPlanKey=GDL0\nbamboo_repository_46497930_name=Jalview Git\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a16e52efe8a069302d4aaa8230ed0dc2e592bcf4\nbamboo_buildTimeStamp=2024-07-26T12:17:32.098+01:00\nbamboo_repository_previous_revision_number=a8367f07f487bcf754bd249b5f90889f7f630aa4\nbamboo_repository_git_branch=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_buildResultKey=JB-GDL0-JOB1-9\nbamboo_repository_branch_name=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_calculate_tree_using_secondary_structure_annotation - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=a16e52efe8a069302d4aaa8230ed0dc2e592bcf4\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\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=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\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-46301459\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_repository_46497930_previous_revision_number=a8367f07f487bcf754bd249b5f90889f7f630aa4\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-GDL0-JOB1\nbamboo_planKey=JB-GDL0\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46497930_branch_name=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_repository_46497930_git_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	26-Jul-2024 12:17:38	
build	26-Jul-2024 12:17:38	> Configure project :
build	26-Jul-2024 12:17:38	Using properties from file './utils/channels/default/channel_gradle.properties'
build	26-Jul-2024 12:17:38	JALVIEW_VERSION is set to '2.11.4.0'
build	26-Jul-2024 12:17:38	HEADLESS BUILD
build	26-Jul-2024 12:17:38	J2S ENABLED
build	26-Jul-2024 12:17:38	Using a BUILD profile.
build	26-Jul-2024 12:17:38	eclipseDir exists
build	26-Jul-2024 12:17:39	
build	26-Jul-2024 12:17:39	> Task :clean
build	26-Jul-2024 12:17:39	> Task :cleanPackageDir
build	26-Jul-2024 12:17:39	> Task :getdownImagesCopy
build	26-Jul-2024 12:17:40	> Task :getdownImagesProcess
build	26-Jul-2024 12:17:40	> Task :getdownImages
build	26-Jul-2024 12:17:40	> Task :copyHelp
build	26-Jul-2024 12:17:42	> Task :buildIndices
build	26-Jul-2024 12:17:43	> Task :copyResources
build	26-Jul-2024 12:17:43	> Task :copyChannelResources
build	26-Jul-2024 12:17:43	
build	26-Jul-2024 12:17:43	> Task :createBuildProperties
build	26-Jul-2024 12:17:43	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	26-Jul-2024 12:17:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-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	26-Jul-2024 12:17:43	
build	26-Jul-2024 12:17:43	> Task :buildResources
build	26-Jul-2024 12:17:43	> Task :copyDocs
build	26-Jul-2024 12:17:44	
build	26-Jul-2024 12:17:44	> Task :convertMdFiles
build	26-Jul-2024 12:17:44	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	26-Jul-2024 12:17:44	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	26-Jul-2024 12:17:44	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	26-Jul-2024 12:17:44	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/build/resources/doc_build/doc/building.html
build	26-Jul-2024 12:17:44	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	26-Jul-2024 12:17:44	
build	26-Jul-2024 12:17:44	> Task :releasesTemplates
build	26-Jul-2024 12:17:44	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	26-Jul-2024 12:17:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-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	26-Jul-2024 12:17:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-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	26-Jul-2024 12:17:44	
build	26-Jul-2024 12:17:44	> Task :prepare
build	26-Jul-2024 12:17:46	
build	26-Jul-2024 12:17:46	> Task :compileJava
build	26-Jul-2024 12:17:46	Setting target compatibility to 11
error	26-Jul-2024 12:17:54	Note: Some input files use or override a deprecated API.
error	26-Jul-2024 12:17:54	Note: Recompile with -Xlint:deprecation for details.
error	26-Jul-2024 12:17:54	Note: Some input files use unchecked or unsafe operations.
error	26-Jul-2024 12:17:54	Note: Recompile with -Xlint:unchecked for details.
build	26-Jul-2024 12:17:54	
build	26-Jul-2024 12:17:54	> Task :processResources
build	26-Jul-2024 12:17:54	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	26-Jul-2024 12:17:54	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/build/resources/doc_build'. Reason: Task ':processResources' 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	26-Jul-2024 12:17:54	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/build/resources/doc_build'. Reason: Task ':processResources' 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	26-Jul-2024 12:17:54	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/build/resources/help_build'. Reason: Task ':processResources' 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	26-Jul-2024 12:17:54	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/build/resources/help_build'. Reason: Task ':processResources' 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	26-Jul-2024 12:17:54	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/build/resources/help_build'. Reason: Task ':processResources' 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	26-Jul-2024 12:17:54	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/build/resources/resources_build'. Reason: Task ':processResources' 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	26-Jul-2024 12:17:54	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/build/resources/resources_build'. Reason: Task ':processResources' 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	26-Jul-2024 12:17:54	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/build/resources/resources_build'. Reason: Task ':processResources' 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	26-Jul-2024 12:17:54	
build	26-Jul-2024 12:17:54	> Task :classes
build	26-Jul-2024 12:17:56	
build	26-Jul-2024 12:17:56	> Task :compileLinkCheck
build	26-Jul-2024 12:17:56	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	26-Jul-2024 12:17:56	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' 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	26-Jul-2024 12:17:56	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' 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	26-Jul-2024 12:17:56	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1/utils'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' 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	26-Jul-2024 12:17:56	
build	26-Jul-2024 12:17:56	> Task :linkCheck
build	26-Jul-2024 12:17:56	Checking help file links
build	26-Jul-2024 12:17:56	
build	26-Jul-2024 12:17:56	Results:
build	26-Jul-2024 12:17:56	156 distinct help targets
build	26-Jul-2024 12:17:56	156 help mappings
build	26-Jul-2024 12:17:56	0 invalid targets
build	26-Jul-2024 12:17:56	31 unused targets
build	26-Jul-2024 12:17:56	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	26-Jul-2024 12:17:56	    overviewprefs: html/features/preferences.html#overview
build	26-Jul-2024 12:17:56	    cdnafeatures: html/features/codingfeatures.html
build	26-Jul-2024 12:17:56	    startupprefs: html/features/preferences.html#startup
build	26-Jul-2024 12:17:56	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	26-Jul-2024 12:17:56	    io.modellerpir: html/io/modellerpir.html
build	26-Jul-2024 12:17:56	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	26-Jul-2024 12:17:56	    pdbmcviewer: html/features/pdbviewer.html
build	26-Jul-2024 12:17:56	    groovy.colours: html/features/groovy.html#groovyColours
build	26-Jul-2024 12:17:56	    seqmappings: html/features/seqmappings.html
build	26-Jul-2024 12:17:56	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	26-Jul-2024 12:17:56	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	26-Jul-2024 12:17:56	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	26-Jul-2024 12:17:56	    search: html/features/search.html
build	26-Jul-2024 12:17:56	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	26-Jul-2024 12:17:56	    alformats: html/io/fileformats.html
build	26-Jul-2024 12:17:56	    strucprefs: html/features/preferences.html#structure
build	26-Jul-2024 12:17:56	    siftsmapping: html/features/siftsmapping.html
build	26-Jul-2024 12:17:56	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	26-Jul-2024 12:17:56	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	26-Jul-2024 12:17:56	    newkeys: html/features/newkeystrokes.html
build	26-Jul-2024 12:17:56	    importvcf.attribs: html/features/importvcf.html#attribs
build	26-Jul-2024 12:17:56	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	26-Jul-2024 12:17:56	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	26-Jul-2024 12:17:56	    jalarchive: html/features/jalarchive.html
build	26-Jul-2024 12:17:56	    newsreader: html/webServices/newsreader.html
build	26-Jul-2024 12:17:56	    jalviewcltool: html/features/commandline.html#script
build	26-Jul-2024 12:17:56	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	26-Jul-2024 12:17:56	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	26-Jul-2024 12:17:56	    paematrixformat: html/io/paematrixformat.html
build	26-Jul-2024 12:17:56	    overview: html/features/overview.html
build	26-Jul-2024 12:17:56	0 invalid map urls
build	26-Jul-2024 12:17:56	0 invalid image attributes
build	26-Jul-2024 12:17:56	482 internal href links (106 with anchors)
build	26-Jul-2024 12:17:56	0 invalid internal href links
build	26-Jul-2024 12:17:56	0 invalid internal anchor links
build	26-Jul-2024 12:17:56	111 external href links
build	26-Jul-2024 12:17:56	External links not verified as internet not available
build	26-Jul-2024 12:17:56	*** Success ***
build	26-Jul-2024 12:17:57	
build	26-Jul-2024 12:17:57	> Task :jar
build	26-Jul-2024 12:17:58	> Task :syncJars
build	26-Jul-2024 12:17:58	> Task :makeDist
build	26-Jul-2024 12:17:58	> Task :getdownWebsiteBuild
build	26-Jul-2024 12:17:59	
build	26-Jul-2024 12:17:59	> Task :getdownDigest
build	26-Jul-2024 12:17:59	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
error	26-Jul-2024 12:17:59	2024/07/26 12:17:58:627 WARNING Starting without install4j classes
error	26-Jul-2024 12:17:59	2024/07/26 12:17:59:145 WARNING Starting without install4j classes
build	26-Jul-2024 12:17:59	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	26-Jul-2024 12:17:59	
build	26-Jul-2024 12:17:59	> Task :getdown
build	26-Jul-2024 12:17:59	
build	26-Jul-2024 12:17:59	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	26-Jul-2024 12:17:59	
build	26-Jul-2024 12:17:59	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	26-Jul-2024 12:17:59	
build	26-Jul-2024 12:17:59	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	26-Jul-2024 12:17:59	
build	26-Jul-2024 12:17:59	Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness.
build	26-Jul-2024 12:17:59	Please consult deprecation warnings for more details.
build	26-Jul-2024 12:17:59	
build	26-Jul-2024 12:17:59	BUILD SUCCESSFUL in 22s
build	26-Jul-2024 12:17:59	21 actionable tasks: 21 executed
simple	26-Jul-2024 12:18:00	Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success
simple	26-Jul-2024 12:18:00	Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command	26-Jul-2024 12:18:00	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_calculate_tree_using_secondary_structure_annotation - Default Job #9 (JB-GDL0-JOB1-9)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL0-JOB1-9-ScriptBuildTask-6228444385494411835.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_dependency_parent_0=JB-GDB580-26\nbamboo_repository_46497930_git_branch=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_46497930_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_repository_revision_number=a16e52efe8a069302d4aaa8230ed0dc2e592bcf4\nbamboo_repository_46497930_revision_number=a16e52efe8a069302d4aaa8230ed0dc2e592bcf4\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL0-JOB1-9\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL0-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL0-JOB1\nbamboo_shortPlanName=feature-JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_planRepository_name=Jalview Git\nbamboo_buildNumber=9\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL0-JOB1-9\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_shortPlanKey=GDL0\nbamboo_repository_46497930_name=Jalview Git\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a16e52efe8a069302d4aaa8230ed0dc2e592bcf4\nbamboo_buildTimeStamp=2024-07-26T12:17:32.098+01:00\nbamboo_repository_previous_revision_number=a8367f07f487bcf754bd249b5f90889f7f630aa4\nbamboo_repository_git_branch=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_buildResultKey=JB-GDL0-JOB1-9\nbamboo_repository_branch_name=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_calculate_tree_using_secondary_structure_annotation - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=a16e52efe8a069302d4aaa8230ed0dc2e592bcf4\nbamboo_CHANNEL=DEVELOP\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/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL0 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\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-46301459\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\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_46497930_previous_revision_number=a8367f07f487bcf754bd249b5f90889f7f630aa4\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-GDL0-JOB1\nbamboo_planKey=JB-GDL0\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46497930_branch_name=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\nbamboo_repository_46497930_git_username=\nbamboo_planRepository_1_branchName=feature/JAL-4386_calculate_tree_using_secondary_structure_annotation\n
simple	26-Jul-2024 12:18:00	Finished task 'Copy JVL file and produce link in HTML' with result: Success
simple	26-Jul-2024 12:18:00	Running post build plugin 'NCover Results Collector'
simple	26-Jul-2024 12:18:00	Running post build plugin 'Artifact Copier'
simple	26-Jul-2024 12:18:00	Publishing an artifact: getdown
simple	26-Jul-2024 12:18:00	Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 236.0 ms
simple	26-Jul-2024 12:18:00	Running post build plugin 'Artifactory Release Management Staging'
simple	26-Jul-2024 12:18:00	Running post build plugin 'Artifactory Build Info Copier'
simple	26-Jul-2024 12:18:00	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	26-Jul-2024 12:18:00	Running post build plugin 'npm Cache Cleanup'
simple	26-Jul-2024 12:18:00	Running post build plugin 'Clover Results Collector'
simple	26-Jul-2024 12:18:00	Running post build plugin 'Docker Container Cleanup'
simple	26-Jul-2024 12:18:00	Finalising the build...
simple	26-Jul-2024 12:18:00	Stopping timer.
simple	26-Jul-2024 12:18:00	Build JB-GDL0-JOB1-9 completed.
simple	26-Jul-2024 12:18:00	Running on server: post build plugin 'NCover Results Collector'
simple	26-Jul-2024 12:18:00	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	26-Jul-2024 12:18:00	Running on server: post build plugin 'Clover Delta Calculator'
simple	26-Jul-2024 12:18:00	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	26-Jul-2024 12:18:00	All post build plugins have finished
simple	26-Jul-2024 12:18:00	Generating build results summary...
simple	26-Jul-2024 12:18:00	Saving build results to disk...
simple	26-Jul-2024 12:18:00	Logging substituted variables...
simple	26-Jul-2024 12:18:00	Indexing build results...
simple	26-Jul-2024 12:18:00	Finished building JB-GDL0-JOB1-9.