simple	18-Nov-2024 10:10:18	Build Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Default Job #1 (JB-GDL45-JOB1-1) started building on agent Default Agent
simple	18-Nov-2024 10:10:18	
simple	18-Nov-2024 10:10:18	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1
simple	18-Nov-2024 10:10:18	Executing build Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Default Job #1 (JB-GDL45-JOB1-1)
simple	18-Nov-2024 10:10:18	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	18-Nov-2024 10:10:18	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1
simple	18-Nov-2024 10:10:18	Updating source code to revision: 5e8bd075739b756cac8f741a47a7de952c45f879
simple	18-Nov-2024 10:10:18	Fetching 'refs/heads/spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure' from 'http://source.jalview.org/git/jalview.git'.
simple	18-Nov-2024 10:10:18	Checking out revision 5e8bd075739b756cac8f741a47a7de952c45f879.
simple	18-Nov-2024 10:10:18	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1/.git'.
simple	18-Nov-2024 10:10:19	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1'...
simple	18-Nov-2024 10:10:19	done.
simple	18-Nov-2024 10:10:29	Switched to a new branch 'spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure'
simple	18-Nov-2024 10:10:29	Branch spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure set up to track remote branch spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure from origin.
simple	18-Nov-2024 10:10:29	Updated source code to revision: 5e8bd075739b756cac8f741a47a7de952c45f879
simple	18-Nov-2024 10:10:29	Finished task 'Checkout Default Repository' with result: Success
simple	18-Nov-2024 10:10:29	Running pre-build action: VCS Version Collector
simple	18-Nov-2024 10:10:29	Running pre-build action: Artifactory Release Staging
command	18-Nov-2024 10:10:29	Substituting variable: ${bamboo.planKey} with JB-GDL45
simple	18-Nov-2024 10:10:29	Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	18-Nov-2024 10:10:29	Bamboo Artifactory Plugin version: 2.6.2
command	18-Nov-2024 10:10:29	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Default Job #1 (JB-GDL45-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL45 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_dependency_parent_0=JB-GDB647-3\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL45-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL45-JOB1\nbamboo_shortPlanName=spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL45-JOB1-1\nbamboo_repository_46498217_name=Jalview Git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_shortPlanKey=GDL45\nbamboo_repository_46498217_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498217_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_buildTimeStamp=2024-11-18T10:04:52.978Z\nbamboo_repository_46498217_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_buildResultKey=JB-GDL45-JOB1-1\nbamboo_repository_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498217_git_username=\nbamboo_planRepository_1_revision=5e8bd075739b756cac8f741a47a7de952c45f879\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=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\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=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498217_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302033\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-GDL45-JOB1\nbamboo_planKey=JB-GDL45\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	18-Nov-2024 10:10:32	
build	18-Nov-2024 10:10:32	> Configure project :
build	18-Nov-2024 10:10:32	Using properties from file './utils/channels/default/channel_gradle.properties'
build	18-Nov-2024 10:10:32	JALVIEW_VERSION is set to '2.11.4.2'
build	18-Nov-2024 10:10:32	HEADLESS BUILD
build	18-Nov-2024 10:10:32	J2S ENABLED
build	18-Nov-2024 10:10:32	Using a BUILD profile.
build	18-Nov-2024 10:10:32	eclipseDir exists
build	18-Nov-2024 10:10:32	
build	18-Nov-2024 10:10:32	> Task :clean
build	18-Nov-2024 10:10:32	> Task :cleanPackageDir UP-TO-DATE
build	18-Nov-2024 10:10:32	> Task :getdownImagesCopy
build	18-Nov-2024 10:10:32	> Task :getdownImagesProcess
build	18-Nov-2024 10:10:32	> Task :getdownImages
build	18-Nov-2024 10:10:32	> Task :copyHelp
build	18-Nov-2024 10:10:35	> Task :buildIndices
build	18-Nov-2024 10:10:35	> Task :copyResources
build	18-Nov-2024 10:10:35	> Task :copyChannelResources
build	18-Nov-2024 10:10:35	
build	18-Nov-2024 10:10:35	> Task :createBuildProperties
build	18-Nov-2024 10:10:35	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	18-Nov-2024 10:10:35	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-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	18-Nov-2024 10:10:35	
build	18-Nov-2024 10:10:35	> Task :buildResources
build	18-Nov-2024 10:10:35	> Task :copyDocs
build	18-Nov-2024 10:10:35	
build	18-Nov-2024 10:10:35	> Task :convertMdFiles
build	18-Nov-2024 10:10:35	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	18-Nov-2024 10:10:35	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	18-Nov-2024 10:10:35	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	18-Nov-2024 10:10:35	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1/build/resources/doc_build/doc/building.html
build	18-Nov-2024 10:10:35	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	18-Nov-2024 10:10:36	
build	18-Nov-2024 10:10:36	> Task :releasesTemplates
build	18-Nov-2024 10:10:36	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	18-Nov-2024 10:10:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-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	18-Nov-2024 10:10:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-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	18-Nov-2024 10:10:36	Stripping rc/test/etc for 2_11_4_2
build	18-Nov-2024 10:10:36	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_2.md
build	18-Nov-2024 10:10:36	
build	18-Nov-2024 10:10:36	> Task :prepare
build	18-Nov-2024 10:10:38	
build	18-Nov-2024 10:10:38	> Task :compileJava
build	18-Nov-2024 10:10:38	Setting target compatibility to 11
error	18-Nov-2024 10:10:45	Note: Some input files use or override a deprecated API.
error	18-Nov-2024 10:10:45	Note: Recompile with -Xlint:deprecation for details.
error	18-Nov-2024 10:10:45	Note: Some input files use unchecked or unsafe operations.
error	18-Nov-2024 10:10:45	Note: Recompile with -Xlint:unchecked for details.
build	18-Nov-2024 10:10:45	
build	18-Nov-2024 10:10:45	> Task :processResources
build	18-Nov-2024 10:10:45	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	18-Nov-2024 10:10:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-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	18-Nov-2024 10:10:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-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	18-Nov-2024 10:10:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-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	18-Nov-2024 10:10:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-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	18-Nov-2024 10:10:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-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	18-Nov-2024 10:10:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-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	18-Nov-2024 10:10:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-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	18-Nov-2024 10:10:45	
build	18-Nov-2024 10:10:45	> Task :classes
build	18-Nov-2024 10:10:47	
build	18-Nov-2024 10:10:47	> Task :compileLinkCheck
build	18-Nov-2024 10:10:47	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	18-Nov-2024 10:10:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-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	18-Nov-2024 10:10:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-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	18-Nov-2024 10:10:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-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	18-Nov-2024 10:10:50	
build	18-Nov-2024 10:10:50	> Task :linkCheck
build	18-Nov-2024 10:10:50	Checking help file links
build	18-Nov-2024 10:12:56	
build	18-Nov-2024 10:12:56	Results:
build	18-Nov-2024 10:12:56	159 distinct help targets
build	18-Nov-2024 10:12:56	159 help mappings
build	18-Nov-2024 10:12:56	0 invalid targets
build	18-Nov-2024 10:12:56	32 unused targets
build	18-Nov-2024 10:12:56	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	18-Nov-2024 10:12:56	    overviewprefs: html/features/preferences.html#overview
build	18-Nov-2024 10:12:56	    cdnafeatures: html/features/codingfeatures.html
build	18-Nov-2024 10:12:56	    startupprefs: html/features/preferences.html#startup
build	18-Nov-2024 10:12:56	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	18-Nov-2024 10:12:56	    io.modellerpir: html/io/modellerpir.html
build	18-Nov-2024 10:12:56	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	18-Nov-2024 10:12:56	    pdbmcviewer: html/features/pdbviewer.html
build	18-Nov-2024 10:12:56	    workingwithpae: html/features/paematrices.html
build	18-Nov-2024 10:12:56	    groovy.colours: html/features/groovy.html#groovyColours
build	18-Nov-2024 10:12:56	    seqmappings: html/features/seqmappings.html
build	18-Nov-2024 10:12:56	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	18-Nov-2024 10:12:56	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	18-Nov-2024 10:12:56	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	18-Nov-2024 10:12:56	    search: html/features/search.html
build	18-Nov-2024 10:12:56	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	18-Nov-2024 10:12:56	    alformats: html/io/fileformats.html
build	18-Nov-2024 10:12:56	    strucprefs: html/features/preferences.html#structure
build	18-Nov-2024 10:12:56	    siftsmapping: html/features/siftsmapping.html
build	18-Nov-2024 10:12:56	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	18-Nov-2024 10:12:56	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	18-Nov-2024 10:12:56	    newkeys: html/features/newkeystrokes.html
build	18-Nov-2024 10:12:56	    importvcf.attribs: html/features/importvcf.html#attribs
build	18-Nov-2024 10:12:56	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	18-Nov-2024 10:12:56	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	18-Nov-2024 10:12:56	    jalarchive: html/features/jalarchive.html
build	18-Nov-2024 10:12:56	    newsreader: html/webServices/newsreader.html
build	18-Nov-2024 10:12:56	    jalviewcltool: html/features/commandline.html#script
build	18-Nov-2024 10:12:56	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	18-Nov-2024 10:12:56	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	18-Nov-2024 10:12:56	    paematrixformat: html/io/paematrixformat.html
build	18-Nov-2024 10:12:56	    overview: html/features/overview.html
build	18-Nov-2024 10:12:56	0 invalid map urls
build	18-Nov-2024 10:12:56	0 invalid image attributes
build	18-Nov-2024 10:12:56	506 internal href links (110 with anchors)
build	18-Nov-2024 10:12:56	0 invalid internal href links
build	18-Nov-2024 10:12:56	0 invalid internal anchor links
build	18-Nov-2024 10:12:56	112 external href links
build	18-Nov-2024 10:12:56	External links not verified as internet not available
build	18-Nov-2024 10:12:56	*** Success ***
build	18-Nov-2024 10:12:57	
build	18-Nov-2024 10:12:57	> Task :jar
build	18-Nov-2024 10:12:57	> Task :syncJars
build	18-Nov-2024 10:12:57	> Task :makeDist
build	18-Nov-2024 10:12:58	> Task :getdownWebsiteBuild
build	18-Nov-2024 10:12:59	
build	18-Nov-2024 10:12:59	> Task :getdownDigest
build	18-Nov-2024 10:12:59	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
error	18-Nov-2024 10:12:59	2024/11/18 10:12:58:454 WARNING Starting without install4j classes
error	18-Nov-2024 10:12:59	2024/11/18 10:12:58:978 WARNING Starting without install4j classes
build	18-Nov-2024 10:12:59	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	18-Nov-2024 10:12:59	
build	18-Nov-2024 10:12:59	> Task :getdown
build	18-Nov-2024 10:12:59	
build	18-Nov-2024 10:12:59	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	18-Nov-2024 10:12:59	
build	18-Nov-2024 10:12:59	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	18-Nov-2024 10:12:59	
build	18-Nov-2024 10:12:59	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	18-Nov-2024 10:12:59	
build	18-Nov-2024 10:12:59	Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness.
build	18-Nov-2024 10:12:59	Please consult deprecation warnings for more details.
build	18-Nov-2024 10:12:59	
build	18-Nov-2024 10:12:59	BUILD SUCCESSFUL in 2m 29s
build	18-Nov-2024 10:12:59	21 actionable tasks: 20 executed, 1 up-to-date
simple	18-Nov-2024 10:13:00	Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success
simple	18-Nov-2024 10:13:00	Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command	18-Nov-2024 10:13:00	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Default Job #1 (JB-GDL45-JOB1-1)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL45-JOB1-1-ScriptBuildTask-4520380723419837089.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_dependency_parent_0=JB-GDB647-3\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL45-JOB1-1\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL45-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL45-JOB1\nbamboo_shortPlanName=spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_planRepository_name=Jalview Git\nbamboo_buildNumber=1\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-GDL45-JOB1-1\nbamboo_repository_46498217_name=Jalview Git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_shortPlanKey=GDL45\nbamboo_repository_46498217_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498217_revision_number=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=5e8bd075739b756cac8f741a47a7de952c45f879\nbamboo_buildTimeStamp=2024-11-18T10:04:52.978Z\nbamboo_repository_46498217_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_repository_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_buildResultKey=JB-GDL45-JOB1-1\nbamboo_repository_branch_name=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498217_git_username=\nbamboo_planRepository_1_revision=5e8bd075739b756cac8f741a47a7de952c45f879\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-GDL45 -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=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\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=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498217_git_branch=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302033\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_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-GDL45-JOB1\nbamboo_planKey=JB-GDL45\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure\n
simple	18-Nov-2024 10:13:00	Finished task 'Copy JVL file and produce link in HTML' with result: Success
simple	18-Nov-2024 10:13:00	Running post build plugin 'NCover Results Collector'
simple	18-Nov-2024 10:13:00	Running post build plugin 'Artifact Copier'
simple	18-Nov-2024 10:13:00	Publishing an artifact: getdown
simple	18-Nov-2024 10:13:00	Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 95.72 ms
simple	18-Nov-2024 10:13:00	Running post build plugin 'Artifactory Release Management Staging'
simple	18-Nov-2024 10:13:00	Running post build plugin 'Artifactory Build Info Copier'
simple	18-Nov-2024 10:13:00	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	18-Nov-2024 10:13:00	Running post build plugin 'npm Cache Cleanup'
simple	18-Nov-2024 10:13:00	Running post build plugin 'Clover Results Collector'
simple	18-Nov-2024 10:13:00	Running post build plugin 'Docker Container Cleanup'
simple	18-Nov-2024 10:13:00	Finalising the build...
simple	18-Nov-2024 10:13:00	Stopping timer.
simple	18-Nov-2024 10:13:00	Build JB-GDL45-JOB1-1 completed.
simple	18-Nov-2024 10:13:00	Running on server: post build plugin 'NCover Results Collector'
simple	18-Nov-2024 10:13:00	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	18-Nov-2024 10:13:00	Running on server: post build plugin 'Clover Delta Calculator'
simple	18-Nov-2024 10:13:00	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	18-Nov-2024 10:13:00	All post build plugins have finished
simple	18-Nov-2024 10:13:00	Generating build results summary...
simple	18-Nov-2024 10:13:00	Saving build results to disk...
simple	18-Nov-2024 10:13:00	Logging substituted variables...
simple	18-Nov-2024 10:13:00	Indexing build results...
simple	18-Nov-2024 10:13:00	Finished building JB-GDL45-JOB1-1.