simple	12-Aug-2024 10:25:29	Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0 - Default Job #2 (JB-GDL7-JOB1-2) started building on agent Default Agent
simple	12-Aug-2024 10:25:29	
simple	12-Aug-2024 10:25:29	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-JOB1
simple	12-Aug-2024 10:25:29	Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0 - Default Job #2 (JB-GDL7-JOB1-2)
simple	12-Aug-2024 10:25:29	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	12-Aug-2024 10:25:29	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-JOB1
simple	12-Aug-2024 10:25:29	Updating source code to revision: 360177d2c0f4550de2be90b5f9536b991123e16f
simple	12-Aug-2024 10:25:29	Fetching 'refs/heads/bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0' from 'http://source.jalview.org/git/jalview.git'.
simple	12-Aug-2024 10:25:29	Checking out revision 360177d2c0f4550de2be90b5f9536b991123e16f.
simple	12-Aug-2024 10:25:30	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164
simple	12-Aug-2024 10:25:30	   4af2311..360177d  bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0 -> origin/bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0
simple	12-Aug-2024 10:25:31	Already on 'bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0'
simple	12-Aug-2024 10:25:31	Your branch is behind 'origin/bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0' by 132 commits, and can be fast-forwarded.
simple	12-Aug-2024 10:25:31	  (use "git pull" to update your local branch)
simple	12-Aug-2024 10:25:32	HEAD is now at 360177d Merge branch 'bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0
simple	12-Aug-2024 10:25:32	Updated source code to revision: 360177d2c0f4550de2be90b5f9536b991123e16f
simple	12-Aug-2024 10:25:32	Finished task 'Checkout Default Repository' with result: Success
simple	12-Aug-2024 10:25:32	Running pre-build action: VCS Version Collector
simple	12-Aug-2024 10:25:32	Running pre-build action: Artifactory Release Staging
command	12-Aug-2024 10:25:32	Substituting variable: ${bamboo.planKey} with JB-GDL7
simple	12-Aug-2024 10:25:32	Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	12-Aug-2024 10:25:32	Bamboo Artifactory Plugin version: 2.6.2
command	12-Aug-2024 10:25:32	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0 - Default Job #2 (JB-GDL7-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL7 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_dependency_parent_0=JB-GDB601-3\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=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_repository_revision_number=360177d2c0f4550de2be90b5f9536b991123e16f\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL7-JOB1-2\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_46497978_git_username=\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL7-JOB1\nbamboo_repository_46497978_revision_number=360177d2c0f4550de2be90b5f9536b991123e16f\nbamboo_shortPlanName=bug-JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\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=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL7-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_repository_46497978_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_shortPlanKey=GDL7\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=360177d2c0f4550de2be90b5f9536b991123e16f\nbamboo_buildTimeStamp=2024-08-12T10:24:28.204+01:00\nbamboo_repository_previous_revision_number=4af2311cac6864a2879463213930dc46ce83c626\nbamboo_repository_git_branch=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_buildResultKey=JB-GDL7-JOB1-2\nbamboo_repository_branch_name=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0 - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=360177d2c0f4550de2be90b5f9536b991123e16f\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=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46497978_previous_revision_number=4af2311cac6864a2879463213930dc46ce83c626\nbamboo_planRepository_branchDisplayName=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46497978_name=Jalview Git\nbamboo_repository_46497978_git_branch=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301555\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_46497978_branch_name=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\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-GDL7-JOB1\nbamboo_planKey=JB-GDL7\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	12-Aug-2024 10:25:33	
build	12-Aug-2024 10:25:33	> Configure project :
build	12-Aug-2024 10:25:33	Using properties from file './utils/channels/default/channel_gradle.properties'
build	12-Aug-2024 10:25:33	Using properties from file './utils/channels/default/channel_gradle.properties'
build	12-Aug-2024 10:25:33	JALVIEW_VERSION is set to '2.11.4.0'
build	12-Aug-2024 10:25:33	HEADLESS BUILD
build	12-Aug-2024 10:25:33	J2S ENABLED
build	12-Aug-2024 10:25:33	Using a BUILD profile.
build	12-Aug-2024 10:25:33	
build	12-Aug-2024 10:25:33	> Task :clean
build	12-Aug-2024 10:25:33	> Task :cleanPackageDir
build	12-Aug-2024 10:25:33	> Task :getdownImagesCopy
build	12-Aug-2024 10:25:34	> Task :getdownImagesProcess
build	12-Aug-2024 10:25:34	> Task :getdownImages
build	12-Aug-2024 10:25:34	> Task :copyHelp
build	12-Aug-2024 10:25:35	> Task :buildIndices
build	12-Aug-2024 10:25:35	> Task :copyResources
build	12-Aug-2024 10:25:35	> Task :copyChannelResources
build	12-Aug-2024 10:25:35	
build	12-Aug-2024 10:25:35	> Task :createBuildProperties
build	12-Aug-2024 10:25:35	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	12-Aug-2024 10:25:35	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:35	
build	12-Aug-2024 10:25:35	> Task :buildResources
build	12-Aug-2024 10:25:36	> Task :copyDocs
build	12-Aug-2024 10:25:36	
build	12-Aug-2024 10:25:36	> Task :convertMdFiles
build	12-Aug-2024 10:25:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	12-Aug-2024 10:25:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	12-Aug-2024 10:25:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	12-Aug-2024 10:25:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-JOB1/build/resources/doc_build/doc/building.html
build	12-Aug-2024 10:25:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	12-Aug-2024 10:25:36	
build	12-Aug-2024 10:25:36	> Task :releasesTemplates
build	12-Aug-2024 10:25:36	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	12-Aug-2024 10:25:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:36	
build	12-Aug-2024 10:25:36	> Task :prepare
build	12-Aug-2024 10:25:38	
build	12-Aug-2024 10:25:38	> Task :compileJava
build	12-Aug-2024 10:25:38	Setting target compatibility to 11
error	12-Aug-2024 10:25:44	Note: Some input files use or override a deprecated API.
error	12-Aug-2024 10:25:44	Note: Recompile with -Xlint:deprecation for details.
error	12-Aug-2024 10:25:44	Note: Some input files use unchecked or unsafe operations.
error	12-Aug-2024 10:25:44	Note: Recompile with -Xlint:unchecked for details.
build	12-Aug-2024 10:25:44	
build	12-Aug-2024 10:25:44	> Task :processResources
build	12-Aug-2024 10:25:44	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	12-Aug-2024 10:25:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:44	
build	12-Aug-2024 10:25:44	> Task :classes
build	12-Aug-2024 10:25:46	
build	12-Aug-2024 10:25:46	> Task :compileLinkCheck
build	12-Aug-2024 10:25:46	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	12-Aug-2024 10:25:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-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	12-Aug-2024 10:25:47	
build	12-Aug-2024 10:25:47	> Task :linkCheck
build	12-Aug-2024 10:25:47	Checking help file links
build	12-Aug-2024 10:25:47	
build	12-Aug-2024 10:25:47	Results:
build	12-Aug-2024 10:25:47	156 distinct help targets
build	12-Aug-2024 10:25:47	156 help mappings
build	12-Aug-2024 10:25:47	0 invalid targets
build	12-Aug-2024 10:25:47	31 unused targets
build	12-Aug-2024 10:25:47	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	12-Aug-2024 10:25:47	    overviewprefs: html/features/preferences.html#overview
build	12-Aug-2024 10:25:47	    cdnafeatures: html/features/codingfeatures.html
build	12-Aug-2024 10:25:47	    startupprefs: html/features/preferences.html#startup
build	12-Aug-2024 10:25:47	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	12-Aug-2024 10:25:47	    io.modellerpir: html/io/modellerpir.html
build	12-Aug-2024 10:25:47	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	12-Aug-2024 10:25:47	    pdbmcviewer: html/features/pdbviewer.html
build	12-Aug-2024 10:25:47	    groovy.colours: html/features/groovy.html#groovyColours
build	12-Aug-2024 10:25:47	    seqmappings: html/features/seqmappings.html
build	12-Aug-2024 10:25:47	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	12-Aug-2024 10:25:47	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	12-Aug-2024 10:25:47	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	12-Aug-2024 10:25:47	    search: html/features/search.html
build	12-Aug-2024 10:25:47	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	12-Aug-2024 10:25:47	    alformats: html/io/fileformats.html
build	12-Aug-2024 10:25:47	    strucprefs: html/features/preferences.html#structure
build	12-Aug-2024 10:25:47	    siftsmapping: html/features/siftsmapping.html
build	12-Aug-2024 10:25:47	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	12-Aug-2024 10:25:47	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	12-Aug-2024 10:25:47	    newkeys: html/features/newkeystrokes.html
build	12-Aug-2024 10:25:47	    importvcf.attribs: html/features/importvcf.html#attribs
build	12-Aug-2024 10:25:47	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	12-Aug-2024 10:25:47	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	12-Aug-2024 10:25:47	    jalarchive: html/features/jalarchive.html
build	12-Aug-2024 10:25:47	    newsreader: html/webServices/newsreader.html
build	12-Aug-2024 10:25:47	    jalviewcltool: html/features/commandline.html#script
build	12-Aug-2024 10:25:47	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	12-Aug-2024 10:25:47	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	12-Aug-2024 10:25:47	    paematrixformat: html/io/paematrixformat.html
build	12-Aug-2024 10:25:47	    overview: html/features/overview.html
build	12-Aug-2024 10:25:47	0 invalid map urls
build	12-Aug-2024 10:25:47	0 invalid image attributes
build	12-Aug-2024 10:25:47	482 internal href links (106 with anchors)
build	12-Aug-2024 10:25:47	0 invalid internal href links
build	12-Aug-2024 10:25:47	0 invalid internal anchor links
build	12-Aug-2024 10:25:47	111 external href links
build	12-Aug-2024 10:25:47	External links not verified as internet not available
build	12-Aug-2024 10:25:47	*** Success ***
build	12-Aug-2024 10:25:48	
build	12-Aug-2024 10:25:48	> Task :jar
build	12-Aug-2024 10:25:49	> Task :syncJars
build	12-Aug-2024 10:25:49	> Task :makeDist
build	12-Aug-2024 10:25:49	> Task :getdownWebsiteBuild
build	12-Aug-2024 10:25:50	
build	12-Aug-2024 10:25:50	> Task :getdownDigest
build	12-Aug-2024 10:25:50	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
build	12-Aug-2024 10:25:50	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
error	12-Aug-2024 10:25:50	2024/08/12 10:25:49:618 WARNING Starting without install4j classes
error	12-Aug-2024 10:25:50	2024/08/12 10:25:50:174 WARNING Starting without install4j classes
build	12-Aug-2024 10:25:50	
build	12-Aug-2024 10:25:50	> Task :getdown
build	12-Aug-2024 10:25:50	
build	12-Aug-2024 10:25:50	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	12-Aug-2024 10:25:50	
build	12-Aug-2024 10:25:50	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	12-Aug-2024 10:25:50	
build	12-Aug-2024 10:25:50	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	12-Aug-2024 10:25:50	
build	12-Aug-2024 10:25:50	Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness.
build	12-Aug-2024 10:25:50	Please consult deprecation warnings for more details.
build	12-Aug-2024 10:25:50	
build	12-Aug-2024 10:25:50	BUILD SUCCESSFUL in 18s
build	12-Aug-2024 10:25:50	21 actionable tasks: 21 executed
simple	12-Aug-2024 10:25:51	Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success
simple	12-Aug-2024 10:25:51	Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command	12-Aug-2024 10:25:51	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0 - Default Job #2 (JB-GDL7-JOB1-2)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL7-JOB1-2-ScriptBuildTask-2234249107875075781.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_dependency_parent_0=JB-GDB601-3\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_repository_revision_number=360177d2c0f4550de2be90b5f9536b991123e16f\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL7-JOB1-2\nbamboo_repository_46497978_git_username=\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL7-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL7-JOB1\nbamboo_repository_46497978_revision_number=360177d2c0f4550de2be90b5f9536b991123e16f\nbamboo_shortPlanName=bug-JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_planRepository_name=Jalview Git\nbamboo_buildNumber=2\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-GDL7-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_repository_46497978_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_shortPlanKey=GDL7\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=360177d2c0f4550de2be90b5f9536b991123e16f\nbamboo_buildTimeStamp=2024-08-12T10:24:28.204+01:00\nbamboo_repository_previous_revision_number=4af2311cac6864a2879463213930dc46ce83c626\nbamboo_repository_git_branch=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_buildResultKey=JB-GDL7-JOB1-2\nbamboo_repository_branch_name=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0 - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=360177d2c0f4550de2be90b5f9536b991123e16f\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-GDL7 -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=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46497978_previous_revision_number=4af2311cac6864a2879463213930dc46ce83c626\nbamboo_planRepository_branchDisplayName=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46497978_name=Jalview Git\nbamboo_repository_46497978_git_branch=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301555\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_46497978_branch_name=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\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-GDL7-JOB1\nbamboo_planKey=JB-GDL7\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0\n
simple	12-Aug-2024 10:25:51	Finished task 'Copy JVL file and produce link in HTML' with result: Success
simple	12-Aug-2024 10:25:51	Running post build plugin 'NCover Results Collector'
simple	12-Aug-2024 10:25:51	Running post build plugin 'Artifact Copier'
simple	12-Aug-2024 10:25:51	Publishing an artifact: getdown
simple	12-Aug-2024 10:25:51	Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 121.6 ms
simple	12-Aug-2024 10:25:51	Running post build plugin 'Artifactory Release Management Staging'
simple	12-Aug-2024 10:25:51	Running post build plugin 'Artifactory Build Info Copier'
simple	12-Aug-2024 10:25:51	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	12-Aug-2024 10:25:51	Running post build plugin 'npm Cache Cleanup'
simple	12-Aug-2024 10:25:51	Running post build plugin 'Clover Results Collector'
simple	12-Aug-2024 10:25:51	Running post build plugin 'Docker Container Cleanup'
simple	12-Aug-2024 10:25:51	Finalising the build...
simple	12-Aug-2024 10:25:51	Stopping timer.
simple	12-Aug-2024 10:25:51	Build JB-GDL7-JOB1-2 completed.
simple	12-Aug-2024 10:25:51	Running on server: post build plugin 'NCover Results Collector'
simple	12-Aug-2024 10:25:51	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	12-Aug-2024 10:25:51	Running on server: post build plugin 'Clover Delta Calculator'
simple	12-Aug-2024 10:25:51	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	12-Aug-2024 10:25:51	All post build plugins have finished
simple	12-Aug-2024 10:25:51	Generating build results summary...
simple	12-Aug-2024 10:25:51	Saving build results to disk...
simple	12-Aug-2024 10:25:51	Logging substituted variables...
simple	12-Aug-2024 10:25:51	Indexing build results...
simple	12-Aug-2024 10:25:51	Finished building JB-GDL7-JOB1-2.