simple	09-Dec-2025 17:02:33	Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4559_old_cli_args_in_JVL_docs - Default Job #1 (JB-GDL115-JOB1-1) started building on agent Default Agent
simple	09-Dec-2025 17:02:33	
simple	09-Dec-2025 17:02:33	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-JOB1
simple	09-Dec-2025 17:02:33	Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4559_old_cli_args_in_JVL_docs - Default Job #1 (JB-GDL115-JOB1-1)
simple	09-Dec-2025 17:02:33	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	09-Dec-2025 17:02:33	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-JOB1
simple	09-Dec-2025 17:02:33	Updating source code to revision: fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b
simple	09-Dec-2025 17:02:33	Fetching 'refs/heads/bug/JAL-4559_old_cli_args_in_JVL_docs' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	09-Dec-2025 17:02:33	Checking out revision fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b.
simple	09-Dec-2025 17:02:33	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-JOB1/.git'.
simple	09-Dec-2025 17:02:33	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-JOB1'...
simple	09-Dec-2025 17:02:33	done.
simple	09-Dec-2025 17:02:40	Switched to a new branch 'bug/JAL-4559_old_cli_args_in_JVL_docs'
simple	09-Dec-2025 17:02:40	Branch bug/JAL-4559_old_cli_args_in_JVL_docs set up to track remote branch bug/JAL-4559_old_cli_args_in_JVL_docs from origin.
simple	09-Dec-2025 17:02:40	Updated source code to revision: fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b
simple	09-Dec-2025 17:02:40	Finished task 'Checkout Default Repository' with result: Success
simple	09-Dec-2025 17:02:40	Running pre-build action: VCS Version Collector
simple	09-Dec-2025 17:02:40	Running pre-build action: Artifactory Release Staging
command	09-Dec-2025 17:02:40	Substituting variable: ${bamboo.planKey} with JB-GDL115
simple	09-Dec-2025 17:02:40	Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	09-Dec-2025 17:02:40	Bamboo Artifactory Plugin version: 2.6.2
command	09-Dec-2025 17:02:40	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4559_old_cli_args_in_JVL_docs - Default Job #1 (JB-GDL115-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL115 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_dependency_parent_0=JB-GDB736-1\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-4559_old_cli_args_in_JVL_docs\nbamboo_repository_revision_number=fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL115-JOB1-1\nbamboo_repository_48168966_git_username=\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-GDL115-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL115-JOB1\nbamboo_shortPlanName=bug-JAL-4559_old_cli_args_in_JVL_docs\nbamboo_planRepository_name=Jalview Gitlab\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-GDL115-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4559_old_cli_args_in_JVL_docs\nbamboo_shortPlanKey=GDL115\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b\nbamboo_repository_48168966_revision_number=fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b\nbamboo_buildTimeStamp=2025-12-09T17:02:32.994Z\nbamboo_repository_git_branch=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_buildResultKey=JB-GDL115-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4559_old_cli_args_in_JVL_docs - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48168966_branch_name=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_repository_name=Jalview Gitlab\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-4559_old_cli_args_in_JVL_docs\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_48168966_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4559_old_cli_args_in_JVL_docs\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_48168966_git_branch=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-47972363\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=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48168966_name=Jalview Gitlab\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-GDL115-JOB1\nbamboo_planKey=JB-GDL115\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4559_old_cli_args_in_JVL_docs\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	09-Dec-2025 17:02:42	
build	09-Dec-2025 17:02:42	> Configure project :
build	09-Dec-2025 17:02:42	Using properties from file './utils/channels/default/channel_gradle.properties'
build	09-Dec-2025 17:02:42	JALVIEW_VERSION is set to '2.11.5.1'
build	09-Dec-2025 17:02:42	HEADLESS BUILD
build	09-Dec-2025 17:02:42	J2S ENABLED
build	09-Dec-2025 17:02:42	Using a BUILD profile.
build	09-Dec-2025 17:02:42	eclipseDir exists
build	09-Dec-2025 17:02:42	
build	09-Dec-2025 17:02:42	> Task :clean
build	09-Dec-2025 17:02:42	> Task :cleanPackageDir UP-TO-DATE
build	09-Dec-2025 17:02:42	> Task :getdownImagesCopy
build	09-Dec-2025 17:02:42	> Task :getdownImagesProcess
build	09-Dec-2025 17:02:42	> Task :getdownImages
build	09-Dec-2025 17:02:42	> Task :copyHelp
build	09-Dec-2025 17:02:45	> Task :buildIndices
build	09-Dec-2025 17:02:45	> Task :copyResources
build	09-Dec-2025 17:02:45	> Task :copyChannelResources
build	09-Dec-2025 17:02:45	
build	09-Dec-2025 17:02:45	> Task :createBuildProperties
build	09-Dec-2025 17:02:45	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:02:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-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	09-Dec-2025 17:02:45	
build	09-Dec-2025 17:02:45	> Task :buildResources
build	09-Dec-2025 17:02:45	> Task :copyDocs
build	09-Dec-2025 17:02:45	
build	09-Dec-2025 17:02:45	> Task :convertMdFiles
build	09-Dec-2025 17:02:45	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	09-Dec-2025 17:02:45	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	09-Dec-2025 17:02:45	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	09-Dec-2025 17:02:45	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-JOB1/build/resources/doc_build/doc/building.html
build	09-Dec-2025 17:02:45	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	09-Dec-2025 17:02:45	
build	09-Dec-2025 17:02:45	> Task :releasesTemplates
build	09-Dec-2025 17:02:45	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:02:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-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	09-Dec-2025 17:02:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-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	09-Dec-2025 17:02:45	Stripping rc/test/etc for 2_11_5_1
build	09-Dec-2025 17:02:45	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md
build	09-Dec-2025 17:02:45	
build	09-Dec-2025 17:02:45	> Task :prepare
build	09-Dec-2025 17:02:48	
build	09-Dec-2025 17:02:48	> Task :compileJava
build	09-Dec-2025 17:02:48	Setting target compatibility to 11
error	09-Dec-2025 17:02:54	Note: Some input files use or override a deprecated API.
error	09-Dec-2025 17:02:54	Note: Recompile with -Xlint:deprecation for details.
error	09-Dec-2025 17:02:54	Note: Some input files use unchecked or unsafe operations.
error	09-Dec-2025 17:02:54	Note: Recompile with -Xlint:unchecked for details.
build	09-Dec-2025 17:02:55	
build	09-Dec-2025 17:02:55	> Task :processResources
build	09-Dec-2025 17:02:55	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:02:55	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-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	09-Dec-2025 17:02:55	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-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	09-Dec-2025 17:02:55	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-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	09-Dec-2025 17:02:55	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-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	09-Dec-2025 17:02:55	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-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	09-Dec-2025 17:02:55	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-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	09-Dec-2025 17:02:55	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-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	09-Dec-2025 17:02:55	
build	09-Dec-2025 17:02:55	> Task :classes
build	09-Dec-2025 17:02:57	
build	09-Dec-2025 17:02:57	> Task :compileLinkCheck
build	09-Dec-2025 17:02:57	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:02:57	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-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	09-Dec-2025 17:02:57	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-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	09-Dec-2025 17:02:57	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-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	09-Dec-2025 17:02:58	
build	09-Dec-2025 17:02:58	> Task :linkCheck
build	09-Dec-2025 17:02:58	Checking help file links
build	09-Dec-2025 17:02:58	
build	09-Dec-2025 17:02:58	Results:
build	09-Dec-2025 17:02:58	161 distinct help targets
build	09-Dec-2025 17:02:58	161 help mappings
build	09-Dec-2025 17:02:58	0 invalid targets
build	09-Dec-2025 17:02:58	31 unused targets
build	09-Dec-2025 17:02:58	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	09-Dec-2025 17:02:58	    overviewprefs: html/features/preferences.html#overview
build	09-Dec-2025 17:02:58	    cdnafeatures: html/features/codingfeatures.html
build	09-Dec-2025 17:02:58	    startupprefs: html/features/preferences.html#startup
build	09-Dec-2025 17:02:58	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	09-Dec-2025 17:02:58	    io.modellerpir: html/io/modellerpir.html
build	09-Dec-2025 17:02:58	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	09-Dec-2025 17:02:58	    pdbmcviewer: html/features/pdbviewer.html
build	09-Dec-2025 17:02:58	    groovy.colours: html/features/groovy.html#groovyColours
build	09-Dec-2025 17:02:58	    seqmappings: html/features/seqmappings.html
build	09-Dec-2025 17:02:58	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	09-Dec-2025 17:02:58	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	09-Dec-2025 17:02:58	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	09-Dec-2025 17:02:58	    search: html/features/search.html
build	09-Dec-2025 17:02:58	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	09-Dec-2025 17:02:58	    alformats: html/io/fileformats.html
build	09-Dec-2025 17:02:58	    strucprefs: html/features/preferences.html#structure
build	09-Dec-2025 17:02:58	    siftsmapping: html/features/siftsmapping.html
build	09-Dec-2025 17:02:58	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	09-Dec-2025 17:02:58	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	09-Dec-2025 17:02:58	    newkeys: html/features/newkeystrokes.html
build	09-Dec-2025 17:02:58	    importvcf.attribs: html/features/importvcf.html#attribs
build	09-Dec-2025 17:02:58	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	09-Dec-2025 17:02:58	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	09-Dec-2025 17:02:58	    jalarchive: html/features/jalarchive.html
build	09-Dec-2025 17:02:58	    newsreader: html/webServices/newsreader.html
build	09-Dec-2025 17:02:58	    jalviewcltool: html/features/commandline.html#script
build	09-Dec-2025 17:02:58	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	09-Dec-2025 17:02:58	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	09-Dec-2025 17:02:58	    paematrixformat: html/io/paematrixformat.html
build	09-Dec-2025 17:02:58	    overview: html/features/overview.html
build	09-Dec-2025 17:02:58	0 invalid map urls
build	09-Dec-2025 17:02:58	0 invalid image attributes
build	09-Dec-2025 17:02:58	520 internal href links (120 with anchors)
build	09-Dec-2025 17:02:58	0 invalid internal href links
build	09-Dec-2025 17:02:58	0 invalid internal anchor links
build	09-Dec-2025 17:02:58	112 external href links
build	09-Dec-2025 17:02:58	External links not verified as internet not available
build	09-Dec-2025 17:02:58	*** Success ***
build	09-Dec-2025 17:02:59	
build	09-Dec-2025 17:02:59	> Task :jar
build	09-Dec-2025 17:02:59	> Task :syncJars
build	09-Dec-2025 17:02:59	> Task :makeDist
build	09-Dec-2025 17:03:00	> Task :getdownWebsiteBuild
build	09-Dec-2025 17:03:01	
build	09-Dec-2025 17:03:01	> Task :getdownDigest
build	09-Dec-2025 17:03:01	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
build	09-Dec-2025 17:03:01	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	09-Dec-2025 17:03:01	
build	09-Dec-2025 17:03:01	> Task :getdown
build	09-Dec-2025 17:03:01	
build	09-Dec-2025 17:03:01	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	09-Dec-2025 17:03:01	
build	09-Dec-2025 17:03:01	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	09-Dec-2025 17:03:01	
build	09-Dec-2025 17:03:01	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	09-Dec-2025 17:03:01	
build	09-Dec-2025 17:03:01	Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness.
build	09-Dec-2025 17:03:01	Please consult deprecation warnings for more details.
build	09-Dec-2025 17:03:01	
build	09-Dec-2025 17:03:01	BUILD SUCCESSFUL in 21s
build	09-Dec-2025 17:03:01	21 actionable tasks: 20 executed, 1 up-to-date
error	09-Dec-2025 17:03:01	2025/12/09 17:03:00:463 WARNING Starting without install4j classes
error	09-Dec-2025 17:03:01	2025/12/09 17:03:01:001 WARNING Starting without install4j classes
simple	09-Dec-2025 17:03:01	Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success
simple	09-Dec-2025 17:03:01	Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command	09-Dec-2025 17:03:01	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4559_old_cli_args_in_JVL_docs - Default Job #1 (JB-GDL115-JOB1-1)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL115-JOB1-1-ScriptBuildTask-4212921654760716588.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_dependency_parent_0=JB-GDB736-1\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_repository_revision_number=fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL115-JOB1-1\nbamboo_repository_48168966_git_username=\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL115-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL115-JOB1\nbamboo_shortPlanName=bug-JAL-4559_old_cli_args_in_JVL_docs\nbamboo_planRepository_name=Jalview Gitlab\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-GDL115-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4559_old_cli_args_in_JVL_docs\nbamboo_shortPlanKey=GDL115\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b\nbamboo_repository_48168966_revision_number=fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b\nbamboo_buildTimeStamp=2025-12-09T17:02:32.994Z\nbamboo_repository_git_branch=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_buildResultKey=JB-GDL115-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4559_old_cli_args_in_JVL_docs - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48168966_branch_name=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_repository_name=Jalview Gitlab\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-GDL115 -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-4559_old_cli_args_in_JVL_docs\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_48168966_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_48168966_git_branch=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-47972363\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=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48168966_name=Jalview Gitlab\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-GDL115-JOB1\nbamboo_planKey=JB-GDL115\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=bug/JAL-4559_old_cli_args_in_JVL_docs\n
simple	09-Dec-2025 17:03:01	Finished task 'Copy JVL file and produce link in HTML' with result: Success
simple	09-Dec-2025 17:03:01	Running post build plugin 'NCover Results Collector'
simple	09-Dec-2025 17:03:01	Running post build plugin 'Artifact Copier'
simple	09-Dec-2025 17:03:01	Publishing an artifact: getdown
simple	09-Dec-2025 17:03:02	Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 127.7 ms
simple	09-Dec-2025 17:03:02	Running post build plugin 'Artifactory Release Management Staging'
simple	09-Dec-2025 17:03:02	Running post build plugin 'Artifactory Build Info Copier'
simple	09-Dec-2025 17:03:02	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	09-Dec-2025 17:03:02	Running post build plugin 'npm Cache Cleanup'
simple	09-Dec-2025 17:03:02	Running post build plugin 'Clover Results Collector'
simple	09-Dec-2025 17:03:02	Running post build plugin 'Docker Container Cleanup'
simple	09-Dec-2025 17:03:02	Finalising the build...
simple	09-Dec-2025 17:03:02	Stopping timer.
simple	09-Dec-2025 17:03:02	Build JB-GDL115-JOB1-1 completed.
simple	09-Dec-2025 17:03:02	Running on server: post build plugin 'NCover Results Collector'
simple	09-Dec-2025 17:03:02	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	09-Dec-2025 17:03:02	Running on server: post build plugin 'Clover Delta Calculator'
simple	09-Dec-2025 17:03:02	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	09-Dec-2025 17:03:02	All post build plugins have finished
simple	09-Dec-2025 17:03:02	Generating build results summary...
simple	09-Dec-2025 17:03:02	Saving build results to disk...
simple	09-Dec-2025 17:03:02	Logging substituted variables...
simple	09-Dec-2025 17:03:02	Indexing build results...
simple	09-Dec-2025 17:03:02	Finished building JB-GDL115-JOB1-1.