simple	09-Dec-2025 17:03:02	Build Jalview Builds - Getdown Plan Channel - bug-JAL-4559_old_cli_args_in_JVL_docs - Default Job #1 (JB-GPC658-JOB1-1) started building on agent Default Agent
simple	09-Dec-2025 17:03:02	
simple	09-Dec-2025 17:03:02	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1
simple	09-Dec-2025 17:03:02	Executing build Jalview Builds - Getdown Plan Channel - bug-JAL-4559_old_cli_args_in_JVL_docs - Default Job #1 (JB-GPC658-JOB1-1)
simple	09-Dec-2025 17:03:02	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	09-Dec-2025 17:03:02	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1
simple	09-Dec-2025 17:03:02	Updating source code to revision: fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b
simple	09-Dec-2025 17:03:02	Fetching 'refs/heads/bug/JAL-4559_old_cli_args_in_JVL_docs' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	09-Dec-2025 17:03:03	Checking out revision fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b.
simple	09-Dec-2025 17:03:03	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/.git'.
simple	09-Dec-2025 17:03:03	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1'...
simple	09-Dec-2025 17:03:03	done.
simple	09-Dec-2025 17:03:07	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 17:03:07	Switched to a new branch 'bug/JAL-4559_old_cli_args_in_JVL_docs'
simple	09-Dec-2025 17:03:07	Updated source code to revision: fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b
simple	09-Dec-2025 17:03:07	Finished task 'Checkout Default Repository' with result: Success
simple	09-Dec-2025 17:03:07	Running pre-build action: VCS Version Collector
simple	09-Dec-2025 17:03:07	Running pre-build action: Artifactory Release Staging
command	09-Dec-2025 17:03:07	Substituting variable: ${bamboo.planKey} with JB-GPC658
simple	09-Dec-2025 17:03:07	Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	09-Dec-2025 17:03:07	Bamboo Artifactory Plugin version: 2.6.2
command	09-Dec-2025 17:03:07	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - bug-JAL-4559_old_cli_args_in_JVL_docs - Default Job #1 (JB-GPC658-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC658 clean shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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-GPC658-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_48168964_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GPC658-JOB1\nbamboo_shortPlanName=bug-JAL-4559_old_cli_args_in_JVL_docs\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_repository_48168964_git_username=\nbamboo_buildNumber=1\nbamboo_repository_48168964_revision_number=fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b\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-GPC658-JOB1-1\nbamboo_repository_48168964_name=Jalview Gitlab\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - bug-JAL-4559_old_cli_args_in_JVL_docs\nbamboo_shortPlanKey=GPC658\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b\nbamboo_buildTimeStamp=2025-12-09T17:02:33.244Z\nbamboo_repository_git_branch=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_buildResultKey=JB-GPC658-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - 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_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48168964_branch_name=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_repository_name=Jalview Gitlab\nbamboo_repository_48168964_git_branch=bug/JAL-4559_old_cli_args_in_JVL_docs\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_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_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-47972359\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_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-GPC658-JOB1\nbamboo_planKey=JB-GPC658\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 17:03:08	
build	09-Dec-2025 17:03:08	> Configure project :
build	09-Dec-2025 17:03:08	Using properties from file './utils/channels/default/channel_gradle.properties'
build	09-Dec-2025 17:03:08	JALVIEW_VERSION is set to '2.11.5.1'
build	09-Dec-2025 17:03:08	HEADLESS BUILD
build	09-Dec-2025 17:03:08	J2S ENABLED
build	09-Dec-2025 17:03:08	Using a BUILD profile.
build	09-Dec-2025 17:03:08	eclipseDir exists
build	09-Dec-2025 17:03:09	
build	09-Dec-2025 17:03:09	> Task :clean
build	09-Dec-2025 17:03:09	> Task :cleanPackageDir UP-TO-DATE
build	09-Dec-2025 17:03:09	> Task :copyHelp
build	09-Dec-2025 17:03:11	> Task :buildIndices
build	09-Dec-2025 17:03:11	> Task :copyResources
build	09-Dec-2025 17:03:11	> Task :copyChannelResources
build	09-Dec-2025 17:03:11	
build	09-Dec-2025 17:03:11	> Task :createBuildProperties
build	09-Dec-2025 17:03:11	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:03:11	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:11	
build	09-Dec-2025 17:03:11	> Task :buildResources
build	09-Dec-2025 17:03:11	> Task :copyDocs
build	09-Dec-2025 17:03:11	
build	09-Dec-2025 17:03:11	> Task :convertMdFiles
build	09-Dec-2025 17:03:11	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	09-Dec-2025 17:03:11	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	09-Dec-2025 17:03:11	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	09-Dec-2025 17:03:11	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/build/resources/doc_build/doc/building.html
build	09-Dec-2025 17:03:11	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	09-Dec-2025 17:03:12	
build	09-Dec-2025 17:03:12	> Task :releasesTemplates
build	09-Dec-2025 17:03:12	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:03:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:12	Stripping rc/test/etc for 2_11_5_1
build	09-Dec-2025 17:03:12	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md
build	09-Dec-2025 17:03:12	
build	09-Dec-2025 17:03:12	> Task :prepare
build	09-Dec-2025 17:03:14	
build	09-Dec-2025 17:03:14	> Task :compileJava
build	09-Dec-2025 17:03:14	Setting target compatibility to 11
error	09-Dec-2025 17:03:19	Note: Some input files use or override a deprecated API.
error	09-Dec-2025 17:03:19	Note: Recompile with -Xlint:deprecation for details.
error	09-Dec-2025 17:03:19	Note: Some input files use unchecked or unsafe operations.
error	09-Dec-2025 17:03:19	Note: Recompile with -Xlint:unchecked for details.
build	09-Dec-2025 17:03:20	
build	09-Dec-2025 17:03:20	> Task :processResources
build	09-Dec-2025 17:03:20	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:03:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:20	
build	09-Dec-2025 17:03:20	> Task :classes
build	09-Dec-2025 17:03:22	
build	09-Dec-2025 17:03:22	> Task :compileLinkCheck
build	09-Dec-2025 17:03:22	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:03:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:23	
build	09-Dec-2025 17:03:23	> Task :linkCheck
build	09-Dec-2025 17:03:23	Checking help file links
build	09-Dec-2025 17:03:23	
build	09-Dec-2025 17:03:23	Results:
build	09-Dec-2025 17:03:23	161 distinct help targets
build	09-Dec-2025 17:03:23	161 help mappings
build	09-Dec-2025 17:03:23	0 invalid targets
build	09-Dec-2025 17:03:23	31 unused targets
build	09-Dec-2025 17:03:23	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	09-Dec-2025 17:03:23	    overviewprefs: html/features/preferences.html#overview
build	09-Dec-2025 17:03:23	    cdnafeatures: html/features/codingfeatures.html
build	09-Dec-2025 17:03:23	    startupprefs: html/features/preferences.html#startup
build	09-Dec-2025 17:03:23	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	09-Dec-2025 17:03:23	    io.modellerpir: html/io/modellerpir.html
build	09-Dec-2025 17:03:23	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	09-Dec-2025 17:03:23	    pdbmcviewer: html/features/pdbviewer.html
build	09-Dec-2025 17:03:23	    groovy.colours: html/features/groovy.html#groovyColours
build	09-Dec-2025 17:03:23	    seqmappings: html/features/seqmappings.html
build	09-Dec-2025 17:03:23	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	09-Dec-2025 17:03:23	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	09-Dec-2025 17:03:23	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	09-Dec-2025 17:03:23	    search: html/features/search.html
build	09-Dec-2025 17:03:23	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	09-Dec-2025 17:03:23	    alformats: html/io/fileformats.html
build	09-Dec-2025 17:03:23	    strucprefs: html/features/preferences.html#structure
build	09-Dec-2025 17:03:23	    siftsmapping: html/features/siftsmapping.html
build	09-Dec-2025 17:03:23	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	09-Dec-2025 17:03:23	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	09-Dec-2025 17:03:23	    newkeys: html/features/newkeystrokes.html
build	09-Dec-2025 17:03:23	    importvcf.attribs: html/features/importvcf.html#attribs
build	09-Dec-2025 17:03:23	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	09-Dec-2025 17:03:23	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	09-Dec-2025 17:03:23	    jalarchive: html/features/jalarchive.html
build	09-Dec-2025 17:03:23	    newsreader: html/webServices/newsreader.html
build	09-Dec-2025 17:03:23	    jalviewcltool: html/features/commandline.html#script
build	09-Dec-2025 17:03:23	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	09-Dec-2025 17:03:23	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	09-Dec-2025 17:03:23	    paematrixformat: html/io/paematrixformat.html
build	09-Dec-2025 17:03:23	    overview: html/features/overview.html
build	09-Dec-2025 17:03:23	0 invalid map urls
build	09-Dec-2025 17:03:23	0 invalid image attributes
build	09-Dec-2025 17:03:23	520 internal href links (120 with anchors)
build	09-Dec-2025 17:03:23	0 invalid internal href links
build	09-Dec-2025 17:03:23	0 invalid internal anchor links
build	09-Dec-2025 17:03:23	112 external href links
build	09-Dec-2025 17:03:23	External links not verified as internet not available
build	09-Dec-2025 17:03:23	*** Success ***
build	09-Dec-2025 17:03:24	
build	09-Dec-2025 17:03:24	> Task :jar
build	09-Dec-2025 17:03:24	> Task :syncJars
build	09-Dec-2025 17:03:24	> Task :makeDist
build	09-Dec-2025 17:03:31	> Task :shadowJar
build	09-Dec-2025 17:03:31	
build	09-Dec-2025 17:03:31	> Task :getdownImagesCopy
build	09-Dec-2025 17:03:31	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:03:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/utils/channels/default/images'. 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 17:03:32	
build	09-Dec-2025 17:03:32	> Task :getdownImagesProcess
build	09-Dec-2025 17:03:32	> Task :getdownImages
build	09-Dec-2025 17:03:32	> Task :getdownWebsiteBuild
build	09-Dec-2025 17:03:33	
build	09-Dec-2025 17:03:33	> Task :getdownDigest
build	09-Dec-2025 17:03:33	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
error	09-Dec-2025 17:03:33	2025/12/09 17:03:32:546 WARNING Starting without install4j classes
error	09-Dec-2025 17:03:33	2025/12/09 17:03:33:058 WARNING Starting without install4j classes
build	09-Dec-2025 17:03:33	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	09-Dec-2025 17:03:33	
build	09-Dec-2025 17:03:33	> Task :getdown
build	09-Dec-2025 17:03:33	
build	09-Dec-2025 17:03:33	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	09-Dec-2025 17:03:33	
build	09-Dec-2025 17:03:33	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 17:03:33	
build	09-Dec-2025 17:03:33	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	09-Dec-2025 17:03:33	
build	09-Dec-2025 17:03:33	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	09-Dec-2025 17:03:33	Please consult deprecation warnings for more details.
build	09-Dec-2025 17:03:33	
build	09-Dec-2025 17:03:33	BUILD SUCCESSFUL in 25s
build	09-Dec-2025 17:03:33	22 actionable tasks: 21 executed, 1 up-to-date
simple	09-Dec-2025 17:03:33	Finished task 'Jalview distribution for Java 11' with result: Success
command	09-Dec-2025 17:03:33	Substituting variable: ${bamboo.planKey} with JB-GPC658
simple	09-Dec-2025 17:03:33	Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	09-Dec-2025 17:03:34	Bamboo Artifactory Plugin version: 2.6.2
command	09-Dec-2025 17:03:34	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - bug-JAL-4559_old_cli_args_in_JVL_docs - Default Job #1 (JB-GPC658-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -x clean -PCHANNEL=BUILD -PJAVA_VERSION=1.8 -Pbamboo_planKey=JB-GPC658 shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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-GPC658-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_48168964_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GPC658-JOB1\nbamboo_shortPlanName=bug-JAL-4559_old_cli_args_in_JVL_docs\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_repository_48168964_git_username=\nbamboo_buildNumber=1\nbamboo_repository_48168964_revision_number=fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b\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-GPC658-JOB1-1\nbamboo_repository_48168964_name=Jalview Gitlab\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - bug-JAL-4559_old_cli_args_in_JVL_docs\nbamboo_shortPlanKey=GPC658\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=fa776299afd684ddf2c7a6c0a6fa55ffe39ab85b\nbamboo_buildTimeStamp=2025-12-09T17:02:33.244Z\nbamboo_repository_git_branch=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_buildResultKey=JB-GPC658-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - 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_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48168964_branch_name=bug/JAL-4559_old_cli_args_in_JVL_docs\nbamboo_repository_name=Jalview Gitlab\nbamboo_repository_48168964_git_branch=bug/JAL-4559_old_cli_args_in_JVL_docs\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-GPC658 clean shadowJar getdown\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_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_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-47972359\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_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-GPC658-JOB1\nbamboo_planKey=JB-GPC658\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 17:03:34	
build	09-Dec-2025 17:03:34	> Configure project :
build	09-Dec-2025 17:03:34	Using properties from file './utils/channels/default/channel_gradle.properties'
build	09-Dec-2025 17:03:34	JALVIEW_VERSION is set to '2.11.5.1'
build	09-Dec-2025 17:03:34	HEADLESS BUILD
build	09-Dec-2025 17:03:34	J2S ENABLED
build	09-Dec-2025 17:03:34	Using a BUILD profile.
build	09-Dec-2025 17:03:34	eclipseDir exists
build	09-Dec-2025 17:03:34	
build	09-Dec-2025 17:03:34	> Task :copyHelp UP-TO-DATE
build	09-Dec-2025 17:03:35	> Task :buildIndices
build	09-Dec-2025 17:03:35	> Task :copyResources UP-TO-DATE
build	09-Dec-2025 17:03:35	> Task :copyChannelResources UP-TO-DATE
build	09-Dec-2025 17:03:35	
build	09-Dec-2025 17:03:35	> Task :createBuildProperties
build	09-Dec-2025 17:03:35	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:03:35	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:35	
build	09-Dec-2025 17:03:35	> Task :buildResources
build	09-Dec-2025 17:03:35	> Task :copyDocs
build	09-Dec-2025 17:03:36	
build	09-Dec-2025 17:03:36	> Task :convertMdFiles
build	09-Dec-2025 17:03:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	09-Dec-2025 17:03:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	09-Dec-2025 17:03:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	09-Dec-2025 17:03:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/build/resources/doc_build/doc/building.html
build	09-Dec-2025 17:03:36	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	09-Dec-2025 17:03:36	
build	09-Dec-2025 17:03:36	> Task :releasesTemplates
build	09-Dec-2025 17:03:36	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:03:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:36	Stripping rc/test/etc for 2_11_5_1
build	09-Dec-2025 17:03:36	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md
build	09-Dec-2025 17:03:36	
build	09-Dec-2025 17:03:36	> Task :prepare
build	09-Dec-2025 17:03:38	
build	09-Dec-2025 17:03:38	> Task :compileJava
build	09-Dec-2025 17:03:38	Setting target compatibility to 1.8
error	09-Dec-2025 17:03:43	Note: Some input files use or override a deprecated API.
error	09-Dec-2025 17:03:43	Note: Recompile with -Xlint:deprecation for details.
error	09-Dec-2025 17:03:43	Note: Some input files use unchecked or unsafe operations.
error	09-Dec-2025 17:03:43	Note: Recompile with -Xlint:unchecked for details.
build	09-Dec-2025 17:03:45	
build	09-Dec-2025 17:03:45	> Task :processResources
build	09-Dec-2025 17:03:45	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:03:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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	09-Dec-2025 17:03:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:45	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:45	
build	09-Dec-2025 17:03:45	> Task :classes
build	09-Dec-2025 17:03:45	> Task :cleanPackageDir
build	09-Dec-2025 17:03:46	
build	09-Dec-2025 17:03:46	> Task :compileLinkCheck
build	09-Dec-2025 17:03:46	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:03:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-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 17:03:47	
build	09-Dec-2025 17:03:47	> Task :linkCheck
build	09-Dec-2025 17:03:47	Checking help file links
build	09-Dec-2025 17:03:47	
build	09-Dec-2025 17:03:47	Results:
build	09-Dec-2025 17:03:47	161 distinct help targets
build	09-Dec-2025 17:03:47	161 help mappings
build	09-Dec-2025 17:03:47	0 invalid targets
build	09-Dec-2025 17:03:47	31 unused targets
build	09-Dec-2025 17:03:47	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	09-Dec-2025 17:03:47	    overviewprefs: html/features/preferences.html#overview
build	09-Dec-2025 17:03:47	    cdnafeatures: html/features/codingfeatures.html
build	09-Dec-2025 17:03:47	    startupprefs: html/features/preferences.html#startup
build	09-Dec-2025 17:03:47	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	09-Dec-2025 17:03:47	    io.modellerpir: html/io/modellerpir.html
build	09-Dec-2025 17:03:47	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	09-Dec-2025 17:03:47	    pdbmcviewer: html/features/pdbviewer.html
build	09-Dec-2025 17:03:47	    groovy.colours: html/features/groovy.html#groovyColours
build	09-Dec-2025 17:03:47	    seqmappings: html/features/seqmappings.html
build	09-Dec-2025 17:03:47	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	09-Dec-2025 17:03:47	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	09-Dec-2025 17:03:47	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	09-Dec-2025 17:03:47	    search: html/features/search.html
build	09-Dec-2025 17:03:47	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	09-Dec-2025 17:03:47	    alformats: html/io/fileformats.html
build	09-Dec-2025 17:03:47	    strucprefs: html/features/preferences.html#structure
build	09-Dec-2025 17:03:47	    siftsmapping: html/features/siftsmapping.html
build	09-Dec-2025 17:03:47	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	09-Dec-2025 17:03:47	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	09-Dec-2025 17:03:47	    newkeys: html/features/newkeystrokes.html
build	09-Dec-2025 17:03:47	    importvcf.attribs: html/features/importvcf.html#attribs
build	09-Dec-2025 17:03:47	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	09-Dec-2025 17:03:47	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	09-Dec-2025 17:03:47	    jalarchive: html/features/jalarchive.html
build	09-Dec-2025 17:03:47	    newsreader: html/webServices/newsreader.html
build	09-Dec-2025 17:03:47	    jalviewcltool: html/features/commandline.html#script
build	09-Dec-2025 17:03:47	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	09-Dec-2025 17:03:47	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	09-Dec-2025 17:03:47	    paematrixformat: html/io/paematrixformat.html
build	09-Dec-2025 17:03:47	    overview: html/features/overview.html
build	09-Dec-2025 17:03:47	0 invalid map urls
build	09-Dec-2025 17:03:47	0 invalid image attributes
build	09-Dec-2025 17:03:47	520 internal href links (120 with anchors)
build	09-Dec-2025 17:03:47	0 invalid internal href links
build	09-Dec-2025 17:03:47	0 invalid internal anchor links
build	09-Dec-2025 17:03:47	112 external href links
build	09-Dec-2025 17:03:47	External links not verified as internet not available
build	09-Dec-2025 17:03:47	*** Success ***
build	09-Dec-2025 17:03:47	
build	09-Dec-2025 17:03:47	> Task :jar
build	09-Dec-2025 17:03:48	> Task :syncJars
build	09-Dec-2025 17:03:48	> Task :makeDist
build	09-Dec-2025 17:03:54	> Task :shadowJar
build	09-Dec-2025 17:03:54	
build	09-Dec-2025 17:03:54	> Task :getdownImagesCopy
build	09-Dec-2025 17:03:54	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	09-Dec-2025 17:03:54	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/utils/channels/default/images'. 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 17:03:54	
build	09-Dec-2025 17:03:54	> Task :getdownImagesProcess
build	09-Dec-2025 17:03:54	> Task :getdownImages
build	09-Dec-2025 17:03:54	> Task :getdownWebsiteBuild
build	09-Dec-2025 17:03:55	
build	09-Dec-2025 17:03:55	> Task :getdownDigest
build	09-Dec-2025 17:03:55	Generating digest file './build/website/docroot/getdown/default/1.8/digest.txt'...
build	09-Dec-2025 17:03:55	Generating digest file './build/website/docroot/getdown/default/1.8/digest2.txt'...
build	09-Dec-2025 17:03:55	
build	09-Dec-2025 17:03:55	> Task :getdown
error	09-Dec-2025 17:03:55	2025/12/09 17:03:54:838 WARNING Starting without install4j classes
build	09-Dec-2025 17:03:55	
error	09-Dec-2025 17:03:55	2025/12/09 17:03:55:285 WARNING Starting without install4j classes
build	09-Dec-2025 17:03:55	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	09-Dec-2025 17:03:55	
build	09-Dec-2025 17:03:55	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 17:03:55	
build	09-Dec-2025 17:03:55	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	09-Dec-2025 17:03:55	
build	09-Dec-2025 17:03:55	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	09-Dec-2025 17:03:55	Please consult deprecation warnings for more details.
build	09-Dec-2025 17:03:55	
build	09-Dec-2025 17:03:55	BUILD SUCCESSFUL in 21s
build	09-Dec-2025 17:03:55	21 actionable tasks: 18 executed, 3 up-to-date
simple	09-Dec-2025 17:03:56	Finished task 'Jalview distribution for Java 8' with result: Success
simple	09-Dec-2025 17:03:56	Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled
simple	09-Dec-2025 17:03:56	Running post build plugin 'NCover Results Collector'
simple	09-Dec-2025 17:03:56	Running post build plugin 'Artifact Copier'
simple	09-Dec-2025 17:03:56	Publishing an artifact: Jalview executables
simple	09-Dec-2025 17:03:56	Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 163.1 ms
simple	09-Dec-2025 17:03:56	Publishing an artifact: install4j installers
error	09-Dec-2025 17:03:56	Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/build/install4j does not exist.
simple	09-Dec-2025 17:03:56	The artifact hasn't been successfully published after 83.38 μs
simple	09-Dec-2025 17:03:56	Publishing an artifact: getdown-channel
error	09-Dec-2025 17:03:56	Unable to publish artifact [getdown-channel]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/getdown/website does not exist.
simple	09-Dec-2025 17:03:56	The artifact hasn't been successfully published after 29.49 μs
simple	09-Dec-2025 17:03:56	Publishing an artifact: Jalview getdown launcher
error	09-Dec-2025 17:03:56	Unable to publish artifact [Jalview getdown launcher]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/getdown/files does not exist.
simple	09-Dec-2025 17:03:56	The artifact hasn't been successfully published after 26.47 μs
simple	09-Dec-2025 17:03:56	Publishing an artifact: getdown build for website
simple	09-Dec-2025 17:03:56	Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 231.0 ms
simple	09-Dec-2025 17:03:56	Publishing an artifact: getdown build for archive
error	09-Dec-2025 17:03:56	Unable to publish artifact [getdown build for archive]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC658-JOB1/build/website/docroot/old does not exist.
simple	09-Dec-2025 17:03:56	The artifact hasn't been successfully published after 82.09 μs
simple	09-Dec-2025 17:03:56	Running post build plugin 'Artifactory Release Management Staging'
simple	09-Dec-2025 17:03:56	Running post build plugin 'Artifactory Build Info Copier'
simple	09-Dec-2025 17:03:56	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	09-Dec-2025 17:03:56	Running post build plugin 'npm Cache Cleanup'
simple	09-Dec-2025 17:03:56	Running post build plugin 'Clover Results Collector'
simple	09-Dec-2025 17:03:56	Running post build plugin 'Docker Container Cleanup'
simple	09-Dec-2025 17:03:56	Finalising the build...
simple	09-Dec-2025 17:03:56	Stopping timer.
simple	09-Dec-2025 17:03:56	Build JB-GPC658-JOB1-1 completed.
simple	09-Dec-2025 17:03:56	Running on server: post build plugin 'NCover Results Collector'
simple	09-Dec-2025 17:03:56	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	09-Dec-2025 17:03:56	Running on server: post build plugin 'Clover Delta Calculator'
simple	09-Dec-2025 17:03:56	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	09-Dec-2025 17:03:56	All post build plugins have finished
simple	09-Dec-2025 17:03:56	Generating build results summary...
simple	09-Dec-2025 17:03:56	Saving build results to disk...
simple	09-Dec-2025 17:03:56	Logging substituted variables...
simple	09-Dec-2025 17:03:56	Indexing build results...
simple	09-Dec-2025 17:03:56	Finished building JB-GPC658-JOB1-1.