simple	28-May-2026 22:14:50	Build Jalview Builds - Getdown Plan Channel - spike-na_hack_JAL-4673 - Default Job #2 (JB-GPC675-JOB1-2) started building on agent Default Agent
simple	28-May-2026 22:14:50	
simple	28-May-2026 22:14:50	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1
simple	28-May-2026 22:14:50	Executing build Jalview Builds - Getdown Plan Channel - spike-na_hack_JAL-4673 - Default Job #2 (JB-GPC675-JOB1-2)
simple	28-May-2026 22:14:50	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	28-May-2026 22:14:50	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1
simple	28-May-2026 22:14:50	Updating source code to revision: 4fc297c20f6f9a295459768bc694729e8c3e8ab5
simple	28-May-2026 22:14:50	Fetching 'refs/heads/spike/na_hack_JAL-4673' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	28-May-2026 22:14:51	Checking out revision 4fc297c20f6f9a295459768bc694729e8c3e8ab5.
simple	28-May-2026 22:14:51	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	28-May-2026 22:14:51	   419944c..4fc297c  spike/na_hack_JAL-4673 -> origin/spike/na_hack_JAL-4673
simple	28-May-2026 22:14:51	Already on 'spike/na_hack_JAL-4673'
simple	28-May-2026 22:14:51	Your branch is behind 'origin/spike/na_hack_JAL-4673' by 4 commits, and can be fast-forwarded.
simple	28-May-2026 22:14:51	  (use "git pull" to update your local branch)
simple	28-May-2026 22:14:51	HEAD is now at 4fc297c JAL-4673 fix tests and add the layered format one,.
simple	28-May-2026 22:14:51	Updated source code to revision: 4fc297c20f6f9a295459768bc694729e8c3e8ab5
simple	28-May-2026 22:14:51	Finished task 'Checkout Default Repository' with result: Success
simple	28-May-2026 22:14:51	Running pre-build action: VCS Version Collector
simple	28-May-2026 22:14:51	Running pre-build action: Artifactory Release Staging
command	28-May-2026 22:14:51	Substituting variable: ${bamboo.planKey} with JB-GPC675
simple	28-May-2026 22:14:51	Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	28-May-2026 22:14:51	Bamboo Artifactory Plugin version: 2.6.2
command	28-May-2026 22:14:51	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - spike-na_hack_JAL-4673 - Default Job #2 (JB-GPC675-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC675 clean shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=spike/na_hack_JAL-4673\nbamboo_dependency_parent_0=JB-GDB752-5\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=spike/na_hack_JAL-4673\nbamboo_repository_revision_number=4fc297c20f6f9a295459768bc694729e8c3e8ab5\nbamboo_repository_48169061_branch_name=spike/na_hack_JAL-4673\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC675-JOB1-2\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-GPC675-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GPC675-JOB1\nbamboo_shortPlanName=spike-na_hack_JAL-4673\nbamboo_planRepository_name=Jalview Gitlab\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-GPC675-JOB1-2\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_48169061_git_username=\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - spike-na_hack_JAL-4673\nbamboo_shortPlanKey=GPC675\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=4fc297c20f6f9a295459768bc694729e8c3e8ab5\nbamboo_buildTimeStamp=2026-05-28T22:14:50.619+01:00\nbamboo_repository_previous_revision_number=419944c76ab539e2c2338580252d8d2c325e87fa\nbamboo_repository_git_branch=spike/na_hack_JAL-4673\nbamboo_buildResultKey=JB-GPC675-JOB1-2\nbamboo_repository_branch_name=spike/na_hack_JAL-4673\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - spike-na_hack_JAL-4673 - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=4fc297c20f6f9a295459768bc694729e8c3e8ab5\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\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_repository_48169061_revision_number=4fc297c20f6f9a295459768bc694729e8c3e8ab5\nbamboo_repository_48169061_name=Jalview Gitlab\nbamboo_repository_48169061_previous_revision_number=419944c76ab539e2c2338580252d8d2c325e87fa\nbamboo_planRepository_branch=spike/na_hack_JAL-4673\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=spike/na_hack_JAL-4673\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=spike/na_hack_JAL-4673\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-47972553\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_48169061_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-GPC675-JOB1\nbamboo_planKey=JB-GPC675\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_48169061_git_branch=spike/na_hack_JAL-4673\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=spike/na_hack_JAL-4673\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	28-May-2026 22:14:53	
build	28-May-2026 22:14:53	> Configure project :
build	28-May-2026 22:14:53	Using properties from file './utils/channels/default/channel_gradle.properties'
build	28-May-2026 22:14:53	JALVIEW_VERSION is set to '2.12.0'
build	28-May-2026 22:14:53	HEADLESS BUILD
build	28-May-2026 22:14:53	J2S ENABLED
build	28-May-2026 22:14:53	Using a BUILD profile.
build	28-May-2026 22:14:53	eclipseDir exists
build	28-May-2026 22:14:53	
build	28-May-2026 22:14:53	> Task :clean
build	28-May-2026 22:14:53	> Task :cleanPackageDir
build	28-May-2026 22:14:53	> Task :copyHelp
build	28-May-2026 22:14:54	> Task :buildIndices
build	28-May-2026 22:14:54	> Task :copyResources
build	28-May-2026 22:14:54	> Task :copyChannelResources
build	28-May-2026 22:14:55	
build	28-May-2026 22:14:55	> Task :createBuildProperties
build	28-May-2026 22:14:55	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	28-May-2026 22:14:55	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:14:55	
build	28-May-2026 22:14:55	> Task :buildResources
build	28-May-2026 22:14:55	> Task :copyDocs
build	28-May-2026 22:14:55	
build	28-May-2026 22:14:55	> Task :convertMdFiles
build	28-May-2026 22:14:55	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	28-May-2026 22:14:55	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	28-May-2026 22:14:55	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	28-May-2026 22:14:55	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
build	28-May-2026 22:14:55	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1/build/resources/doc_build/doc/building.html
build	28-May-2026 22:14:55	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1/build/resources/doc_build/doc/addingWebClient.html
build	28-May-2026 22:14:55	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	28-May-2026 22:14:55	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
build	28-May-2026 22:14:55	
build	28-May-2026 22:14:55	> Task :releasesTemplates
build	28-May-2026 22:14:55	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	28-May-2026 22:14:55	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:14:55	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:14:55	Stripping rc/test/etc for 2_12_0
build	28-May-2026 22:14:55	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1/help/markdown/whatsnew/whatsnew-2_12_0.md
build	28-May-2026 22:14:55	
build	28-May-2026 22:14:55	> Task :prepare
build	28-May-2026 22:14:57	
build	28-May-2026 22:14:57	> Task :compileJava
build	28-May-2026 22:14:57	Setting target compatibility to 11
error	28-May-2026 22:15:03	Note: Some input files use or override a deprecated API.
error	28-May-2026 22:15:03	Note: Recompile with -Xlint:deprecation for details.
error	28-May-2026 22:15:03	Note: Some input files use unchecked or unsafe operations.
error	28-May-2026 22:15:03	Note: Recompile with -Xlint:unchecked for details.
build	28-May-2026 22:15:04	
build	28-May-2026 22:15:04	> Task :processResources
build	28-May-2026 22:15:04	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	28-May-2026 22:15:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:15:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:15:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:15:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:15:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:15:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:15:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:15:04	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:15:04	
build	28-May-2026 22:15:04	> Task :classes
build	28-May-2026 22:15:05	
build	28-May-2026 22:15:05	> Task :compileLinkCheck
build	28-May-2026 22:15:05	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	28-May-2026 22:15:05	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:15:05	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:15:05	
build	28-May-2026 22:15:05	> Task :linkCheck
build	28-May-2026 22:15:05	Checking help file links
build	28-May-2026 22:15:05	
build	28-May-2026 22:15:05	Results:
build	28-May-2026 22:15:05	162 distinct help targets
build	28-May-2026 22:15:05	162 help mappings
build	28-May-2026 22:15:05	0 invalid targets
build	28-May-2026 22:15:05	31 unused targets
build	28-May-2026 22:15:05	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	28-May-2026 22:15:05	    overviewprefs: html/features/preferences.html#overview
build	28-May-2026 22:15:05	    cdnafeatures: html/features/codingfeatures.html
build	28-May-2026 22:15:05	    startupprefs: html/features/preferences.html#startup
build	28-May-2026 22:15:05	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	28-May-2026 22:15:05	    io.modellerpir: html/io/modellerpir.html
build	28-May-2026 22:15:05	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	28-May-2026 22:15:05	    pdbmcviewer: html/features/pdbviewer.html
build	28-May-2026 22:15:05	    groovy.colours: html/features/groovy.html#groovyColours
build	28-May-2026 22:15:05	    seqmappings: html/features/seqmappings.html
build	28-May-2026 22:15:05	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	28-May-2026 22:15:05	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	28-May-2026 22:15:05	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	28-May-2026 22:15:05	    search: html/features/search.html
build	28-May-2026 22:15:05	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	28-May-2026 22:15:05	    alformats: html/io/fileformats.html
build	28-May-2026 22:15:05	    strucprefs: html/features/preferences.html#structure
build	28-May-2026 22:15:05	    siftsmapping: html/features/siftsmapping.html
build	28-May-2026 22:15:05	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	28-May-2026 22:15:05	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	28-May-2026 22:15:05	    newkeys: html/features/newkeystrokes.html
build	28-May-2026 22:15:05	    importvcf.attribs: html/features/importvcf.html#attribs
build	28-May-2026 22:15:05	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	28-May-2026 22:15:05	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	28-May-2026 22:15:05	    jalarchive: html/features/jalarchive.html
build	28-May-2026 22:15:05	    newsreader: html/webServices/newsreader.html
build	28-May-2026 22:15:05	    jalviewcltool: html/features/commandline.html#script
build	28-May-2026 22:15:05	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	28-May-2026 22:15:05	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	28-May-2026 22:15:05	    paematrixformat: html/io/paematrixformat.html
build	28-May-2026 22:15:05	    overview: html/features/overview.html
build	28-May-2026 22:15:05	0 invalid map urls
build	28-May-2026 22:15:05	0 invalid image attributes
build	28-May-2026 22:15:05	520 internal href links (119 with anchors)
build	28-May-2026 22:15:05	0 invalid internal href links
build	28-May-2026 22:15:05	0 invalid internal anchor links
build	28-May-2026 22:15:05	113 external href links
build	28-May-2026 22:15:05	External links not verified as internet not available
build	28-May-2026 22:15:05	*** Success ***
build	28-May-2026 22:15:06	
build	28-May-2026 22:15:06	> Task :jar
build	28-May-2026 22:15:06	> Task :syncJars
build	28-May-2026 22:15:06	> Task :makeDist
build	28-May-2026 22:15:14	> Task :shadowJar
build	28-May-2026 22:15:14	
build	28-May-2026 22:15:14	> Task :getdownImagesCopy
build	28-May-2026 22:15:14	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	28-May-2026 22:15:14	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-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	28-May-2026 22:15:15	
build	28-May-2026 22:15:15	> Task :getdownImagesProcess
build	28-May-2026 22:15:15	> Task :getdownImages
build	28-May-2026 22:15:15	> Task :getdownWebsiteBuild
build	28-May-2026 22:15:16	
build	28-May-2026 22:15:16	> Task :getdownDigest
build	28-May-2026 22:15:16	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
build	28-May-2026 22:15:16	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
error	28-May-2026 22:15:16	2026/05/28 22:15:15:557 WARNING Starting without install4j classes
error	28-May-2026 22:15:16	2026/05/28 22:15:16:166 WARNING Starting without install4j classes
build	28-May-2026 22:15:16	
build	28-May-2026 22:15:16	> Task :getdown
build	28-May-2026 22:15:16	
build	28-May-2026 22:15:16	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	28-May-2026 22:15:16	
build	28-May-2026 22:15:16	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	28-May-2026 22:15:16	
build	28-May-2026 22:15:16	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	28-May-2026 22:15:16	
build	28-May-2026 22:15:16	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	28-May-2026 22:15:16	Please consult deprecation warnings for more details.
build	28-May-2026 22:15:16	
build	28-May-2026 22:15:16	BUILD SUCCESSFUL in 25s
build	28-May-2026 22:15:16	22 actionable tasks: 22 executed
simple	28-May-2026 22:15:17	Finished task 'Jalview distribution for Java 11' with result: Success
simple	28-May-2026 22:15:17	Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled
simple	28-May-2026 22:15:17	Running post build plugin 'NCover Results Collector'
simple	28-May-2026 22:15:17	Running post build plugin 'Artifact Copier'
simple	28-May-2026 22:15:17	Publishing an artifact: Jalview executables
simple	28-May-2026 22:15:17	Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 204.0 ms
simple	28-May-2026 22:15:17	Publishing an artifact: install4j installers
error	28-May-2026 22:15:17	Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1/build/install4j does not exist.
simple	28-May-2026 22:15:17	The artifact hasn't been successfully published after 3.554 ms
simple	28-May-2026 22:15:17	Publishing an artifact: getdown-channel
error	28-May-2026 22:15:17	Unable to publish artifact [getdown-channel]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1/getdown/website does not exist.
simple	28-May-2026 22:15:17	The artifact hasn't been successfully published after 112.0 μs
simple	28-May-2026 22:15:17	Publishing an artifact: Jalview getdown launcher
error	28-May-2026 22:15:17	Unable to publish artifact [Jalview getdown launcher]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1/getdown/files does not exist.
simple	28-May-2026 22:15:17	The artifact hasn't been successfully published after 39.81 μs
simple	28-May-2026 22:15:17	Publishing an artifact: getdown build for website
simple	28-May-2026 22:15:17	Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 189.7 ms
simple	28-May-2026 22:15:17	Publishing an artifact: getdown build for archive
error	28-May-2026 22:15:17	Unable to publish artifact [getdown build for archive]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC675-JOB1/build/website/docroot/old does not exist.
simple	28-May-2026 22:15:17	The artifact hasn't been successfully published after 200.6 μs
simple	28-May-2026 22:15:17	Running post build plugin 'Artifactory Release Management Staging'
simple	28-May-2026 22:15:17	Running post build plugin 'Artifactory Build Info Copier'
simple	28-May-2026 22:15:17	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	28-May-2026 22:15:17	Running post build plugin 'npm Cache Cleanup'
simple	28-May-2026 22:15:17	Running post build plugin 'Clover Results Collector'
simple	28-May-2026 22:15:17	Running post build plugin 'Docker Container Cleanup'
simple	28-May-2026 22:15:17	Finalising the build...
simple	28-May-2026 22:15:17	Stopping timer.
simple	28-May-2026 22:15:17	Build JB-GPC675-JOB1-2 completed.
simple	28-May-2026 22:15:17	Running on server: post build plugin 'NCover Results Collector'
simple	28-May-2026 22:15:17	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	28-May-2026 22:15:17	Running on server: post build plugin 'Clover Delta Calculator'
simple	28-May-2026 22:15:17	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	28-May-2026 22:15:17	All post build plugins have finished
simple	28-May-2026 22:15:17	Generating build results summary...
simple	28-May-2026 22:15:17	Saving build results to disk...
simple	28-May-2026 22:15:17	Logging substituted variables...
simple	28-May-2026 22:15:17	Indexing build results...
simple	28-May-2026 22:15:17	Finished building JB-GPC675-JOB1-2.