simple	05-Dec-2025 18:07:03	Build Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again - Default Job #9 (JB-GPC657-JOB1-9) started building on agent Default Agent
simple	05-Dec-2025 18:07:03	
simple	05-Dec-2025 18:07:03	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1
simple	05-Dec-2025 18:07:03	Executing build Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again - Default Job #9 (JB-GPC657-JOB1-9)
simple	05-Dec-2025 18:07:03	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	05-Dec-2025 18:07:03	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1
simple	05-Dec-2025 18:07:03	Updating source code to revision: 93fb58cbe20343f44ca1822ba33a9713771dea50
simple	05-Dec-2025 18:07:03	Fetching 'refs/heads/patch/JAL-4606_again_and_again' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	05-Dec-2025 18:07:03	Checking out revision 93fb58cbe20343f44ca1822ba33a9713771dea50.
simple	05-Dec-2025 18:07:03	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	05-Dec-2025 18:07:03	   23d7741..93fb58c  patch/JAL-4606_again_and_again -> origin/patch/JAL-4606_again_and_again
simple	05-Dec-2025 18:07:03	Already on 'patch/JAL-4606_again_and_again'
simple	05-Dec-2025 18:07:03	Your branch is behind 'origin/patch/JAL-4606_again_and_again' by 1 commit, and can be fast-forwarded.
simple	05-Dec-2025 18:07:03	  (use "git pull" to update your local branch)
simple	05-Dec-2025 18:07:04	HEAD is now at 93fb58c JAL-4638 patch out original normalise patch for JAL-4606
simple	05-Dec-2025 18:07:04	Updated source code to revision: 93fb58cbe20343f44ca1822ba33a9713771dea50
simple	05-Dec-2025 18:07:04	Finished task 'Checkout Default Repository' with result: Success
simple	05-Dec-2025 18:07:04	Running pre-build action: VCS Version Collector
simple	05-Dec-2025 18:07:04	Running pre-build action: Artifactory Release Staging
command	05-Dec-2025 18:07:04	Substituting variable: ${bamboo.planKey} with JB-GPC657
simple	05-Dec-2025 18:07:04	Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	05-Dec-2025 18:07:04	Bamboo Artifactory Plugin version: 2.6.2
command	05-Dec-2025 18:07:04	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again - Default Job #9 (JB-GPC657-JOB1-9)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC657 clean shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4606_again_and_again\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4606_again_and_again\nbamboo_repository_revision_number=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC657-JOB1-9\nbamboo_repository_46498625_branch_name=patch/JAL-4606_again_and_again\nbamboo_repository_46498625_git_branch=patch/JAL-4606_again_and_again\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-GPC657-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GPC657-JOB1\nbamboo_shortPlanName=patch-JAL-4606_again_and_again\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=9\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-GPC657-JOB1-9\nbamboo_repository_46498625_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 - patch-JAL-4606_again_and_again\nbamboo_shortPlanKey=GPC657\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_buildTimeStamp=2025-12-05T18:07:03.641Z\nbamboo_repository_previous_revision_number=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_planRepository_previousRevision=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_repository_git_branch=patch/JAL-4606_again_and_again\nbamboo_buildResultKey=JB-GPC657-JOB1-9\nbamboo_repository_branch_name=patch/JAL-4606_again_and_again\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498625_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_1_revision=93fb58cbe20343f44ca1822ba33a9713771dea50\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_repository_46498625_git_username=\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_dependenciesDisabled=false\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=patch/JAL-4606_again_and_again\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_repository_46498625_previous_revision_number=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_repository_46498625_revision_number=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_planRepository_branchDisplayName=patch/JAL-4606_again_and_again\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4606_again_and_again\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-46302819\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_ManualBuildTriggerReason_userName=jprocter\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-GPC657-JOB1\nbamboo_planKey=JB-GPC657\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4606_again_and_again\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	05-Dec-2025 18:07:04	
build	05-Dec-2025 18:07:04	> Configure project :
build	05-Dec-2025 18:07:04	Using properties from file './utils/channels/default/channel_gradle.properties'
build	05-Dec-2025 18:07:04	JALVIEW_VERSION is set to '2.11.5.1'
build	05-Dec-2025 18:07:04	HEADLESS BUILD
build	05-Dec-2025 18:07:04	J2S ENABLED
build	05-Dec-2025 18:07:04	Using a BUILD profile.
build	05-Dec-2025 18:07:04	eclipseDir exists
build	05-Dec-2025 18:07:05	
build	05-Dec-2025 18:07:05	> Task :clean
build	05-Dec-2025 18:07:05	> Task :cleanPackageDir
build	05-Dec-2025 18:07:05	> Task :copyHelp
build	05-Dec-2025 18:07:06	> Task :buildIndices
build	05-Dec-2025 18:07:06	> Task :copyResources
build	05-Dec-2025 18:07:06	> Task :copyChannelResources
build	05-Dec-2025 18:07:06	
build	05-Dec-2025 18:07:06	> Task :createBuildProperties
build	05-Dec-2025 18:07:06	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	05-Dec-2025 18:07:06	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:06	
build	05-Dec-2025 18:07:06	> Task :buildResources
build	05-Dec-2025 18:07:06	> Task :copyDocs
build	05-Dec-2025 18:07:06	
build	05-Dec-2025 18:07:06	> Task :convertMdFiles
build	05-Dec-2025 18:07:06	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	05-Dec-2025 18:07:06	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	05-Dec-2025 18:07:06	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	05-Dec-2025 18:07:06	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/building.html
build	05-Dec-2025 18:07:06	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	05-Dec-2025 18:07:06	
build	05-Dec-2025 18:07:06	> Task :releasesTemplates
build	05-Dec-2025 18:07:06	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	05-Dec-2025 18:07:06	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:06	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:06	Stripping rc/test/etc for 2_11_5_1
build	05-Dec-2025 18:07:06	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md
build	05-Dec-2025 18:07:06	
build	05-Dec-2025 18:07:06	> Task :prepare
build	05-Dec-2025 18:07:08	
build	05-Dec-2025 18:07:08	> Task :compileJava
build	05-Dec-2025 18:07:08	Setting target compatibility to 11
error	05-Dec-2025 18:07:12	Note: Some input files use or override a deprecated API.
error	05-Dec-2025 18:07:12	Note: Recompile with -Xlint:deprecation for details.
error	05-Dec-2025 18:07:12	Note: Some input files use unchecked or unsafe operations.
error	05-Dec-2025 18:07:12	Note: Recompile with -Xlint:unchecked for details.
build	05-Dec-2025 18:07:12	
build	05-Dec-2025 18:07:12	> Task :processResources
build	05-Dec-2025 18:07:12	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	05-Dec-2025 18:07:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:12	
build	05-Dec-2025 18:07:12	> Task :classes
build	05-Dec-2025 18:07:13	
build	05-Dec-2025 18:07:13	> Task :compileLinkCheck
build	05-Dec-2025 18:07:13	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	05-Dec-2025 18:07:13	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:13	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:13	
build	05-Dec-2025 18:07:13	> Task :linkCheck
build	05-Dec-2025 18:07:13	Checking help file links
build	05-Dec-2025 18:07:13	
build	05-Dec-2025 18:07:13	Results:
build	05-Dec-2025 18:07:13	161 distinct help targets
build	05-Dec-2025 18:07:13	161 help mappings
build	05-Dec-2025 18:07:13	0 invalid targets
build	05-Dec-2025 18:07:13	31 unused targets
build	05-Dec-2025 18:07:13	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	05-Dec-2025 18:07:13	    overviewprefs: html/features/preferences.html#overview
build	05-Dec-2025 18:07:13	    cdnafeatures: html/features/codingfeatures.html
build	05-Dec-2025 18:07:13	    startupprefs: html/features/preferences.html#startup
build	05-Dec-2025 18:07:13	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	05-Dec-2025 18:07:13	    io.modellerpir: html/io/modellerpir.html
build	05-Dec-2025 18:07:13	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	05-Dec-2025 18:07:13	    pdbmcviewer: html/features/pdbviewer.html
build	05-Dec-2025 18:07:13	    groovy.colours: html/features/groovy.html#groovyColours
build	05-Dec-2025 18:07:13	    seqmappings: html/features/seqmappings.html
build	05-Dec-2025 18:07:13	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	05-Dec-2025 18:07:13	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	05-Dec-2025 18:07:13	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	05-Dec-2025 18:07:13	    search: html/features/search.html
build	05-Dec-2025 18:07:13	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	05-Dec-2025 18:07:13	    alformats: html/io/fileformats.html
build	05-Dec-2025 18:07:13	    strucprefs: html/features/preferences.html#structure
build	05-Dec-2025 18:07:13	    siftsmapping: html/features/siftsmapping.html
build	05-Dec-2025 18:07:13	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	05-Dec-2025 18:07:13	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	05-Dec-2025 18:07:13	    newkeys: html/features/newkeystrokes.html
build	05-Dec-2025 18:07:13	    importvcf.attribs: html/features/importvcf.html#attribs
build	05-Dec-2025 18:07:13	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	05-Dec-2025 18:07:13	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	05-Dec-2025 18:07:13	    jalarchive: html/features/jalarchive.html
build	05-Dec-2025 18:07:13	    newsreader: html/webServices/newsreader.html
build	05-Dec-2025 18:07:13	    jalviewcltool: html/features/commandline.html#script
build	05-Dec-2025 18:07:13	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	05-Dec-2025 18:07:13	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	05-Dec-2025 18:07:13	    paematrixformat: html/io/paematrixformat.html
build	05-Dec-2025 18:07:13	    overview: html/features/overview.html
build	05-Dec-2025 18:07:13	0 invalid map urls
build	05-Dec-2025 18:07:13	0 invalid image attributes
build	05-Dec-2025 18:07:13	520 internal href links (120 with anchors)
build	05-Dec-2025 18:07:13	0 invalid internal href links
build	05-Dec-2025 18:07:13	0 invalid internal anchor links
build	05-Dec-2025 18:07:13	112 external href links
build	05-Dec-2025 18:07:13	External links not verified as internet not available
build	05-Dec-2025 18:07:13	*** Success ***
build	05-Dec-2025 18:07:14	
build	05-Dec-2025 18:07:14	> Task :jar
build	05-Dec-2025 18:07:14	> Task :syncJars
build	05-Dec-2025 18:07:14	> Task :makeDist
build	05-Dec-2025 18:07:20	> Task :shadowJar
build	05-Dec-2025 18:07:20	
build	05-Dec-2025 18:07:20	> Task :getdownImagesCopy
build	05-Dec-2025 18:07:20	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	05-Dec-2025 18:07:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:21	
build	05-Dec-2025 18:07:21	> Task :getdownImagesProcess
build	05-Dec-2025 18:07:21	> Task :getdownImages
build	05-Dec-2025 18:07:21	> Task :getdownWebsiteBuild
build	05-Dec-2025 18:07:22	
build	05-Dec-2025 18:07:22	> Task :getdownDigest
build	05-Dec-2025 18:07:22	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
error	05-Dec-2025 18:07:22	2025/12/05 18:07:21:581 WARNING Starting without install4j classes
error	05-Dec-2025 18:07:22	2025/12/05 18:07:22:109 WARNING Starting without install4j classes
build	05-Dec-2025 18:07:22	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	05-Dec-2025 18:07:22	
build	05-Dec-2025 18:07:22	> Task :getdown
build	05-Dec-2025 18:07:22	
build	05-Dec-2025 18:07:22	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	05-Dec-2025 18:07:22	
build	05-Dec-2025 18:07:22	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	05-Dec-2025 18:07:22	
build	05-Dec-2025 18:07:22	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	05-Dec-2025 18:07:22	
build	05-Dec-2025 18:07:22	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	05-Dec-2025 18:07:22	Please consult deprecation warnings for more details.
build	05-Dec-2025 18:07:22	
build	05-Dec-2025 18:07:22	BUILD SUCCESSFUL in 18s
build	05-Dec-2025 18:07:22	22 actionable tasks: 22 executed
simple	05-Dec-2025 18:07:23	Finished task 'Jalview distribution for Java 11' with result: Success
command	05-Dec-2025 18:07:23	Substituting variable: ${bamboo.planKey} with JB-GPC657
simple	05-Dec-2025 18:07:23	Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	05-Dec-2025 18:07:23	Bamboo Artifactory Plugin version: 2.6.2
command	05-Dec-2025 18:07:23	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again - Default Job #9 (JB-GPC657-JOB1-9)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -x clean -PCHANNEL=BUILD -PJAVA_VERSION=1.8 -Pbamboo_planKey=JB-GPC657 shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4606_again_and_again\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4606_again_and_again\nbamboo_repository_revision_number=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC657-JOB1-9\nbamboo_repository_46498625_branch_name=patch/JAL-4606_again_and_again\nbamboo_repository_46498625_git_branch=patch/JAL-4606_again_and_again\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-GPC657-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GPC657-JOB1\nbamboo_shortPlanName=patch-JAL-4606_again_and_again\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=9\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-GPC657-JOB1-9\nbamboo_repository_46498625_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 - patch-JAL-4606_again_and_again\nbamboo_shortPlanKey=GPC657\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_buildTimeStamp=2025-12-05T18:07:03.641Z\nbamboo_repository_previous_revision_number=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_planRepository_previousRevision=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_repository_git_branch=patch/JAL-4606_again_and_again\nbamboo_buildResultKey=JB-GPC657-JOB1-9\nbamboo_repository_branch_name=patch/JAL-4606_again_and_again\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498625_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_1_revision=93fb58cbe20343f44ca1822ba33a9713771dea50\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_repository_46498625_git_username=\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-GPC657 clean shadowJar getdown\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_dependenciesDisabled=false\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=patch/JAL-4606_again_and_again\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_repository_46498625_previous_revision_number=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=23d77417fa19d86491740b13213c4e5f6fe8c8ca\nbamboo_repository_46498625_revision_number=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_planRepository_branchDisplayName=patch/JAL-4606_again_and_again\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4606_again_and_again\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-46302819\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_ManualBuildTriggerReason_userName=jprocter\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-GPC657-JOB1\nbamboo_planKey=JB-GPC657\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4606_again_and_again\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	05-Dec-2025 18:07:23	
build	05-Dec-2025 18:07:23	> Configure project :
build	05-Dec-2025 18:07:23	Using properties from file './utils/channels/default/channel_gradle.properties'
build	05-Dec-2025 18:07:23	JALVIEW_VERSION is set to '2.11.5.1'
build	05-Dec-2025 18:07:23	HEADLESS BUILD
build	05-Dec-2025 18:07:23	J2S ENABLED
build	05-Dec-2025 18:07:23	Using a BUILD profile.
build	05-Dec-2025 18:07:23	eclipseDir exists
build	05-Dec-2025 18:07:23	
build	05-Dec-2025 18:07:23	> Task :copyHelp UP-TO-DATE
build	05-Dec-2025 18:07:24	> Task :buildIndices
build	05-Dec-2025 18:07:24	> Task :copyResources UP-TO-DATE
build	05-Dec-2025 18:07:24	> Task :copyChannelResources UP-TO-DATE
build	05-Dec-2025 18:07:24	
build	05-Dec-2025 18:07:24	> Task :createBuildProperties
build	05-Dec-2025 18:07:24	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	05-Dec-2025 18:07:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:24	
build	05-Dec-2025 18:07:24	> Task :buildResources
build	05-Dec-2025 18:07:24	> Task :copyDocs
build	05-Dec-2025 18:07:25	
build	05-Dec-2025 18:07:25	> Task :convertMdFiles
build	05-Dec-2025 18:07:25	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	05-Dec-2025 18:07:25	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	05-Dec-2025 18:07:25	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	05-Dec-2025 18:07:25	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/building.html
build	05-Dec-2025 18:07:25	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	05-Dec-2025 18:07:25	
build	05-Dec-2025 18:07:25	> Task :releasesTemplates
build	05-Dec-2025 18:07:25	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	05-Dec-2025 18:07:25	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:25	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:25	Stripping rc/test/etc for 2_11_5_1
build	05-Dec-2025 18:07:25	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md
build	05-Dec-2025 18:07:25	
build	05-Dec-2025 18:07:25	> Task :prepare
build	05-Dec-2025 18:07:27	
build	05-Dec-2025 18:07:27	> Task :compileJava
build	05-Dec-2025 18:07:27	Setting target compatibility to 1.8
error	05-Dec-2025 18:07:30	Note: Some input files use or override a deprecated API.
error	05-Dec-2025 18:07:30	Note: Recompile with -Xlint:deprecation for details.
error	05-Dec-2025 18:07:30	Note: Some input files use unchecked or unsafe operations.
error	05-Dec-2025 18:07:30	Note: Recompile with -Xlint:unchecked for details.
build	05-Dec-2025 18:07:31	
build	05-Dec-2025 18:07:31	> Task :processResources
build	05-Dec-2025 18:07:31	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	05-Dec-2025 18:07:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:31	
build	05-Dec-2025 18:07:31	> Task :classes
build	05-Dec-2025 18:07:31	> Task :cleanPackageDir
build	05-Dec-2025 18:07:32	
build	05-Dec-2025 18:07:32	> Task :compileLinkCheck
build	05-Dec-2025 18:07:32	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	05-Dec-2025 18:07:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:32	
build	05-Dec-2025 18:07:32	> Task :linkCheck
build	05-Dec-2025 18:07:32	Checking help file links
build	05-Dec-2025 18:07:32	
build	05-Dec-2025 18:07:32	Results:
build	05-Dec-2025 18:07:32	161 distinct help targets
build	05-Dec-2025 18:07:32	161 help mappings
build	05-Dec-2025 18:07:32	0 invalid targets
build	05-Dec-2025 18:07:32	31 unused targets
build	05-Dec-2025 18:07:32	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	05-Dec-2025 18:07:32	    overviewprefs: html/features/preferences.html#overview
build	05-Dec-2025 18:07:32	    cdnafeatures: html/features/codingfeatures.html
build	05-Dec-2025 18:07:32	    startupprefs: html/features/preferences.html#startup
build	05-Dec-2025 18:07:32	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	05-Dec-2025 18:07:32	    io.modellerpir: html/io/modellerpir.html
build	05-Dec-2025 18:07:32	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	05-Dec-2025 18:07:32	    pdbmcviewer: html/features/pdbviewer.html
build	05-Dec-2025 18:07:32	    groovy.colours: html/features/groovy.html#groovyColours
build	05-Dec-2025 18:07:32	    seqmappings: html/features/seqmappings.html
build	05-Dec-2025 18:07:32	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	05-Dec-2025 18:07:32	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	05-Dec-2025 18:07:32	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	05-Dec-2025 18:07:32	    search: html/features/search.html
build	05-Dec-2025 18:07:32	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	05-Dec-2025 18:07:32	    alformats: html/io/fileformats.html
build	05-Dec-2025 18:07:32	    strucprefs: html/features/preferences.html#structure
build	05-Dec-2025 18:07:32	    siftsmapping: html/features/siftsmapping.html
build	05-Dec-2025 18:07:32	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	05-Dec-2025 18:07:32	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	05-Dec-2025 18:07:32	    newkeys: html/features/newkeystrokes.html
build	05-Dec-2025 18:07:32	    importvcf.attribs: html/features/importvcf.html#attribs
build	05-Dec-2025 18:07:32	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	05-Dec-2025 18:07:32	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	05-Dec-2025 18:07:32	    jalarchive: html/features/jalarchive.html
build	05-Dec-2025 18:07:32	    newsreader: html/webServices/newsreader.html
build	05-Dec-2025 18:07:32	    jalviewcltool: html/features/commandline.html#script
build	05-Dec-2025 18:07:32	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	05-Dec-2025 18:07:32	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	05-Dec-2025 18:07:32	    paematrixformat: html/io/paematrixformat.html
build	05-Dec-2025 18:07:32	    overview: html/features/overview.html
build	05-Dec-2025 18:07:32	0 invalid map urls
build	05-Dec-2025 18:07:32	0 invalid image attributes
build	05-Dec-2025 18:07:32	520 internal href links (120 with anchors)
build	05-Dec-2025 18:07:32	0 invalid internal href links
build	05-Dec-2025 18:07:32	0 invalid internal anchor links
build	05-Dec-2025 18:07:32	112 external href links
build	05-Dec-2025 18:07:32	External links not verified as internet not available
build	05-Dec-2025 18:07:32	*** Success ***
build	05-Dec-2025 18:07:33	
build	05-Dec-2025 18:07:33	> Task :jar
build	05-Dec-2025 18:07:33	> Task :syncJars
build	05-Dec-2025 18:07:33	> Task :makeDist
build	05-Dec-2025 18:07:38	> Task :shadowJar
build	05-Dec-2025 18:07:38	
build	05-Dec-2025 18:07:38	> Task :getdownImagesCopy
build	05-Dec-2025 18:07:38	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	05-Dec-2025 18:07:38	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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	05-Dec-2025 18:07:39	
build	05-Dec-2025 18:07:39	> Task :getdownImagesProcess
build	05-Dec-2025 18:07:39	> Task :getdownImages
build	05-Dec-2025 18:07:39	> Task :getdownWebsiteBuild
build	05-Dec-2025 18:07:40	
build	05-Dec-2025 18:07:40	> Task :getdownDigest
build	05-Dec-2025 18:07:40	Generating digest file './build/website/docroot/getdown/default/1.8/digest.txt'...
error	05-Dec-2025 18:07:40	2025/12/05 18:07:39:416 WARNING Starting without install4j classes
error	05-Dec-2025 18:07:40	2025/12/05 18:07:39:933 WARNING Starting without install4j classes
build	05-Dec-2025 18:07:40	Generating digest file './build/website/docroot/getdown/default/1.8/digest2.txt'...
build	05-Dec-2025 18:07:40	
build	05-Dec-2025 18:07:40	> Task :getdown
build	05-Dec-2025 18:07:40	
build	05-Dec-2025 18:07:40	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	05-Dec-2025 18:07:40	
build	05-Dec-2025 18:07:40	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	05-Dec-2025 18:07:40	
build	05-Dec-2025 18:07:40	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	05-Dec-2025 18:07:40	
build	05-Dec-2025 18:07:40	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	05-Dec-2025 18:07:40	Please consult deprecation warnings for more details.
build	05-Dec-2025 18:07:40	
build	05-Dec-2025 18:07:40	BUILD SUCCESSFUL in 17s
build	05-Dec-2025 18:07:40	21 actionable tasks: 18 executed, 3 up-to-date
simple	05-Dec-2025 18:07:40	Finished task 'Jalview distribution for Java 8' with result: Success
simple	05-Dec-2025 18:07:40	Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled
simple	05-Dec-2025 18:07:40	Running post build plugin 'NCover Results Collector'
simple	05-Dec-2025 18:07:40	Running post build plugin 'Artifact Copier'
simple	05-Dec-2025 18:07:40	Publishing an artifact: Jalview executables
simple	05-Dec-2025 18:07:41	Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 154.5 ms
simple	05-Dec-2025 18:07:41	Publishing an artifact: install4j installers
error	05-Dec-2025 18:07:41	Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/install4j does not exist.
simple	05-Dec-2025 18:07:41	The artifact hasn't been successfully published after 90.38 μs
simple	05-Dec-2025 18:07:41	Publishing an artifact: getdown-channel
error	05-Dec-2025 18:07:41	Unable to publish artifact [getdown-channel]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/getdown/website does not exist.
simple	05-Dec-2025 18:07:41	The artifact hasn't been successfully published after 55.11 μs
simple	05-Dec-2025 18:07:41	Publishing an artifact: Jalview getdown launcher
error	05-Dec-2025 18:07:41	Unable to publish artifact [Jalview getdown launcher]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/getdown/files does not exist.
simple	05-Dec-2025 18:07:41	The artifact hasn't been successfully published after 62.50 μs
simple	05-Dec-2025 18:07:41	Publishing an artifact: getdown build for website
simple	05-Dec-2025 18:07:41	Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 223.6 ms
simple	05-Dec-2025 18:07:41	Publishing an artifact: getdown build for archive
error	05-Dec-2025 18:07:41	Unable to publish artifact [getdown build for archive]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/website/docroot/old does not exist.
simple	05-Dec-2025 18:07:41	The artifact hasn't been successfully published after 124.7 μs
simple	05-Dec-2025 18:07:41	Running post build plugin 'Artifactory Release Management Staging'
simple	05-Dec-2025 18:07:41	Running post build plugin 'Artifactory Build Info Copier'
simple	05-Dec-2025 18:07:41	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	05-Dec-2025 18:07:41	Running post build plugin 'npm Cache Cleanup'
simple	05-Dec-2025 18:07:41	Running post build plugin 'Clover Results Collector'
simple	05-Dec-2025 18:07:41	Running post build plugin 'Docker Container Cleanup'
simple	05-Dec-2025 18:07:41	Finalising the build...
simple	05-Dec-2025 18:07:41	Stopping timer.
simple	05-Dec-2025 18:07:41	Build JB-GPC657-JOB1-9 completed.
simple	05-Dec-2025 18:07:41	Running on server: post build plugin 'NCover Results Collector'
simple	05-Dec-2025 18:07:41	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	05-Dec-2025 18:07:41	Running on server: post build plugin 'Clover Delta Calculator'
simple	05-Dec-2025 18:07:41	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	05-Dec-2025 18:07:41	All post build plugins have finished
simple	05-Dec-2025 18:07:41	Generating build results summary...
simple	05-Dec-2025 18:07:41	Saving build results to disk...
simple	05-Dec-2025 18:07:41	Logging substituted variables...
simple	05-Dec-2025 18:07:41	Indexing build results...
simple	05-Dec-2025 18:07:41	Finished building JB-GPC657-JOB1-9.