simple	15-Nov-2024 14:07:50	Build Jalview Builds - Getdown Plan Channel - features-JAL-3914_modelqualityscores_v2115 - Default Job #1 (JB-GPC579-JOB1-1) started building on agent Default Agent
simple	15-Nov-2024 14:07:50	
simple	15-Nov-2024 14:07:50	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1
simple	15-Nov-2024 14:07:50	Executing build Jalview Builds - Getdown Plan Channel - features-JAL-3914_modelqualityscores_v2115 - Default Job #1 (JB-GPC579-JOB1-1)
simple	15-Nov-2024 14:07:50	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	15-Nov-2024 14:07:50	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1
simple	15-Nov-2024 14:07:50	Updating source code to revision: 8dbe9206561daac950b4154da519d7aad4cfeaee
simple	15-Nov-2024 14:07:50	Fetching 'refs/heads/features/JAL-3914_modelqualityscores_v2115' from 'http://source.jalview.org/git/jalview.git'.
simple	15-Nov-2024 14:07:50	Checking out revision 8dbe9206561daac950b4154da519d7aad4cfeaee.
simple	15-Nov-2024 14:07:50	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/.git'.
simple	15-Nov-2024 14:07:50	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1'...
simple	15-Nov-2024 14:07:50	done.
simple	15-Nov-2024 14:07:54	Switched to a new branch 'features/JAL-3914_modelqualityscores_v2115'
simple	15-Nov-2024 14:07:54	Branch features/JAL-3914_modelqualityscores_v2115 set up to track remote branch features/JAL-3914_modelqualityscores_v2115 from origin.
simple	15-Nov-2024 14:07:54	Updated source code to revision: 8dbe9206561daac950b4154da519d7aad4cfeaee
simple	15-Nov-2024 14:07:54	Finished task 'Checkout Default Repository' with result: Success
simple	15-Nov-2024 14:07:54	Running pre-build action: VCS Version Collector
simple	15-Nov-2024 14:07:54	Running pre-build action: Artifactory Release Staging
command	15-Nov-2024 14:07:54	Substituting variable: ${bamboo.planKey} with JB-GPC579
simple	15-Nov-2024 14:07:54	Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	15-Nov-2024 14:07:54	Bamboo Artifactory Plugin version: 2.6.2
command	15-Nov-2024 14:07:54	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - features-JAL-3914_modelqualityscores_v2115 - Default Job #1 (JB-GPC579-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC579 clean shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=features/JAL-3914_modelqualityscores_v2115\nbamboo_dependency_parent_0=JB-GDB646-1\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=features/JAL-3914_modelqualityscores_v2115\nbamboo_repository_revision_number=8dbe9206561daac950b4154da519d7aad4cfeaee\nbamboo_repository_46498210_name=Jalview Git\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC579-JOB1-1\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-GPC579-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GPC579-JOB1\nbamboo_shortPlanName=features-JAL-3914_modelqualityscores_v2115\nbamboo_repository_46498210_revision_number=8dbe9206561daac950b4154da519d7aad4cfeaee\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC579-JOB1-1\nbamboo_repository_46498210_git_branch=features/JAL-3914_modelqualityscores_v2115\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498210_git_username=\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - features-JAL-3914_modelqualityscores_v2115\nbamboo_shortPlanKey=GPC579\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=8dbe9206561daac950b4154da519d7aad4cfeaee\nbamboo_buildTimeStamp=2024-11-15T14:05:08.818Z\nbamboo_repository_git_branch=features/JAL-3914_modelqualityscores_v2115\nbamboo_buildResultKey=JB-GPC579-JOB1-1\nbamboo_repository_branch_name=features/JAL-3914_modelqualityscores_v2115\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - features-JAL-3914_modelqualityscores_v2115 - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498210_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_1_revision=8dbe9206561daac950b4154da519d7aad4cfeaee\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498210_branch_name=features/JAL-3914_modelqualityscores_v2115\nbamboo_repository_name=Jalview Git\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=features/JAL-3914_modelqualityscores_v2115\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=features/JAL-3914_modelqualityscores_v2115\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=features/JAL-3914_modelqualityscores_v2115\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-46302019\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=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1\nbamboo_planKey=JB-GPC579\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=features/JAL-3914_modelqualityscores_v2115\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	15-Nov-2024 14:07:55	
build	15-Nov-2024 14:07:55	> Configure project :
build	15-Nov-2024 14:07:55	Using properties from file './utils/channels/default/channel_gradle.properties'
build	15-Nov-2024 14:07:55	JALVIEW_VERSION is set to '2.11.4.2'
build	15-Nov-2024 14:07:55	HEADLESS BUILD
build	15-Nov-2024 14:07:55	J2S ENABLED
build	15-Nov-2024 14:07:55	Using a BUILD profile.
build	15-Nov-2024 14:07:55	eclipseDir exists
build	15-Nov-2024 14:07:55	
build	15-Nov-2024 14:07:55	> Task :clean
build	15-Nov-2024 14:07:55	> Task :cleanPackageDir UP-TO-DATE
build	15-Nov-2024 14:07:55	> Task :copyHelp
build	15-Nov-2024 14:07:58	> Task :buildIndices
build	15-Nov-2024 14:07:58	> Task :copyResources
build	15-Nov-2024 14:07:58	> Task :copyChannelResources
build	15-Nov-2024 14:07:58	
build	15-Nov-2024 14:07:58	> Task :createBuildProperties
build	15-Nov-2024 14:07:58	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	15-Nov-2024 14:07:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:07:58	
build	15-Nov-2024 14:07:58	> Task :buildResources
build	15-Nov-2024 14:07:58	> Task :copyDocs
build	15-Nov-2024 14:07:58	
build	15-Nov-2024 14:07:58	> Task :convertMdFiles
build	15-Nov-2024 14:07:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	15-Nov-2024 14:07:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	15-Nov-2024 14:07:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	15-Nov-2024 14:07:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/build/resources/doc_build/doc/building.html
build	15-Nov-2024 14:07:58	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	15-Nov-2024 14:07:58	
build	15-Nov-2024 14:07:58	> Task :releasesTemplates
build	15-Nov-2024 14:07:58	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	15-Nov-2024 14:07:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:07:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:07:58	Stripping rc/test/etc for 2_11_4_2
build	15-Nov-2024 14:07:58	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_2.md
build	15-Nov-2024 14:07:58	
build	15-Nov-2024 14:07:58	> Task :prepare
build	15-Nov-2024 14:08:00	
build	15-Nov-2024 14:08:00	> Task :compileJava
build	15-Nov-2024 14:08:00	Setting target compatibility to 11
error	15-Nov-2024 14:08:07	Note: Some input files use or override a deprecated API.
error	15-Nov-2024 14:08:07	Note: Recompile with -Xlint:deprecation for details.
error	15-Nov-2024 14:08:07	Note: Some input files use unchecked or unsafe operations.
error	15-Nov-2024 14:08:07	Note: Recompile with -Xlint:unchecked for details.
build	15-Nov-2024 14:08:08	
build	15-Nov-2024 14:08:08	> Task :processResources
build	15-Nov-2024 14:08:08	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	15-Nov-2024 14:08:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:08:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:08:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:08:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:08:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:08:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:08:08	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:08:08	
build	15-Nov-2024 14:08:08	> Task :classes
build	15-Nov-2024 14:08:10	
build	15-Nov-2024 14:08:10	> Task :compileLinkCheck
build	15-Nov-2024 14:08:10	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	15-Nov-2024 14:08:10	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:08:10	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:08:12	
build	15-Nov-2024 14:08:12	> Task :linkCheck
build	15-Nov-2024 14:08:12	Checking help file links
build	15-Nov-2024 14:10:19	
build	15-Nov-2024 14:10:19	Results:
build	15-Nov-2024 14:10:19	159 distinct help targets
build	15-Nov-2024 14:10:19	159 help mappings
build	15-Nov-2024 14:10:19	0 invalid targets
build	15-Nov-2024 14:10:19	32 unused targets
build	15-Nov-2024 14:10:19	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	15-Nov-2024 14:10:19	    overviewprefs: html/features/preferences.html#overview
build	15-Nov-2024 14:10:19	    cdnafeatures: html/features/codingfeatures.html
build	15-Nov-2024 14:10:19	    startupprefs: html/features/preferences.html#startup
build	15-Nov-2024 14:10:19	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	15-Nov-2024 14:10:19	    io.modellerpir: html/io/modellerpir.html
build	15-Nov-2024 14:10:19	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	15-Nov-2024 14:10:19	    pdbmcviewer: html/features/pdbviewer.html
build	15-Nov-2024 14:10:19	    workingwithpae: html/features/paematrices.html
build	15-Nov-2024 14:10:19	    groovy.colours: html/features/groovy.html#groovyColours
build	15-Nov-2024 14:10:19	    seqmappings: html/features/seqmappings.html
build	15-Nov-2024 14:10:19	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	15-Nov-2024 14:10:19	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	15-Nov-2024 14:10:19	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	15-Nov-2024 14:10:19	    search: html/features/search.html
build	15-Nov-2024 14:10:19	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	15-Nov-2024 14:10:19	    alformats: html/io/fileformats.html
build	15-Nov-2024 14:10:19	    strucprefs: html/features/preferences.html#structure
build	15-Nov-2024 14:10:19	    siftsmapping: html/features/siftsmapping.html
build	15-Nov-2024 14:10:19	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	15-Nov-2024 14:10:19	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	15-Nov-2024 14:10:19	    newkeys: html/features/newkeystrokes.html
build	15-Nov-2024 14:10:19	    importvcf.attribs: html/features/importvcf.html#attribs
build	15-Nov-2024 14:10:19	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	15-Nov-2024 14:10:19	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	15-Nov-2024 14:10:19	    jalarchive: html/features/jalarchive.html
build	15-Nov-2024 14:10:19	    newsreader: html/webServices/newsreader.html
build	15-Nov-2024 14:10:19	    jalviewcltool: html/features/commandline.html#script
build	15-Nov-2024 14:10:19	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	15-Nov-2024 14:10:19	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	15-Nov-2024 14:10:19	    paematrixformat: html/io/paematrixformat.html
build	15-Nov-2024 14:10:19	    overview: html/features/overview.html
build	15-Nov-2024 14:10:19	0 invalid map urls
build	15-Nov-2024 14:10:19	0 invalid image attributes
build	15-Nov-2024 14:10:19	506 internal href links (110 with anchors)
build	15-Nov-2024 14:10:19	0 invalid internal href links
build	15-Nov-2024 14:10:19	0 invalid internal anchor links
build	15-Nov-2024 14:10:19	112 external href links
build	15-Nov-2024 14:10:19	External links not verified as internet not available
build	15-Nov-2024 14:10:19	*** Success ***
build	15-Nov-2024 14:10:20	
build	15-Nov-2024 14:10:20	> Task :jar
build	15-Nov-2024 14:10:20	> Task :syncJars
build	15-Nov-2024 14:10:20	> Task :makeDist
build	15-Nov-2024 14:10:29	> Task :shadowJar
build	15-Nov-2024 14:10:29	
build	15-Nov-2024 14:10:29	> Task :getdownImagesCopy
build	15-Nov-2024 14:10:29	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	15-Nov-2024 14:10:29	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:29	
build	15-Nov-2024 14:10:29	> Task :getdownImagesProcess
build	15-Nov-2024 14:10:29	> Task :getdownImages
build	15-Nov-2024 14:10:29	> Task :getdownWebsiteBuild
build	15-Nov-2024 14:10:31	
build	15-Nov-2024 14:10:31	> Task :getdownDigest
build	15-Nov-2024 14:10:31	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
error	15-Nov-2024 14:10:31	2024/11/15 14:10:30:070 WARNING Starting without install4j classes
error	15-Nov-2024 14:10:31	2024/11/15 14:10:30:644 WARNING Starting without install4j classes
build	15-Nov-2024 14:10:31	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	15-Nov-2024 14:10:31	
build	15-Nov-2024 14:10:31	> Task :getdown
build	15-Nov-2024 14:10:31	
build	15-Nov-2024 14:10:31	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	15-Nov-2024 14:10:31	
build	15-Nov-2024 14:10:31	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	15-Nov-2024 14:10:31	
build	15-Nov-2024 14:10:31	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	15-Nov-2024 14:10:31	
build	15-Nov-2024 14:10:31	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	15-Nov-2024 14:10:31	Please consult deprecation warnings for more details.
build	15-Nov-2024 14:10:31	
build	15-Nov-2024 14:10:31	BUILD SUCCESSFUL in 2m 36s
build	15-Nov-2024 14:10:31	22 actionable tasks: 21 executed, 1 up-to-date
simple	15-Nov-2024 14:10:31	Finished task 'Jalview distribution for Java 11' with result: Success
command	15-Nov-2024 14:10:31	Substituting variable: ${bamboo.planKey} with JB-GPC579
simple	15-Nov-2024 14:10:31	Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	15-Nov-2024 14:10:31	Bamboo Artifactory Plugin version: 2.6.2
command	15-Nov-2024 14:10:31	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - features-JAL-3914_modelqualityscores_v2115 - Default Job #1 (JB-GPC579-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-GPC579 shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=features/JAL-3914_modelqualityscores_v2115\nbamboo_dependency_parent_0=JB-GDB646-1\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=features/JAL-3914_modelqualityscores_v2115\nbamboo_repository_revision_number=8dbe9206561daac950b4154da519d7aad4cfeaee\nbamboo_repository_46498210_name=Jalview Git\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC579-JOB1-1\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-GPC579-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GPC579-JOB1\nbamboo_shortPlanName=features-JAL-3914_modelqualityscores_v2115\nbamboo_repository_46498210_revision_number=8dbe9206561daac950b4154da519d7aad4cfeaee\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC579-JOB1-1\nbamboo_repository_46498210_git_branch=features/JAL-3914_modelqualityscores_v2115\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498210_git_username=\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - features-JAL-3914_modelqualityscores_v2115\nbamboo_shortPlanKey=GPC579\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=8dbe9206561daac950b4154da519d7aad4cfeaee\nbamboo_buildTimeStamp=2024-11-15T14:05:08.818Z\nbamboo_repository_git_branch=features/JAL-3914_modelqualityscores_v2115\nbamboo_buildResultKey=JB-GPC579-JOB1-1\nbamboo_repository_branch_name=features/JAL-3914_modelqualityscores_v2115\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - features-JAL-3914_modelqualityscores_v2115 - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498210_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_1_revision=8dbe9206561daac950b4154da519d7aad4cfeaee\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498210_branch_name=features/JAL-3914_modelqualityscores_v2115\nbamboo_repository_name=Jalview Git\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC579 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=features/JAL-3914_modelqualityscores_v2115\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=features/JAL-3914_modelqualityscores_v2115\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=features/JAL-3914_modelqualityscores_v2115\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-46302019\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=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1\nbamboo_planKey=JB-GPC579\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=features/JAL-3914_modelqualityscores_v2115\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	15-Nov-2024 14:10:32	
build	15-Nov-2024 14:10:32	> Configure project :
build	15-Nov-2024 14:10:32	Using properties from file './utils/channels/default/channel_gradle.properties'
build	15-Nov-2024 14:10:32	JALVIEW_VERSION is set to '2.11.4.2'
build	15-Nov-2024 14:10:32	HEADLESS BUILD
build	15-Nov-2024 14:10:32	J2S ENABLED
build	15-Nov-2024 14:10:32	Using a BUILD profile.
build	15-Nov-2024 14:10:32	eclipseDir exists
build	15-Nov-2024 14:10:32	
build	15-Nov-2024 14:10:32	> Task :copyHelp UP-TO-DATE
build	15-Nov-2024 14:10:33	> Task :buildIndices
build	15-Nov-2024 14:10:33	> Task :copyResources UP-TO-DATE
build	15-Nov-2024 14:10:33	> Task :copyChannelResources UP-TO-DATE
build	15-Nov-2024 14:10:33	
build	15-Nov-2024 14:10:33	> Task :createBuildProperties
build	15-Nov-2024 14:10:33	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	15-Nov-2024 14:10:33	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:33	
build	15-Nov-2024 14:10:33	> Task :buildResources
build	15-Nov-2024 14:10:33	> Task :copyDocs
build	15-Nov-2024 14:10:34	
build	15-Nov-2024 14:10:34	> Task :convertMdFiles
build	15-Nov-2024 14:10:34	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	15-Nov-2024 14:10:34	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	15-Nov-2024 14:10:34	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	15-Nov-2024 14:10:34	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/build/resources/doc_build/doc/building.html
build	15-Nov-2024 14:10:34	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	15-Nov-2024 14:10:34	
build	15-Nov-2024 14:10:34	> Task :releasesTemplates
build	15-Nov-2024 14:10:34	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	15-Nov-2024 14:10:34	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:34	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:34	Stripping rc/test/etc for 2_11_4_2
build	15-Nov-2024 14:10:34	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_2.md
build	15-Nov-2024 14:10:34	
build	15-Nov-2024 14:10:34	> Task :prepare
build	15-Nov-2024 14:10:36	
build	15-Nov-2024 14:10:36	> Task :compileJava
build	15-Nov-2024 14:10:36	Setting target compatibility to 1.8
error	15-Nov-2024 14:10:42	Note: Some input files use or override a deprecated API.
error	15-Nov-2024 14:10:42	Note: Recompile with -Xlint:deprecation for details.
error	15-Nov-2024 14:10:42	Note: Some input files use unchecked or unsafe operations.
error	15-Nov-2024 14:10:42	Note: Recompile with -Xlint:unchecked for details.
build	15-Nov-2024 14:10:44	
build	15-Nov-2024 14:10:44	> Task :processResources
build	15-Nov-2024 14:10:44	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	15-Nov-2024 14:10:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:44	
build	15-Nov-2024 14:10:44	> Task :classes
build	15-Nov-2024 14:10:44	> Task :cleanPackageDir
build	15-Nov-2024 14:10:46	
build	15-Nov-2024 14:10:46	> Task :compileLinkCheck
build	15-Nov-2024 14:10:46	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	15-Nov-2024 14:10:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:46	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:10:48	
build	15-Nov-2024 14:10:48	> Task :linkCheck
build	15-Nov-2024 14:10:48	Checking help file links
build	15-Nov-2024 14:12:53	
build	15-Nov-2024 14:12:53	Results:
build	15-Nov-2024 14:12:53	159 distinct help targets
build	15-Nov-2024 14:12:53	159 help mappings
build	15-Nov-2024 14:12:53	0 invalid targets
build	15-Nov-2024 14:12:53	32 unused targets
build	15-Nov-2024 14:12:53	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	15-Nov-2024 14:12:53	    overviewprefs: html/features/preferences.html#overview
build	15-Nov-2024 14:12:53	    cdnafeatures: html/features/codingfeatures.html
build	15-Nov-2024 14:12:53	    startupprefs: html/features/preferences.html#startup
build	15-Nov-2024 14:12:53	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	15-Nov-2024 14:12:53	    io.modellerpir: html/io/modellerpir.html
build	15-Nov-2024 14:12:53	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	15-Nov-2024 14:12:53	    pdbmcviewer: html/features/pdbviewer.html
build	15-Nov-2024 14:12:53	    workingwithpae: html/features/paematrices.html
build	15-Nov-2024 14:12:53	    groovy.colours: html/features/groovy.html#groovyColours
build	15-Nov-2024 14:12:53	    seqmappings: html/features/seqmappings.html
build	15-Nov-2024 14:12:53	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	15-Nov-2024 14:12:53	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	15-Nov-2024 14:12:53	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	15-Nov-2024 14:12:53	    search: html/features/search.html
build	15-Nov-2024 14:12:53	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	15-Nov-2024 14:12:53	    alformats: html/io/fileformats.html
build	15-Nov-2024 14:12:53	    strucprefs: html/features/preferences.html#structure
build	15-Nov-2024 14:12:53	    siftsmapping: html/features/siftsmapping.html
build	15-Nov-2024 14:12:53	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	15-Nov-2024 14:12:53	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	15-Nov-2024 14:12:53	    newkeys: html/features/newkeystrokes.html
build	15-Nov-2024 14:12:53	    importvcf.attribs: html/features/importvcf.html#attribs
build	15-Nov-2024 14:12:53	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	15-Nov-2024 14:12:53	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	15-Nov-2024 14:12:53	    jalarchive: html/features/jalarchive.html
build	15-Nov-2024 14:12:53	    newsreader: html/webServices/newsreader.html
build	15-Nov-2024 14:12:53	    jalviewcltool: html/features/commandline.html#script
build	15-Nov-2024 14:12:53	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	15-Nov-2024 14:12:53	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	15-Nov-2024 14:12:53	    paematrixformat: html/io/paematrixformat.html
build	15-Nov-2024 14:12:53	    overview: html/features/overview.html
build	15-Nov-2024 14:12:53	0 invalid map urls
build	15-Nov-2024 14:12:53	0 invalid image attributes
build	15-Nov-2024 14:12:53	506 internal href links (110 with anchors)
build	15-Nov-2024 14:12:53	0 invalid internal href links
build	15-Nov-2024 14:12:53	0 invalid internal anchor links
build	15-Nov-2024 14:12:53	112 external href links
build	15-Nov-2024 14:12:53	External links not verified as internet not available
build	15-Nov-2024 14:12:53	*** Success ***
build	15-Nov-2024 14:12:54	
build	15-Nov-2024 14:12:54	> Task :jar
build	15-Nov-2024 14:12:54	> Task :syncJars
build	15-Nov-2024 14:12:54	> Task :makeDist
build	15-Nov-2024 14:13:01	> Task :shadowJar
build	15-Nov-2024 14:13:01	
build	15-Nov-2024 14:13:01	> Task :getdownImagesCopy
build	15-Nov-2024 14:13:01	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	15-Nov-2024 14:13:01	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-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	15-Nov-2024 14:13:01	
build	15-Nov-2024 14:13:01	> Task :getdownImagesProcess
build	15-Nov-2024 14:13:01	> Task :getdownImages
build	15-Nov-2024 14:13:02	> Task :getdownWebsiteBuild
build	15-Nov-2024 14:13:03	
build	15-Nov-2024 14:13:03	> Task :getdownDigest
build	15-Nov-2024 14:13:03	Generating digest file './build/website/docroot/getdown/default/1.8/digest.txt'...
error	15-Nov-2024 14:13:03	2024/11/15 14:13:02:384 WARNING Starting without install4j classes
error	15-Nov-2024 14:13:03	2024/11/15 14:13:02:884 WARNING Starting without install4j classes
build	15-Nov-2024 14:13:03	Generating digest file './build/website/docroot/getdown/default/1.8/digest2.txt'...
build	15-Nov-2024 14:13:03	
build	15-Nov-2024 14:13:03	> Task :getdown
build	15-Nov-2024 14:13:03	
build	15-Nov-2024 14:13:03	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	15-Nov-2024 14:13:03	
build	15-Nov-2024 14:13:03	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	15-Nov-2024 14:13:03	
build	15-Nov-2024 14:13:03	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	15-Nov-2024 14:13:03	
build	15-Nov-2024 14:13:03	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	15-Nov-2024 14:13:03	Please consult deprecation warnings for more details.
build	15-Nov-2024 14:13:03	
build	15-Nov-2024 14:13:03	BUILD SUCCESSFUL in 2m 31s
build	15-Nov-2024 14:13:03	21 actionable tasks: 18 executed, 3 up-to-date
simple	15-Nov-2024 14:13:03	Finished task 'Jalview distribution for Java 8' with result: Success
simple	15-Nov-2024 14:13:03	Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled
simple	15-Nov-2024 14:13:03	Running post build plugin 'NCover Results Collector'
simple	15-Nov-2024 14:13:03	Running post build plugin 'Artifact Copier'
simple	15-Nov-2024 14:13:03	Publishing an artifact: Jalview executables
simple	15-Nov-2024 14:13:04	Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 182.2 ms
simple	15-Nov-2024 14:13:04	Publishing an artifact: install4j installers
error	15-Nov-2024 14:13:04	Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/build/install4j does not exist.
simple	15-Nov-2024 14:13:04	The artifact hasn't been successfully published after 101.5 μs
simple	15-Nov-2024 14:13:04	Publishing an artifact: getdown-channel
error	15-Nov-2024 14:13:04	Unable to publish artifact [getdown-channel]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/getdown/website does not exist.
simple	15-Nov-2024 14:13:04	The artifact hasn't been successfully published after 59.56 μs
simple	15-Nov-2024 14:13:04	Publishing an artifact: Jalview getdown launcher
error	15-Nov-2024 14:13:04	Unable to publish artifact [Jalview getdown launcher]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/getdown/files does not exist.
simple	15-Nov-2024 14:13:04	The artifact hasn't been successfully published after 41.49 μs
simple	15-Nov-2024 14:13:04	Publishing an artifact: getdown build for website
simple	15-Nov-2024 14:13:04	Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 287.4 ms
simple	15-Nov-2024 14:13:04	Publishing an artifact: getdown build for archive
error	15-Nov-2024 14:13:04	Unable to publish artifact [getdown build for archive]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC579-JOB1/build/website/docroot/old does not exist.
simple	15-Nov-2024 14:13:04	The artifact hasn't been successfully published after 114.3 μs
simple	15-Nov-2024 14:13:04	Running post build plugin 'Artifactory Release Management Staging'
simple	15-Nov-2024 14:13:04	Running post build plugin 'Artifactory Build Info Copier'
simple	15-Nov-2024 14:13:04	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	15-Nov-2024 14:13:04	Running post build plugin 'npm Cache Cleanup'
simple	15-Nov-2024 14:13:04	Running post build plugin 'Clover Results Collector'
simple	15-Nov-2024 14:13:04	Running post build plugin 'Docker Container Cleanup'
simple	15-Nov-2024 14:13:04	Finalising the build...
simple	15-Nov-2024 14:13:04	Stopping timer.
simple	15-Nov-2024 14:13:04	Build JB-GPC579-JOB1-1 completed.
simple	15-Nov-2024 14:13:04	Running on server: post build plugin 'NCover Results Collector'
simple	15-Nov-2024 14:13:04	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	15-Nov-2024 14:13:04	Running on server: post build plugin 'Clover Delta Calculator'
simple	15-Nov-2024 14:13:04	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	15-Nov-2024 14:13:04	All post build plugins have finished
simple	15-Nov-2024 14:13:04	Generating build results summary...
simple	15-Nov-2024 14:13:04	Saving build results to disk...
simple	15-Nov-2024 14:13:04	Logging substituted variables...
simple	15-Nov-2024 14:13:04	Indexing build results...
simple	15-Nov-2024 14:13:04	Finished building JB-GPC579-JOB1-1.