simple	11-Nov-2024 15:22:22	Build Jalview Builds - Getdown Plan Channel - features-JAL-4489_cluster_pca_and_pasimap - Default Job #1 (JB-GPC575-JOB1-1) started building on agent Default Agent
simple	11-Nov-2024 15:22:22	
simple	11-Nov-2024 15:22:22	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1
simple	11-Nov-2024 15:22:22	Executing build Jalview Builds - Getdown Plan Channel - features-JAL-4489_cluster_pca_and_pasimap - Default Job #1 (JB-GPC575-JOB1-1)
simple	11-Nov-2024 15:22:22	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	11-Nov-2024 15:22:22	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1
simple	11-Nov-2024 15:22:22	Updating source code to revision: f6be36d7152321642e41db9d8bdbd2580431541e
simple	11-Nov-2024 15:22:22	Fetching 'refs/heads/features/JAL-4489_cluster_pca_and_pasimap' from 'http://source.jalview.org/git/jalview.git'.
simple	11-Nov-2024 15:22:22	Checking out revision f6be36d7152321642e41db9d8bdbd2580431541e.
simple	11-Nov-2024 15:22:22	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/.git'.
simple	11-Nov-2024 15:22:22	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1'...
simple	11-Nov-2024 15:22:22	done.
simple	11-Nov-2024 15:22:33	Branch features/JAL-4489_cluster_pca_and_pasimap set up to track remote branch features/JAL-4489_cluster_pca_and_pasimap from origin.
simple	11-Nov-2024 15:22:33	Switched to a new branch 'features/JAL-4489_cluster_pca_and_pasimap'
simple	11-Nov-2024 15:22:33	Updated source code to revision: f6be36d7152321642e41db9d8bdbd2580431541e
simple	11-Nov-2024 15:22:33	Finished task 'Checkout Default Repository' with result: Success
simple	11-Nov-2024 15:22:33	Running pre-build action: VCS Version Collector
simple	11-Nov-2024 15:22:33	Running pre-build action: Artifactory Release Staging
command	11-Nov-2024 15:22:33	Substituting variable: ${bamboo.planKey} with JB-GPC575
simple	11-Nov-2024 15:22:33	Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	11-Nov-2024 15:22:33	Bamboo Artifactory Plugin version: 2.6.2
command	11-Nov-2024 15:22:33	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - features-JAL-4489_cluster_pca_and_pasimap - Default Job #1 (JB-GPC575-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC575 clean shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_dependency_parent_0=JB-GDB642-3\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-4489_cluster_pca_and_pasimap\nbamboo_repository_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC575-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_46498186_name=Jalview Git\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GPC575-JOB1\nbamboo_shortPlanName=features-JAL-4489_cluster_pca_and_pasimap\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-GPC575-JOB1-1\nbamboo_repository_46498186_git_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - features-JAL-4489_cluster_pca_and_pasimap\nbamboo_shortPlanKey=GPC575\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498186_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_buildTimeStamp=2024-11-11T15:22:22.027Z\nbamboo_repository_git_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_buildResultKey=JB-GPC575-JOB1-1\nbamboo_repository_branch_name=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - features-JAL-4489_cluster_pca_and_pasimap - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=f6be36d7152321642e41db9d8bdbd2580431541e\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\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-4489_cluster_pca_and_pasimap\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46498186_git_username=\nbamboo_planRepository_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=features/JAL-4489_cluster_pca_and_pasimap\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-46301971\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_repository_46498186_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\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_repository_46498186_branch_name=features/JAL-4489_cluster_pca_and_pasimap\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-GPC575-JOB1\nbamboo_planKey=JB-GPC575\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=features/JAL-4489_cluster_pca_and_pasimap\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	11-Nov-2024 15:22:35	
build	11-Nov-2024 15:22:35	> Configure project :
build	11-Nov-2024 15:22:35	Using properties from file './utils/channels/default/channel_gradle.properties'
build	11-Nov-2024 15:22:35	JALVIEW_VERSION is set to '2.11.4.1'
build	11-Nov-2024 15:22:35	HEADLESS BUILD
build	11-Nov-2024 15:22:35	J2S ENABLED
build	11-Nov-2024 15:22:35	Using a BUILD profile.
build	11-Nov-2024 15:22:35	eclipseDir exists
build	11-Nov-2024 15:22:36	
build	11-Nov-2024 15:22:36	> Task :clean
build	11-Nov-2024 15:22:36	> Task :cleanPackageDir UP-TO-DATE
build	11-Nov-2024 15:22:36	> Task :copyHelp
build	11-Nov-2024 15:22:38	> Task :buildIndices
build	11-Nov-2024 15:22:38	> Task :copyResources
build	11-Nov-2024 15:22:38	> Task :copyChannelResources
build	11-Nov-2024 15:22:38	
build	11-Nov-2024 15:22:38	> Task :createBuildProperties
build	11-Nov-2024 15:22:38	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:22:38	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:22:38	
build	11-Nov-2024 15:22:38	> Task :buildResources
build	11-Nov-2024 15:22:38	> Task :copyDocs
build	11-Nov-2024 15:22:39	
build	11-Nov-2024 15:22:39	> Task :convertMdFiles
build	11-Nov-2024 15:22:39	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	11-Nov-2024 15:22:39	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	11-Nov-2024 15:22:39	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	11-Nov-2024 15:22:39	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/build/resources/doc_build/doc/building.html
build	11-Nov-2024 15:22:39	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	11-Nov-2024 15:22:39	
build	11-Nov-2024 15:22:39	> Task :releasesTemplates
build	11-Nov-2024 15:22:39	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:22:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:22:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:22:39	Stripping rc/test/etc for 2_11_4_1
build	11-Nov-2024 15:22:39	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_1.md
build	11-Nov-2024 15:22:39	
build	11-Nov-2024 15:22:39	> Task :prepare
build	11-Nov-2024 15:22:41	
build	11-Nov-2024 15:22:41	> Task :compileJava
build	11-Nov-2024 15:22:41	Setting target compatibility to 11
error	11-Nov-2024 15:22:48	Note: Some input files use or override a deprecated API.
error	11-Nov-2024 15:22:48	Note: Recompile with -Xlint:deprecation for details.
error	11-Nov-2024 15:22:48	Note: Some input files use unchecked or unsafe operations.
error	11-Nov-2024 15:22:48	Note: Recompile with -Xlint:unchecked for details.
build	11-Nov-2024 15:22:48	
build	11-Nov-2024 15:22:48	> Task :processResources
build	11-Nov-2024 15:22:48	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:22:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:22:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:22:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:22:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:22:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:22:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:22:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:22:48	
build	11-Nov-2024 15:22:48	> Task :classes
build	11-Nov-2024 15:22:50	
build	11-Nov-2024 15:22:50	> Task :compileLinkCheck
build	11-Nov-2024 15:22:50	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:22:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:22:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:22:53	
build	11-Nov-2024 15:22:53	> Task :linkCheck
build	11-Nov-2024 15:22:53	Checking help file links
build	11-Nov-2024 15:25:00	
build	11-Nov-2024 15:25:00	Results:
build	11-Nov-2024 15:25:00	159 distinct help targets
build	11-Nov-2024 15:25:00	159 help mappings
build	11-Nov-2024 15:25:00	0 invalid targets
build	11-Nov-2024 15:25:00	32 unused targets
build	11-Nov-2024 15:25:00	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	11-Nov-2024 15:25:00	    overviewprefs: html/features/preferences.html#overview
build	11-Nov-2024 15:25:00	    cdnafeatures: html/features/codingfeatures.html
build	11-Nov-2024 15:25:00	    startupprefs: html/features/preferences.html#startup
build	11-Nov-2024 15:25:00	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	11-Nov-2024 15:25:00	    io.modellerpir: html/io/modellerpir.html
build	11-Nov-2024 15:25:00	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	11-Nov-2024 15:25:00	    pdbmcviewer: html/features/pdbviewer.html
build	11-Nov-2024 15:25:00	    workingwithpae: html/features/paematrices.html
build	11-Nov-2024 15:25:00	    groovy.colours: html/features/groovy.html#groovyColours
build	11-Nov-2024 15:25:00	    seqmappings: html/features/seqmappings.html
build	11-Nov-2024 15:25:00	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	11-Nov-2024 15:25:00	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	11-Nov-2024 15:25:00	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	11-Nov-2024 15:25:00	    search: html/features/search.html
build	11-Nov-2024 15:25:00	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	11-Nov-2024 15:25:00	    alformats: html/io/fileformats.html
build	11-Nov-2024 15:25:00	    strucprefs: html/features/preferences.html#structure
build	11-Nov-2024 15:25:00	    siftsmapping: html/features/siftsmapping.html
build	11-Nov-2024 15:25:00	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	11-Nov-2024 15:25:00	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	11-Nov-2024 15:25:00	    newkeys: html/features/newkeystrokes.html
build	11-Nov-2024 15:25:00	    importvcf.attribs: html/features/importvcf.html#attribs
build	11-Nov-2024 15:25:00	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	11-Nov-2024 15:25:00	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	11-Nov-2024 15:25:00	    jalarchive: html/features/jalarchive.html
build	11-Nov-2024 15:25:00	    newsreader: html/webServices/newsreader.html
build	11-Nov-2024 15:25:00	    jalviewcltool: html/features/commandline.html#script
build	11-Nov-2024 15:25:00	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	11-Nov-2024 15:25:00	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	11-Nov-2024 15:25:00	    paematrixformat: html/io/paematrixformat.html
build	11-Nov-2024 15:25:00	    overview: html/features/overview.html
build	11-Nov-2024 15:25:00	0 invalid map urls
build	11-Nov-2024 15:25:00	0 invalid image attributes
build	11-Nov-2024 15:25:00	508 internal href links (110 with anchors)
build	11-Nov-2024 15:25:00	0 invalid internal href links
build	11-Nov-2024 15:25:00	0 invalid internal anchor links
build	11-Nov-2024 15:25:00	113 external href links
build	11-Nov-2024 15:25:00	External links not verified as internet not available
build	11-Nov-2024 15:25:00	*** Success ***
build	11-Nov-2024 15:25:01	
build	11-Nov-2024 15:25:01	> Task :jar
build	11-Nov-2024 15:25:01	> Task :syncJars
build	11-Nov-2024 15:25:01	> Task :makeDist
build	11-Nov-2024 15:25:10	> Task :shadowJar
build	11-Nov-2024 15:25:11	
build	11-Nov-2024 15:25:11	> Task :getdownImagesCopy
build	11-Nov-2024 15:25:11	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:25:11	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:11	
build	11-Nov-2024 15:25:11	> Task :getdownImagesProcess
build	11-Nov-2024 15:25:11	> Task :getdownImages
build	11-Nov-2024 15:25:12	> Task :getdownWebsiteBuild
build	11-Nov-2024 15:25:13	
build	11-Nov-2024 15:25:13	> Task :getdownDigest
build	11-Nov-2024 15:25:13	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
build	11-Nov-2024 15:25:13	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	11-Nov-2024 15:25:13	
build	11-Nov-2024 15:25:13	> Task :getdown
build	11-Nov-2024 15:25:13	
build	11-Nov-2024 15:25:13	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	11-Nov-2024 15:25:13	
build	11-Nov-2024 15:25:13	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	11-Nov-2024 15:25:13	
build	11-Nov-2024 15:25:13	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	11-Nov-2024 15:25:13	
build	11-Nov-2024 15:25:13	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	11-Nov-2024 15:25:13	Please consult deprecation warnings for more details.
build	11-Nov-2024 15:25:13	
build	11-Nov-2024 15:25:13	BUILD SUCCESSFUL in 2m 40s
build	11-Nov-2024 15:25:13	22 actionable tasks: 21 executed, 1 up-to-date
error	11-Nov-2024 15:25:13	2024/11/11 15:25:12:344 WARNING Starting without install4j classes
error	11-Nov-2024 15:25:13	2024/11/11 15:25:12:902 WARNING Starting without install4j classes
simple	11-Nov-2024 15:25:13	Finished task 'Jalview distribution for Java 11' with result: Success
command	11-Nov-2024 15:25:13	Substituting variable: ${bamboo.planKey} with JB-GPC575
simple	11-Nov-2024 15:25:13	Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	11-Nov-2024 15:25:13	Bamboo Artifactory Plugin version: 2.6.2
command	11-Nov-2024 15:25:13	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - features-JAL-4489_cluster_pca_and_pasimap - Default Job #1 (JB-GPC575-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-GPC575 shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_dependency_parent_0=JB-GDB642-3\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-4489_cluster_pca_and_pasimap\nbamboo_repository_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC575-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_46498186_name=Jalview Git\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GPC575-JOB1\nbamboo_shortPlanName=features-JAL-4489_cluster_pca_and_pasimap\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-GPC575-JOB1-1\nbamboo_repository_46498186_git_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - features-JAL-4489_cluster_pca_and_pasimap\nbamboo_shortPlanKey=GPC575\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498186_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=f6be36d7152321642e41db9d8bdbd2580431541e\nbamboo_buildTimeStamp=2024-11-11T15:22:22.027Z\nbamboo_repository_git_branch=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_buildResultKey=JB-GPC575-JOB1-1\nbamboo_repository_branch_name=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - features-JAL-4489_cluster_pca_and_pasimap - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=f6be36d7152321642e41db9d8bdbd2580431541e\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\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-GPC575 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-4489_cluster_pca_and_pasimap\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46498186_git_username=\nbamboo_planRepository_branchDisplayName=features/JAL-4489_cluster_pca_and_pasimap\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=features/JAL-4489_cluster_pca_and_pasimap\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-46301971\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_repository_46498186_revision_number=f6be36d7152321642e41db9d8bdbd2580431541e\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_repository_46498186_branch_name=features/JAL-4489_cluster_pca_and_pasimap\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-GPC575-JOB1\nbamboo_planKey=JB-GPC575\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=features/JAL-4489_cluster_pca_and_pasimap\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	11-Nov-2024 15:25:14	
build	11-Nov-2024 15:25:14	> Configure project :
build	11-Nov-2024 15:25:14	Using properties from file './utils/channels/default/channel_gradle.properties'
build	11-Nov-2024 15:25:14	JALVIEW_VERSION is set to '2.11.4.1'
build	11-Nov-2024 15:25:14	HEADLESS BUILD
build	11-Nov-2024 15:25:14	J2S ENABLED
build	11-Nov-2024 15:25:14	Using a BUILD profile.
build	11-Nov-2024 15:25:14	eclipseDir exists
build	11-Nov-2024 15:25:15	
build	11-Nov-2024 15:25:15	> Task :copyHelp UP-TO-DATE
build	11-Nov-2024 15:25:16	> Task :buildIndices
build	11-Nov-2024 15:25:16	> Task :copyResources UP-TO-DATE
build	11-Nov-2024 15:25:16	> Task :copyChannelResources UP-TO-DATE
build	11-Nov-2024 15:25:16	
build	11-Nov-2024 15:25:16	> Task :createBuildProperties
build	11-Nov-2024 15:25:16	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:25:16	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:16	
build	11-Nov-2024 15:25:16	> Task :buildResources
build	11-Nov-2024 15:25:16	> Task :copyDocs
build	11-Nov-2024 15:25:16	
build	11-Nov-2024 15:25:16	> Task :convertMdFiles
build	11-Nov-2024 15:25:16	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	11-Nov-2024 15:25:16	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	11-Nov-2024 15:25:16	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	11-Nov-2024 15:25:16	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/build/resources/doc_build/doc/building.html
build	11-Nov-2024 15:25:16	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	11-Nov-2024 15:25:16	
build	11-Nov-2024 15:25:16	> Task :releasesTemplates
build	11-Nov-2024 15:25:16	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:25:16	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:16	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:16	Stripping rc/test/etc for 2_11_4_1
build	11-Nov-2024 15:25:16	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_1.md
build	11-Nov-2024 15:25:16	
build	11-Nov-2024 15:25:16	> Task :prepare
build	11-Nov-2024 15:25:18	
build	11-Nov-2024 15:25:18	> Task :compileJava
build	11-Nov-2024 15:25:18	Setting target compatibility to 1.8
error	11-Nov-2024 15:25:24	Note: Some input files use or override a deprecated API.
error	11-Nov-2024 15:25:24	Note: Recompile with -Xlint:deprecation for details.
error	11-Nov-2024 15:25:24	Note: Some input files use unchecked or unsafe operations.
error	11-Nov-2024 15:25:24	Note: Recompile with -Xlint:unchecked for details.
build	11-Nov-2024 15:25:27	
build	11-Nov-2024 15:25:27	> Task :processResources
build	11-Nov-2024 15:25:27	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:25:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:27	
build	11-Nov-2024 15:25:27	> Task :classes
build	11-Nov-2024 15:25:27	> Task :cleanPackageDir
build	11-Nov-2024 15:25:28	
build	11-Nov-2024 15:25:28	> Task :compileLinkCheck
build	11-Nov-2024 15:25:28	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:25:28	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:28	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:25:30	
build	11-Nov-2024 15:25:30	> Task :linkCheck
build	11-Nov-2024 15:25:30	Checking help file links
build	11-Nov-2024 15:27:35	
build	11-Nov-2024 15:27:35	Results:
build	11-Nov-2024 15:27:35	159 distinct help targets
build	11-Nov-2024 15:27:35	159 help mappings
build	11-Nov-2024 15:27:35	0 invalid targets
build	11-Nov-2024 15:27:35	32 unused targets
build	11-Nov-2024 15:27:35	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	11-Nov-2024 15:27:35	    overviewprefs: html/features/preferences.html#overview
build	11-Nov-2024 15:27:35	    cdnafeatures: html/features/codingfeatures.html
build	11-Nov-2024 15:27:35	    startupprefs: html/features/preferences.html#startup
build	11-Nov-2024 15:27:35	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	11-Nov-2024 15:27:35	    io.modellerpir: html/io/modellerpir.html
build	11-Nov-2024 15:27:35	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	11-Nov-2024 15:27:35	    pdbmcviewer: html/features/pdbviewer.html
build	11-Nov-2024 15:27:35	    workingwithpae: html/features/paematrices.html
build	11-Nov-2024 15:27:35	    groovy.colours: html/features/groovy.html#groovyColours
build	11-Nov-2024 15:27:35	    seqmappings: html/features/seqmappings.html
build	11-Nov-2024 15:27:35	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	11-Nov-2024 15:27:35	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	11-Nov-2024 15:27:35	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	11-Nov-2024 15:27:35	    search: html/features/search.html
build	11-Nov-2024 15:27:35	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	11-Nov-2024 15:27:35	    alformats: html/io/fileformats.html
build	11-Nov-2024 15:27:35	    strucprefs: html/features/preferences.html#structure
build	11-Nov-2024 15:27:35	    siftsmapping: html/features/siftsmapping.html
build	11-Nov-2024 15:27:35	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	11-Nov-2024 15:27:35	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	11-Nov-2024 15:27:35	    newkeys: html/features/newkeystrokes.html
build	11-Nov-2024 15:27:35	    importvcf.attribs: html/features/importvcf.html#attribs
build	11-Nov-2024 15:27:35	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	11-Nov-2024 15:27:35	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	11-Nov-2024 15:27:35	    jalarchive: html/features/jalarchive.html
build	11-Nov-2024 15:27:35	    newsreader: html/webServices/newsreader.html
build	11-Nov-2024 15:27:35	    jalviewcltool: html/features/commandline.html#script
build	11-Nov-2024 15:27:35	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	11-Nov-2024 15:27:35	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	11-Nov-2024 15:27:35	    paematrixformat: html/io/paematrixformat.html
build	11-Nov-2024 15:27:35	    overview: html/features/overview.html
build	11-Nov-2024 15:27:35	0 invalid map urls
build	11-Nov-2024 15:27:35	0 invalid image attributes
build	11-Nov-2024 15:27:35	508 internal href links (110 with anchors)
build	11-Nov-2024 15:27:35	0 invalid internal href links
build	11-Nov-2024 15:27:35	0 invalid internal anchor links
build	11-Nov-2024 15:27:35	113 external href links
build	11-Nov-2024 15:27:35	External links not verified as internet not available
build	11-Nov-2024 15:27:35	*** Success ***
build	11-Nov-2024 15:27:36	
build	11-Nov-2024 15:27:36	> Task :jar
build	11-Nov-2024 15:27:37	> Task :syncJars
build	11-Nov-2024 15:27:37	> Task :makeDist
build	11-Nov-2024 15:27:44	> Task :shadowJar
build	11-Nov-2024 15:27:44	
build	11-Nov-2024 15:27:44	> Task :getdownImagesCopy
build	11-Nov-2024 15:27:44	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	11-Nov-2024 15:27:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-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	11-Nov-2024 15:27:44	
build	11-Nov-2024 15:27:44	> Task :getdownImagesProcess
build	11-Nov-2024 15:27:44	> Task :getdownImages
build	11-Nov-2024 15:27:44	> Task :getdownWebsiteBuild
error	11-Nov-2024 15:27:46	2024/11/11 15:27:44:924 WARNING Starting without install4j classes
build	11-Nov-2024 15:27:46	
build	11-Nov-2024 15:27:46	> Task :getdownDigest
build	11-Nov-2024 15:27:46	Generating digest file './build/website/docroot/getdown/default/1.8/digest.txt'...
error	11-Nov-2024 15:27:46	2024/11/11 15:27:45:514 WARNING Starting without install4j classes
build	11-Nov-2024 15:27:46	Generating digest file './build/website/docroot/getdown/default/1.8/digest2.txt'...
build	11-Nov-2024 15:27:46	
build	11-Nov-2024 15:27:46	> Task :getdown
build	11-Nov-2024 15:27:46	
build	11-Nov-2024 15:27:46	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	11-Nov-2024 15:27:46	
build	11-Nov-2024 15:27:46	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	11-Nov-2024 15:27:46	
build	11-Nov-2024 15:27:46	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	11-Nov-2024 15:27:46	
build	11-Nov-2024 15:27:46	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	11-Nov-2024 15:27:46	Please consult deprecation warnings for more details.
build	11-Nov-2024 15:27:46	
build	11-Nov-2024 15:27:46	BUILD SUCCESSFUL in 2m 32s
build	11-Nov-2024 15:27:46	21 actionable tasks: 18 executed, 3 up-to-date
simple	11-Nov-2024 15:27:46	Finished task 'Jalview distribution for Java 8' with result: Success
simple	11-Nov-2024 15:27:46	Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled
simple	11-Nov-2024 15:27:46	Running post build plugin 'NCover Results Collector'
simple	11-Nov-2024 15:27:46	Running post build plugin 'Artifact Copier'
simple	11-Nov-2024 15:27:46	Publishing an artifact: Jalview executables
simple	11-Nov-2024 15:27:46	Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 157.6 ms
simple	11-Nov-2024 15:27:46	Publishing an artifact: install4j installers
error	11-Nov-2024 15:27:46	Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/build/install4j does not exist.
simple	11-Nov-2024 15:27:46	The artifact hasn't been successfully published after 1.373 ms
simple	11-Nov-2024 15:27:46	Publishing an artifact: getdown-channel
error	11-Nov-2024 15:27:46	Unable to publish artifact [getdown-channel]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/getdown/website does not exist.
simple	11-Nov-2024 15:27:46	The artifact hasn't been successfully published after 60.96 μs
simple	11-Nov-2024 15:27:46	Publishing an artifact: Jalview getdown launcher
error	11-Nov-2024 15:27:46	Unable to publish artifact [Jalview getdown launcher]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/getdown/files does not exist.
simple	11-Nov-2024 15:27:46	The artifact hasn't been successfully published after 41.36 μs
simple	11-Nov-2024 15:27:46	Publishing an artifact: getdown build for website
simple	11-Nov-2024 15:27:46	Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 306.0 ms
simple	11-Nov-2024 15:27:46	Publishing an artifact: getdown build for archive
error	11-Nov-2024 15:27:46	Unable to publish artifact [getdown build for archive]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC575-JOB1/build/website/docroot/old does not exist.
simple	11-Nov-2024 15:27:46	The artifact hasn't been successfully published after 104.3 μs
simple	11-Nov-2024 15:27:46	Running post build plugin 'Artifactory Release Management Staging'
simple	11-Nov-2024 15:27:46	Running post build plugin 'Artifactory Build Info Copier'
simple	11-Nov-2024 15:27:46	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	11-Nov-2024 15:27:46	Running post build plugin 'npm Cache Cleanup'
simple	11-Nov-2024 15:27:46	Running post build plugin 'Clover Results Collector'
simple	11-Nov-2024 15:27:46	Running post build plugin 'Docker Container Cleanup'
simple	11-Nov-2024 15:27:46	Finalising the build...
simple	11-Nov-2024 15:27:46	Stopping timer.
simple	11-Nov-2024 15:27:46	Build JB-GPC575-JOB1-1 completed.
simple	11-Nov-2024 15:27:46	Running on server: post build plugin 'NCover Results Collector'
simple	11-Nov-2024 15:27:46	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	11-Nov-2024 15:27:46	Running on server: post build plugin 'Clover Delta Calculator'
simple	11-Nov-2024 15:27:46	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	11-Nov-2024 15:27:46	All post build plugins have finished
simple	11-Nov-2024 15:27:46	Generating build results summary...
simple	11-Nov-2024 15:27:46	Saving build results to disk...
simple	11-Nov-2024 15:27:46	Logging substituted variables...
simple	11-Nov-2024 15:27:46	Indexing build results...
simple	11-Nov-2024 15:27:46	Finished building JB-GPC575-JOB1-1.