simple	21-Nov-2024 23:54:51	Build Jalview Builds - Getdown DEVELOP Launchers - JAL-4474_jalview.ps1_not_working - Default Job #2 (JB-GDL36-JOB1-2) started building on agent Default Agent
simple	21-Nov-2024 23:54:51	
simple	21-Nov-2024 23:54:51	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-JOB1
simple	21-Nov-2024 23:54:51	Executing build Jalview Builds - Getdown DEVELOP Launchers - JAL-4474_jalview.ps1_not_working - Default Job #2 (JB-GDL36-JOB1-2)
simple	21-Nov-2024 23:54:51	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	21-Nov-2024 23:54:51	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-JOB1
simple	21-Nov-2024 23:54:51	Updating source code to revision: 52750109fdb60b7b8d936d4624a8a39d5a722fb2
simple	21-Nov-2024 23:54:51	Fetching 'refs/heads/JAL-4474_jalview.ps1_not_working' from 'http://source.jalview.org/git/jalview.git'.
simple	21-Nov-2024 23:54:52	Checking out revision 52750109fdb60b7b8d936d4624a8a39d5a722fb2.
simple	21-Nov-2024 23:54:54	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164
simple	21-Nov-2024 23:54:54	   1da3b80..5275010  JAL-4474_jalview.ps1_not_working -> origin/JAL-4474_jalview.ps1_not_working
simple	21-Nov-2024 23:54:54	   946589c..72a0f1e  bug/JAL-4477_unmapped_filename_characters -> origin/bug/JAL-4477_unmapped_filename_characters
simple	21-Nov-2024 23:54:54	 * [new branch]      bug/JAL-4482_gradle_task_linkCheck_fails -> origin/bug/JAL-4482_gradle_task_linkCheck_fails
simple	21-Nov-2024 23:54:54	   9fb123c..544bd63  develop    -> origin/develop
simple	21-Nov-2024 23:54:54	 * [new branch]      experiment/JAL-4386_JAL-4435_with_HSB_colours -> origin/experiment/JAL-4386_JAL-4435_with_HSB_colours
simple	21-Nov-2024 23:54:54	 * [new branch]      experiment/JAL-4386_experimental_string_to_colour_scheme_methods -> origin/experiment/JAL-4386_experimental_string_to_colour_scheme_methods
simple	21-Nov-2024 23:54:54	   e1ff67b..1c79fdc  feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels
simple	21-Nov-2024 23:54:54	 * [new branch]      features/JAL-3914_modelqualityscores_v2115 -> origin/features/JAL-3914_modelqualityscores_v2115
simple	21-Nov-2024 23:54:54	 * [new branch]      features/JAL-4489_cluster_pca_and_pasimap -> origin/features/JAL-4489_cluster_pca_and_pasimap
simple	21-Nov-2024 23:54:54	 * [new branch]      features/JAL-4489_clustering_and_pca_pasimap_views -> origin/features/JAL-4489_clustering_and_pca_pasimap_views
simple	21-Nov-2024 23:54:54	 * [new branch]      improvement/JAL-4485_not_finding_chimerax_on_managed_desktop -> origin/improvement/JAL-4485_not_finding_chimerax_on_managed_desktop
simple	21-Nov-2024 23:54:54	 * [new branch]      patch/JAL-4077_jmolsaveloadwindows -> origin/patch/JAL-4077_jmolsaveloadwindows
simple	21-Nov-2024 23:54:54	 * [new branch]      spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure -> origin/spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure
simple	21-Nov-2024 23:55:02	Already on 'JAL-4474_jalview.ps1_not_working'
simple	21-Nov-2024 23:55:02	Your branch is behind 'origin/JAL-4474_jalview.ps1_not_working' by 7 commits, and can be fast-forwarded.
simple	21-Nov-2024 23:55:02	  (use "git pull" to update your local branch)
simple	21-Nov-2024 23:55:02	HEAD is now at 5275010 Merge branch 'bug/JAL-4477_unmapped_filename_characters' into JAL-4474_jalview.ps1_not_working
simple	21-Nov-2024 23:55:02	Updated source code to revision: 52750109fdb60b7b8d936d4624a8a39d5a722fb2
simple	21-Nov-2024 23:55:02	Finished task 'Checkout Default Repository' with result: Success
simple	21-Nov-2024 23:55:02	Running pre-build action: VCS Version Collector
simple	21-Nov-2024 23:55:02	Running pre-build action: Artifactory Release Staging
command	21-Nov-2024 23:55:02	Substituting variable: ${bamboo.planKey} with JB-GDL36
simple	21-Nov-2024 23:55:02	Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	21-Nov-2024 23:55:02	Bamboo Artifactory Plugin version: 2.6.2
command	21-Nov-2024 23:55:02	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - JAL-4474_jalview.ps1_not_working - Default Job #2 (JB-GDL36-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL36 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-JOB1\n ... using extra environment variables: \nbamboo_repository_46498163_name=Jalview Git\nbamboo_planRepository_1_branch=JAL-4474_jalview.ps1_not_working\nbamboo_dependency_parent_0=JB-GDB638-2\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=JAL-4474_jalview.ps1_not_working\nbamboo_repository_revision_number=52750109fdb60b7b8d936d4624a8a39d5a722fb2\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL36-JOB1-2\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL36-JOB1\nbamboo_shortPlanName=JAL-4474_jalview.ps1_not_working\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL36-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - JAL-4474_jalview.ps1_not_working\nbamboo_shortPlanKey=GDL36\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=52750109fdb60b7b8d936d4624a8a39d5a722fb2\nbamboo_buildTimeStamp=2024-11-21T23:54:51.131Z\nbamboo_repository_previous_revision_number=1da3b80194892879ba275911738cdb4372a29ad4\nbamboo_repository_git_branch=JAL-4474_jalview.ps1_not_working\nbamboo_buildResultKey=JB-GDL36-JOB1-2\nbamboo_repository_branch_name=JAL-4474_jalview.ps1_not_working\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - JAL-4474_jalview.ps1_not_working - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=52750109fdb60b7b8d936d4624a8a39d5a722fb2\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\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/\nbamboo_repository_46498163_revision_number=52750109fdb60b7b8d936d4624a8a39d5a722fb2\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=JAL-4474_jalview.ps1_not_working\nbamboo_repository_46498163_git_username=\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=JAL-4474_jalview.ps1_not_working\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=JAL-4474_jalview.ps1_not_working\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-46301925\nbamboo_repository_46498163_branch_name=JAL-4474_jalview.ps1_not_working\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\nbamboo_repository_46498163_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nUSER=bamboo\nbamboo_repository_46498163_git_branch=JAL-4474_jalview.ps1_not_working\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-GDL36-JOB1\nbamboo_planKey=JB-GDL36\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498163_previous_revision_number=1da3b80194892879ba275911738cdb4372a29ad4\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=JAL-4474_jalview.ps1_not_working\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	21-Nov-2024 23:55:05	
build	21-Nov-2024 23:55:05	> Configure project :
build	21-Nov-2024 23:55:05	Using properties from file './utils/channels/default/channel_gradle.properties'
build	21-Nov-2024 23:55:05	JALVIEW_VERSION is set to '2.11.4.1'
build	21-Nov-2024 23:55:05	HEADLESS BUILD
build	21-Nov-2024 23:55:05	J2S ENABLED
build	21-Nov-2024 23:55:05	Using a BUILD profile.
build	21-Nov-2024 23:55:05	eclipseDir exists
build	21-Nov-2024 23:55:06	
build	21-Nov-2024 23:55:06	> Task :clean
build	21-Nov-2024 23:55:06	> Task :cleanPackageDir
build	21-Nov-2024 23:55:06	> Task :getdownImagesCopy
build	21-Nov-2024 23:55:07	> Task :getdownImagesProcess
build	21-Nov-2024 23:55:07	> Task :getdownImages
build	21-Nov-2024 23:55:08	> Task :copyHelp
build	21-Nov-2024 23:55:12	> Task :buildIndices
build	21-Nov-2024 23:55:12	> Task :copyResources
build	21-Nov-2024 23:55:12	> Task :copyChannelResources
build	21-Nov-2024 23:55:12	
build	21-Nov-2024 23:55:12	> Task :createBuildProperties
build	21-Nov-2024 23:55:12	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	21-Nov-2024 23:55:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-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	21-Nov-2024 23:55:12	
build	21-Nov-2024 23:55:12	> Task :buildResources
build	21-Nov-2024 23:55:12	> Task :copyDocs
build	21-Nov-2024 23:55:12	
build	21-Nov-2024 23:55:12	> Task :convertMdFiles
build	21-Nov-2024 23:55:12	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	21-Nov-2024 23:55:12	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	21-Nov-2024 23:55:12	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	21-Nov-2024 23:55:12	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-JOB1/build/resources/doc_build/doc/building.html
build	21-Nov-2024 23:55:12	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	21-Nov-2024 23:55:13	
build	21-Nov-2024 23:55:13	> Task :releasesTemplates
build	21-Nov-2024 23:55:13	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	21-Nov-2024 23:55:13	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-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	21-Nov-2024 23:55:13	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-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	21-Nov-2024 23:55:13	Stripping rc/test/etc for 2_11_4_1
build	21-Nov-2024 23:55:13	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_1.md
build	21-Nov-2024 23:55:13	
build	21-Nov-2024 23:55:13	> Task :prepare
build	21-Nov-2024 23:55:15	
build	21-Nov-2024 23:55:15	> Task :compileJava
build	21-Nov-2024 23:55:15	Setting target compatibility to 11
error	21-Nov-2024 23:55:26	Note: Some input files use or override a deprecated API.
error	21-Nov-2024 23:55:26	Note: Recompile with -Xlint:deprecation for details.
error	21-Nov-2024 23:55:26	Note: Some input files use unchecked or unsafe operations.
error	21-Nov-2024 23:55:26	Note: Recompile with -Xlint:unchecked for details.
build	21-Nov-2024 23:55:27	
build	21-Nov-2024 23:55:27	> Task :processResources
build	21-Nov-2024 23:55:27	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	21-Nov-2024 23:55:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-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	21-Nov-2024 23:55:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-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	21-Nov-2024 23:55:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-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	21-Nov-2024 23:55:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-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	21-Nov-2024 23:55:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-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	21-Nov-2024 23:55:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-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	21-Nov-2024 23:55:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-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	21-Nov-2024 23:55:27	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-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	21-Nov-2024 23:55:27	
build	21-Nov-2024 23:55:27	> Task :classes
build	21-Nov-2024 23:55:29	
build	21-Nov-2024 23:55:29	> Task :compileLinkCheck
build	21-Nov-2024 23:55:29	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	21-Nov-2024 23:55:29	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-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	21-Nov-2024 23:55:29	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-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	21-Nov-2024 23:55:29	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-JOB1/utils'. 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	21-Nov-2024 23:55:31	
build	21-Nov-2024 23:55:31	> Task :linkCheck
build	21-Nov-2024 23:55:31	Checking help file links
build	21-Nov-2024 23:57:37	
build	21-Nov-2024 23:57:37	Results:
build	21-Nov-2024 23:57:37	159 distinct help targets
build	21-Nov-2024 23:57:37	159 help mappings
build	21-Nov-2024 23:57:37	0 invalid targets
build	21-Nov-2024 23:57:37	32 unused targets
build	21-Nov-2024 23:57:37	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	21-Nov-2024 23:57:37	    overviewprefs: html/features/preferences.html#overview
build	21-Nov-2024 23:57:37	    cdnafeatures: html/features/codingfeatures.html
build	21-Nov-2024 23:57:37	    startupprefs: html/features/preferences.html#startup
build	21-Nov-2024 23:57:37	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	21-Nov-2024 23:57:37	    io.modellerpir: html/io/modellerpir.html
build	21-Nov-2024 23:57:37	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	21-Nov-2024 23:57:37	    pdbmcviewer: html/features/pdbviewer.html
build	21-Nov-2024 23:57:37	    workingwithpae: html/features/paematrices.html
build	21-Nov-2024 23:57:37	    groovy.colours: html/features/groovy.html#groovyColours
build	21-Nov-2024 23:57:37	    seqmappings: html/features/seqmappings.html
build	21-Nov-2024 23:57:37	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	21-Nov-2024 23:57:37	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	21-Nov-2024 23:57:37	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	21-Nov-2024 23:57:37	    search: html/features/search.html
build	21-Nov-2024 23:57:37	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	21-Nov-2024 23:57:37	    alformats: html/io/fileformats.html
build	21-Nov-2024 23:57:37	    strucprefs: html/features/preferences.html#structure
build	21-Nov-2024 23:57:37	    siftsmapping: html/features/siftsmapping.html
build	21-Nov-2024 23:57:37	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	21-Nov-2024 23:57:37	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	21-Nov-2024 23:57:37	    newkeys: html/features/newkeystrokes.html
build	21-Nov-2024 23:57:37	    importvcf.attribs: html/features/importvcf.html#attribs
build	21-Nov-2024 23:57:37	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	21-Nov-2024 23:57:37	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	21-Nov-2024 23:57:37	    jalarchive: html/features/jalarchive.html
build	21-Nov-2024 23:57:37	    newsreader: html/webServices/newsreader.html
build	21-Nov-2024 23:57:37	    jalviewcltool: html/features/commandline.html#script
build	21-Nov-2024 23:57:37	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	21-Nov-2024 23:57:37	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	21-Nov-2024 23:57:37	    paematrixformat: html/io/paematrixformat.html
build	21-Nov-2024 23:57:37	    overview: html/features/overview.html
build	21-Nov-2024 23:57:37	0 invalid map urls
build	21-Nov-2024 23:57:37	0 invalid image attributes
build	21-Nov-2024 23:57:37	508 internal href links (110 with anchors)
build	21-Nov-2024 23:57:37	0 invalid internal href links
build	21-Nov-2024 23:57:37	0 invalid internal anchor links
build	21-Nov-2024 23:57:37	113 external href links
build	21-Nov-2024 23:57:37	External links not verified as internet not available
build	21-Nov-2024 23:57:37	*** Success ***
build	21-Nov-2024 23:57:38	
build	21-Nov-2024 23:57:38	> Task :jar
build	21-Nov-2024 23:57:39	> Task :syncJars
build	21-Nov-2024 23:57:39	> Task :makeDist
build	21-Nov-2024 23:57:39	> Task :getdownWebsiteBuild
build	21-Nov-2024 23:57:41	
build	21-Nov-2024 23:57:41	> Task :getdownDigest
build	21-Nov-2024 23:57:41	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
build	21-Nov-2024 23:57:41	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	21-Nov-2024 23:57:41	
build	21-Nov-2024 23:57:41	> Task :getdown
build	21-Nov-2024 23:57:41	
build	21-Nov-2024 23:57:41	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	21-Nov-2024 23:57:41	
build	21-Nov-2024 23:57:41	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	21-Nov-2024 23:57:41	
build	21-Nov-2024 23:57:41	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	21-Nov-2024 23:57:41	
build	21-Nov-2024 23:57:41	Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness.
build	21-Nov-2024 23:57:41	Please consult deprecation warnings for more details.
build	21-Nov-2024 23:57:41	
build	21-Nov-2024 23:57:41	BUILD SUCCESSFUL in 2m 38s
build	21-Nov-2024 23:57:41	21 actionable tasks: 21 executed
error	21-Nov-2024 23:57:41	2024/11/21 23:57:39:912 WARNING Starting without install4j classes
error	21-Nov-2024 23:57:41	2024/11/21 23:57:40:477 WARNING Starting without install4j classes
simple	21-Nov-2024 23:57:41	Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success
simple	21-Nov-2024 23:57:41	Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command	21-Nov-2024 23:57:41	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - JAL-4474_jalview.ps1_not_working - Default Job #2 (JB-GDL36-JOB1-2)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL36-JOB1-2-ScriptBuildTask-171218980929460023.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-JOB1\n ... using extra environment variables: \nbamboo_repository_46498163_name=Jalview Git\nbamboo_planRepository_1_branch=JAL-4474_jalview.ps1_not_working\nbamboo_dependency_parent_0=JB-GDB638-2\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=JAL-4474_jalview.ps1_not_working\nbamboo_repository_revision_number=52750109fdb60b7b8d936d4624a8a39d5a722fb2\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL36-JOB1-2\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL36-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL36-JOB1\nbamboo_shortPlanName=JAL-4474_jalview.ps1_not_working\nbamboo_planRepository_name=Jalview Git\nbamboo_buildNumber=2\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-GDL36-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - JAL-4474_jalview.ps1_not_working\nbamboo_shortPlanKey=GDL36\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=52750109fdb60b7b8d936d4624a8a39d5a722fb2\nbamboo_buildTimeStamp=2024-11-21T23:54:51.131Z\nbamboo_repository_previous_revision_number=1da3b80194892879ba275911738cdb4372a29ad4\nbamboo_repository_git_branch=JAL-4474_jalview.ps1_not_working\nbamboo_buildResultKey=JB-GDL36-JOB1-2\nbamboo_repository_branch_name=JAL-4474_jalview.ps1_not_working\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - JAL-4474_jalview.ps1_not_working - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=52750109fdb60b7b8d936d4624a8a39d5a722fb2\nbamboo_CHANNEL=DEVELOP\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-GDL36 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_repository_46498163_revision_number=52750109fdb60b7b8d936d4624a8a39d5a722fb2\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=JAL-4474_jalview.ps1_not_working\nbamboo_repository_46498163_git_username=\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=JAL-4474_jalview.ps1_not_working\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=JAL-4474_jalview.ps1_not_working\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-46301925\nbamboo_repository_46498163_branch_name=JAL-4474_jalview.ps1_not_working\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\nbamboo_repository_46498163_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_46498163_git_branch=JAL-4474_jalview.ps1_not_working\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-GDL36-JOB1\nbamboo_planKey=JB-GDL36\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498163_previous_revision_number=1da3b80194892879ba275911738cdb4372a29ad4\nbamboo_planRepository_1_branchName=JAL-4474_jalview.ps1_not_working\n
simple	21-Nov-2024 23:57:41	Finished task 'Copy JVL file and produce link in HTML' with result: Success
simple	21-Nov-2024 23:57:41	Running post build plugin 'NCover Results Collector'
simple	21-Nov-2024 23:57:41	Running post build plugin 'Artifact Copier'
simple	21-Nov-2024 23:57:41	Publishing an artifact: getdown
simple	21-Nov-2024 23:57:41	Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 106.8 ms
simple	21-Nov-2024 23:57:41	Running post build plugin 'Artifactory Release Management Staging'
simple	21-Nov-2024 23:57:41	Running post build plugin 'Artifactory Build Info Copier'
simple	21-Nov-2024 23:57:41	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	21-Nov-2024 23:57:41	Running post build plugin 'npm Cache Cleanup'
simple	21-Nov-2024 23:57:41	Running post build plugin 'Clover Results Collector'
simple	21-Nov-2024 23:57:41	Running post build plugin 'Docker Container Cleanup'
simple	21-Nov-2024 23:57:41	Finalising the build...
simple	21-Nov-2024 23:57:41	Stopping timer.
simple	21-Nov-2024 23:57:41	Build JB-GDL36-JOB1-2 completed.
simple	21-Nov-2024 23:57:41	Running on server: post build plugin 'NCover Results Collector'
simple	21-Nov-2024 23:57:41	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	21-Nov-2024 23:57:41	Running on server: post build plugin 'Clover Delta Calculator'
simple	21-Nov-2024 23:57:41	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	21-Nov-2024 23:57:41	All post build plugins have finished
simple	21-Nov-2024 23:57:41	Generating build results summary...
simple	21-Nov-2024 23:57:41	Saving build results to disk...
simple	21-Nov-2024 23:57:41	Logging substituted variables...
simple	21-Nov-2024 23:57:41	Indexing build results...
simple	21-Nov-2024 23:57:41	Finished building JB-GDL36-JOB1-2.