simple	21-Nov-2024 12:14:59	Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4477_unmapped_filename_characters - Default Job #4 (JB-GDL35-JOB1-4) started building on agent Default Agent
simple	21-Nov-2024 12:14:59	
simple	21-Nov-2024 12:14:59	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-JOB1
simple	21-Nov-2024 12:14:59	Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4477_unmapped_filename_characters - Default Job #4 (JB-GDL35-JOB1-4)
simple	21-Nov-2024 12:14:59	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	21-Nov-2024 12:14:59	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-JOB1
simple	21-Nov-2024 12:14:59	Updating source code to revision: 72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9
simple	21-Nov-2024 12:14:59	Fetching 'refs/heads/bug/JAL-4477_unmapped_filename_characters' from 'http://source.jalview.org/git/jalview.git'.
simple	21-Nov-2024 12:15:00	Checking out revision 72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9.
simple	21-Nov-2024 12:15:01	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164
simple	21-Nov-2024 12:15:01	   946589c..72a0f1e  bug/JAL-4477_unmapped_filename_characters -> origin/bug/JAL-4477_unmapped_filename_characters
simple	21-Nov-2024 12:15:01	 * [new branch]      JAL-4474_jalview.ps1_not_working -> origin/JAL-4474_jalview.ps1_not_working
simple	21-Nov-2024 12:15:01	 * [new branch]      bug/JAL-4482_gradle_task_linkCheck_fails -> origin/bug/JAL-4482_gradle_task_linkCheck_fails
simple	21-Nov-2024 12:15:01	   9fb123c..544bd63  develop    -> origin/develop
simple	21-Nov-2024 12:15:01	 * [new branch]      experiment/JAL-4386_JAL-4435_with_HSB_colours -> origin/experiment/JAL-4386_JAL-4435_with_HSB_colours
simple	21-Nov-2024 12:15:01	 * [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 12:15:01	   e1ff67b..1c79fdc  feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels
simple	21-Nov-2024 12:15:01	 * [new branch]      features/JAL-3914_modelqualityscores_v2115 -> origin/features/JAL-3914_modelqualityscores_v2115
simple	21-Nov-2024 12:15:01	 * [new branch]      features/JAL-4489_cluster_pca_and_pasimap -> origin/features/JAL-4489_cluster_pca_and_pasimap
simple	21-Nov-2024 12:15:01	 * [new branch]      features/JAL-4489_clustering_and_pca_pasimap_views -> origin/features/JAL-4489_clustering_and_pca_pasimap_views
simple	21-Nov-2024 12:15:01	 * [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 12:15:01	 * [new branch]      patch/JAL-4077_jmolsaveloadwindows -> origin/patch/JAL-4077_jmolsaveloadwindows
simple	21-Nov-2024 12:15:01	 * [new branch]      spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure -> origin/spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure
simple	21-Nov-2024 12:15:01	Your branch is behind 'origin/bug/JAL-4477_unmapped_filename_characters' by 17 commits, and can be fast-forwarded.
simple	21-Nov-2024 12:15:01	  (use "git pull" to update your local branch)
simple	21-Nov-2024 12:15:01	Already on 'bug/JAL-4477_unmapped_filename_characters'
simple	21-Nov-2024 12:15:01	HEAD is now at 72a0f1e JAL-4491 Allow getdown to download missing cert-chain certificates if not in the cacerts bundle (Jalview already does this). Recompile.
simple	21-Nov-2024 12:15:01	Updated source code to revision: 72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9
simple	21-Nov-2024 12:15:01	Finished task 'Checkout Default Repository' with result: Success
simple	21-Nov-2024 12:15:01	Running pre-build action: VCS Version Collector
simple	21-Nov-2024 12:15:01	Running pre-build action: Artifactory Release Staging
command	21-Nov-2024 12:15:01	Substituting variable: ${bamboo.planKey} with JB-GDL35
simple	21-Nov-2024 12:15:01	Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	21-Nov-2024 12:15:01	Bamboo Artifactory Plugin version: 2.6.2
command	21-Nov-2024 12:15:01	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4477_unmapped_filename_characters - Default Job #4 (JB-GDL35-JOB1-4)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL35 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4477_unmapped_filename_characters\nbamboo_dependency_parent_0=JB-GDB637-7\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=bug/JAL-4477_unmapped_filename_characters\nbamboo_repository_revision_number=72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL35-JOB1-4\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-GDL35-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL35-JOB1\nbamboo_shortPlanName=bug-JAL-4477_unmapped_filename_characters\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=4\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_46498156_git_branch=bug/JAL-4477_unmapped_filename_characters\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL35-JOB1-4\nbamboo_repository_46498156_previous_revision_number=946589ccc914b87a71083c00865593596f643b77\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498156_name=Jalview Git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4477_unmapped_filename_characters\nbamboo_shortPlanKey=GDL35\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498156_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=72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9\nbamboo_buildTimeStamp=2024-11-21T12:14:59.097Z\nbamboo_repository_previous_revision_number=946589ccc914b87a71083c00865593596f643b77\nbamboo_repository_git_branch=bug/JAL-4477_unmapped_filename_characters\nbamboo_buildResultKey=JB-GDL35-JOB1-4\nbamboo_repository_branch_name=bug/JAL-4477_unmapped_filename_characters\nbamboo_repository_46498156_git_username=\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4477_unmapped_filename_characters - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9\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/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46498156_branch_name=bug/JAL-4477_unmapped_filename_characters\nbamboo_planRepository_branch=bug/JAL-4477_unmapped_filename_characters\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=bug/JAL-4477_unmapped_filename_characters\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4477_unmapped_filename_characters\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-46301911\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-GDL35-JOB1\nbamboo_planKey=JB-GDL35\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498156_revision_number=72a0f1e4f4a4dd3e87e6b968fb704b2f61d145d9\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4477_unmapped_filename_characters\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 12:15:06	
build	21-Nov-2024 12:15:06	> Configure project :
build	21-Nov-2024 12:15:06	Using properties from file './utils/channels/default/channel_gradle.properties'
build	21-Nov-2024 12:15:06	JALVIEW_VERSION is set to '2.11.4.2'
build	21-Nov-2024 12:15:06	HEADLESS BUILD
build	21-Nov-2024 12:15:06	J2S ENABLED
build	21-Nov-2024 12:15:06	Using a BUILD profile.
build	21-Nov-2024 12:15:06	eclipseDir exists
build	21-Nov-2024 12:15:06	
build	21-Nov-2024 12:15:06	> Task :clean
build	21-Nov-2024 12:15:06	> Task :cleanPackageDir
build	21-Nov-2024 12:15:06	> Task :getdownImagesCopy
build	21-Nov-2024 12:15:07	> Task :getdownImagesProcess
build	21-Nov-2024 12:15:07	> Task :getdownImages
build	21-Nov-2024 12:15:08	> Task :copyHelp
build	21-Nov-2024 12:15:11	> Task :buildIndices
build	21-Nov-2024 12:15:12	> Task :copyResources
build	21-Nov-2024 12:15:12	> Task :copyChannelResources
build	21-Nov-2024 12:15:12	
build	21-Nov-2024 12:15:12	> Task :createBuildProperties
build	21-Nov-2024 12:15:12	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	21-Nov-2024 12:15:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:12	
build	21-Nov-2024 12:15:12	> Task :buildResources
build	21-Nov-2024 12:15:12	> Task :copyDocs
build	21-Nov-2024 12:15:12	
build	21-Nov-2024 12:15:12	> Task :convertMdFiles
build	21-Nov-2024 12:15:12	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	21-Nov-2024 12:15:12	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	21-Nov-2024 12:15:12	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	21-Nov-2024 12:15:12	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-JOB1/build/resources/doc_build/doc/building.html
build	21-Nov-2024 12:15:12	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	21-Nov-2024 12:15:12	
build	21-Nov-2024 12:15:12	> Task :releasesTemplates
build	21-Nov-2024 12:15:12	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	21-Nov-2024 12:15:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:12	Stripping rc/test/etc for 2_11_4_2
build	21-Nov-2024 12:15:12	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_2.md
build	21-Nov-2024 12:15:12	
build	21-Nov-2024 12:15:12	> Task :prepare
build	21-Nov-2024 12:15:14	
build	21-Nov-2024 12:15:14	> Task :compileJava
build	21-Nov-2024 12:15:14	Setting target compatibility to 11
error	21-Nov-2024 12:15:24	Note: Some input files use or override a deprecated API.
error	21-Nov-2024 12:15:24	Note: Recompile with -Xlint:deprecation for details.
error	21-Nov-2024 12:15:24	Note: Some input files use unchecked or unsafe operations.
error	21-Nov-2024 12:15:24	Note: Recompile with -Xlint:unchecked for details.
build	21-Nov-2024 12:15:24	
build	21-Nov-2024 12:15:24	> Task :processResources
build	21-Nov-2024 12:15:24	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	21-Nov-2024 12:15:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:24	
build	21-Nov-2024 12:15:24	> Task :classes
build	21-Nov-2024 12:15:26	
build	21-Nov-2024 12:15:26	> Task :compileLinkCheck
build	21-Nov-2024 12:15:26	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	21-Nov-2024 12:15:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-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 12:15:28	
build	21-Nov-2024 12:15:28	> Task :linkCheck
build	21-Nov-2024 12:15:28	Checking help file links
build	21-Nov-2024 12:17:33	Invalid anchor: experimental at line 92 of /help/html/menus/desktopMenu.html
build	21-Nov-2024 12:17:34	
build	21-Nov-2024 12:17:34	Results:
build	21-Nov-2024 12:17:34	159 distinct help targets
build	21-Nov-2024 12:17:34	159 help mappings
build	21-Nov-2024 12:17:34	0 invalid targets
build	21-Nov-2024 12:17:34	32 unused targets
build	21-Nov-2024 12:17:34	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	21-Nov-2024 12:17:34	    overviewprefs: html/features/preferences.html#overview
build	21-Nov-2024 12:17:34	    cdnafeatures: html/features/codingfeatures.html
build	21-Nov-2024 12:17:34	    startupprefs: html/features/preferences.html#startup
build	21-Nov-2024 12:17:34	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	21-Nov-2024 12:17:34	    io.modellerpir: html/io/modellerpir.html
error	21-Nov-2024 12:17:34	
build	21-Nov-2024 12:17:34	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
error	21-Nov-2024 12:17:34	FAILURE: Build failed with an exception.
build	21-Nov-2024 12:17:34	    pdbmcviewer: html/features/pdbviewer.html
error	21-Nov-2024 12:17:34	
build	21-Nov-2024 12:17:34	    workingwithpae: html/features/paematrices.html
error	21-Nov-2024 12:17:34	* What went wrong:
error	21-Nov-2024 12:17:34	Execution failed for task ':linkCheck'.
error	21-Nov-2024 12:17:34	> Process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' finished with non-zero exit value 1
error	21-Nov-2024 12:17:34	
error	21-Nov-2024 12:17:34	* Try:
error	21-Nov-2024 12:17:34	> Run with --stacktrace option to get the stack trace.
build	21-Nov-2024 12:17:34	    groovy.colours: html/features/groovy.html#groovyColours
build	21-Nov-2024 12:17:34	    seqmappings: html/features/seqmappings.html
build	21-Nov-2024 12:17:34	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	21-Nov-2024 12:17:34	    splitframe.mirrorfonts: html/features/splitView.html#mirror
error	21-Nov-2024 12:17:34	> Run with --info or --debug option to get more log output.
error	21-Nov-2024 12:17:34	> Run with --scan to get full insights.
error	21-Nov-2024 12:17:34	
build	21-Nov-2024 12:17:34	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	21-Nov-2024 12:17:34	    search: html/features/search.html
build	21-Nov-2024 12:17:34	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
error	21-Nov-2024 12:17:34	* Get more help at https://help.gradle.org
error	21-Nov-2024 12:17:34	
error	21-Nov-2024 12:17:34	BUILD FAILED in 2m 32s
build	21-Nov-2024 12:17:34	    alformats: html/io/fileformats.html
build	21-Nov-2024 12:17:34	    strucprefs: html/features/preferences.html#structure
build	21-Nov-2024 12:17:34	    siftsmapping: html/features/siftsmapping.html
build	21-Nov-2024 12:17:34	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	21-Nov-2024 12:17:34	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	21-Nov-2024 12:17:34	    newkeys: html/features/newkeystrokes.html
build	21-Nov-2024 12:17:34	    importvcf.attribs: html/features/importvcf.html#attribs
build	21-Nov-2024 12:17:34	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	21-Nov-2024 12:17:34	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	21-Nov-2024 12:17:34	    jalarchive: html/features/jalarchive.html
build	21-Nov-2024 12:17:34	    newsreader: html/webServices/newsreader.html
build	21-Nov-2024 12:17:34	    jalviewcltool: html/features/commandline.html#script
build	21-Nov-2024 12:17:34	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	21-Nov-2024 12:17:34	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	21-Nov-2024 12:17:34	    paematrixformat: html/io/paematrixformat.html
build	21-Nov-2024 12:17:34	    overview: html/features/overview.html
build	21-Nov-2024 12:17:34	0 invalid map urls
build	21-Nov-2024 12:17:34	0 invalid image attributes
build	21-Nov-2024 12:17:34	506 internal href links (110 with anchors)
build	21-Nov-2024 12:17:34	0 invalid internal href links
build	21-Nov-2024 12:17:34	1 invalid internal anchor links
build	21-Nov-2024 12:17:34	112 external href links
build	21-Nov-2024 12:17:34	External links not verified as internet not available
build	21-Nov-2024 12:17:34	*** Failed ***
build	21-Nov-2024 12:17:34	
build	21-Nov-2024 12:17:34	> Task :linkCheck FAILED
build	21-Nov-2024 12:17:34	
build	21-Nov-2024 12:17:34	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	21-Nov-2024 12:17:34	
build	21-Nov-2024 12:17:34	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 12:17:34	
build	21-Nov-2024 12:17:34	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	21-Nov-2024 12:17:34	
build	21-Nov-2024 12:17:34	Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness.
build	21-Nov-2024 12:17:34	Please consult deprecation warnings for more details.
build	21-Nov-2024 12:17:34	16 actionable tasks: 16 executed
simple	21-Nov-2024 12:17:34	
simple	21-Nov-2024 12:17:34	Failing task since return code of [/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL35 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown] was 1 while expected 0
simple	21-Nov-2024 12:17:34	Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Failed
simple	21-Nov-2024 12:17:34	Running post build plugin 'NCover Results Collector'
simple	21-Nov-2024 12:17:34	Running post build plugin 'Artifact Copier'
simple	21-Nov-2024 12:17:34	Publishing an artifact: getdown
error	21-Nov-2024 12:17:34	Unable to publish artifact [getdown]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL35-JOB1/build/website/docroot/getdown/default/11 does not exist.
simple	21-Nov-2024 12:17:34	The artifact hasn't been successfully published after 2.306 ms
simple	21-Nov-2024 12:17:34	Running post build plugin 'Artifactory Release Management Staging'
simple	21-Nov-2024 12:17:34	Running post build plugin 'Artifactory Build Info Copier'
simple	21-Nov-2024 12:17:34	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	21-Nov-2024 12:17:34	Running post build plugin 'npm Cache Cleanup'
simple	21-Nov-2024 12:17:34	Running post build plugin 'Clover Results Collector'
simple	21-Nov-2024 12:17:34	Running post build plugin 'Docker Container Cleanup'
simple	21-Nov-2024 12:17:34	Finalising the build...
simple	21-Nov-2024 12:17:34	Stopping timer.
simple	21-Nov-2024 12:17:34	Build JB-GDL35-JOB1-4 completed.
simple	21-Nov-2024 12:17:34	Running on server: post build plugin 'NCover Results Collector'
simple	21-Nov-2024 12:17:34	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	21-Nov-2024 12:17:34	Running on server: post build plugin 'Clover Delta Calculator'
simple	21-Nov-2024 12:17:34	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	21-Nov-2024 12:17:34	All post build plugins have finished
simple	21-Nov-2024 12:17:34	Generating build results summary...
simple	21-Nov-2024 12:17:34	Saving build results to disk...
simple	21-Nov-2024 12:17:34	Logging substituted variables...
simple	21-Nov-2024 12:17:34	Indexing build results...
simple	21-Nov-2024 12:17:34	Finished building JB-GDL35-JOB1-4.