simple	27-Nov-2025 17:35:16	Build Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job #1 (JB-GPC654-JOB1-1) started building on agent Default Agent
simple	27-Nov-2025 17:35:16	
simple	27-Nov-2025 17:35:16	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1
simple	27-Nov-2025 17:35:16	Executing build Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job #1 (JB-GPC654-JOB1-1)
simple	27-Nov-2025 17:35:16	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	27-Nov-2025 17:35:16	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1
simple	27-Nov-2025 17:35:16	Updating source code to revision: acbb7d39481e53918a63f69cd008b4f6bbd7a588
simple	27-Nov-2025 17:35:16	Fetching 'refs/heads/bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	27-Nov-2025 17:35:16	Checking out revision acbb7d39481e53918a63f69cd008b4f6bbd7a588.
simple	27-Nov-2025 17:35:16	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/.git'.
simple	27-Nov-2025 17:35:16	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1'...
simple	27-Nov-2025 17:35:16	done.
simple	27-Nov-2025 17:35:24	Switched to a new branch 'bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus'
simple	27-Nov-2025 17:35:24	Branch bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus set up to track remote branch bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus from origin.
simple	27-Nov-2025 17:35:24	Updated source code to revision: acbb7d39481e53918a63f69cd008b4f6bbd7a588
simple	27-Nov-2025 17:35:24	Finished task 'Checkout Default Repository' with result: Success
simple	27-Nov-2025 17:35:24	Running pre-build action: VCS Version Collector
simple	27-Nov-2025 17:35:24	Running pre-build action: Artifactory Release Staging
command	27-Nov-2025 17:35:24	Substituting variable: ${bamboo.planKey} with JB-GPC654
simple	27-Nov-2025 17:35:24	Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	27-Nov-2025 17:35:24	Bamboo Artifactory Plugin version: 2.6.2
command	27-Nov-2025 17:35:25	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job #1 (JB-GPC654-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC654 clean shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_dependency_parent_0=JB-GDB729-5\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-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_repository_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC654-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GPC654-JOB1\nbamboo_shortPlanName=bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_46498600_name=Jalview Gitlab\nbamboo_repository_46498600_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC654-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_shortPlanKey=GPC654\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_buildTimeStamp=2025-11-27T17:19:12.535Z\nbamboo_repository_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_buildResultKey=JB-GPC654-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\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=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_46498600_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_planRepository_1_type=gitv2\nbamboo_repository_46498600_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_planRepository_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\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_repository_46498600_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_plan_storageTag=plan-46302771\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=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1\nbamboo_planKey=JB-GPC654\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498600_git_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	27-Nov-2025 17:35:27	
build	27-Nov-2025 17:35:27	> Configure project :
build	27-Nov-2025 17:35:27	Using properties from file './utils/channels/default/channel_gradle.properties'
build	27-Nov-2025 17:35:27	JALVIEW_VERSION is set to '2.11.5.1'
build	27-Nov-2025 17:35:27	HEADLESS BUILD
build	27-Nov-2025 17:35:27	J2S ENABLED
build	27-Nov-2025 17:35:27	Using a BUILD profile.
build	27-Nov-2025 17:35:27	eclipseDir exists
build	27-Nov-2025 17:35:27	
build	27-Nov-2025 17:35:27	> Task :clean
build	27-Nov-2025 17:35:27	> Task :cleanPackageDir UP-TO-DATE
build	27-Nov-2025 17:35:27	> Task :copyHelp
build	27-Nov-2025 17:35:29	> Task :buildIndices
build	27-Nov-2025 17:35:29	> Task :copyResources
build	27-Nov-2025 17:35:29	> Task :copyChannelResources
build	27-Nov-2025 17:35:29	
build	27-Nov-2025 17:35:29	> Task :createBuildProperties
build	27-Nov-2025 17:35:29	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:35:29	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:35:29	
build	27-Nov-2025 17:35:29	> Task :buildResources
build	27-Nov-2025 17:35:29	> Task :copyDocs
build	27-Nov-2025 17:35:29	
build	27-Nov-2025 17:35:29	> Task :convertMdFiles
build	27-Nov-2025 17:35:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	27-Nov-2025 17:35:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	27-Nov-2025 17:35:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	27-Nov-2025 17:35:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/building.html
build	27-Nov-2025 17:35:29	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	27-Nov-2025 17:35:31	
build	27-Nov-2025 17:35:31	> Task :releasesTemplates
build	27-Nov-2025 17:35:31	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:35:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:35:31	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:35:31	Stripping rc/test/etc for 2_11_5_1
build	27-Nov-2025 17:35:31	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md
build	27-Nov-2025 17:35:31	
build	27-Nov-2025 17:35:31	> Task :prepare
build	27-Nov-2025 17:35:32	
build	27-Nov-2025 17:35:32	> Task :compileJava
build	27-Nov-2025 17:35:32	Setting target compatibility to 11
build	27-Nov-2025 17:35:39	
build	27-Nov-2025 17:35:39	> Task :processResources
build	27-Nov-2025 17:35:39	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:35:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:35:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:35:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:35:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:35:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:35:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:35:39	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:35:39	
build	27-Nov-2025 17:35:39	> Task :classes
error	27-Nov-2025 17:35:39	Note: Some input files use or override a deprecated API.
error	27-Nov-2025 17:35:39	Note: Recompile with -Xlint:deprecation for details.
error	27-Nov-2025 17:35:39	Note: Some input files use unchecked or unsafe operations.
error	27-Nov-2025 17:35:39	Note: Recompile with -Xlint:unchecked for details.
build	27-Nov-2025 17:35:41	
build	27-Nov-2025 17:35:41	> Task :compileLinkCheck
build	27-Nov-2025 17:35:41	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:35:41	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:35:41	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:35:45	
build	27-Nov-2025 17:35:45	> Task :linkCheck
build	27-Nov-2025 17:35:45	Checking help file links
build	27-Nov-2025 17:37:51	
build	27-Nov-2025 17:37:51	Results:
build	27-Nov-2025 17:37:51	161 distinct help targets
build	27-Nov-2025 17:37:51	161 help mappings
build	27-Nov-2025 17:37:51	0 invalid targets
build	27-Nov-2025 17:37:51	31 unused targets
build	27-Nov-2025 17:37:52	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	27-Nov-2025 17:37:52	    overviewprefs: html/features/preferences.html#overview
build	27-Nov-2025 17:37:52	    cdnafeatures: html/features/codingfeatures.html
build	27-Nov-2025 17:37:52	    startupprefs: html/features/preferences.html#startup
build	27-Nov-2025 17:37:52	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	27-Nov-2025 17:37:52	    io.modellerpir: html/io/modellerpir.html
build	27-Nov-2025 17:37:52	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	27-Nov-2025 17:37:52	    pdbmcviewer: html/features/pdbviewer.html
build	27-Nov-2025 17:37:52	    groovy.colours: html/features/groovy.html#groovyColours
build	27-Nov-2025 17:37:52	    seqmappings: html/features/seqmappings.html
build	27-Nov-2025 17:37:52	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	27-Nov-2025 17:37:52	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	27-Nov-2025 17:37:52	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	27-Nov-2025 17:37:52	    search: html/features/search.html
build	27-Nov-2025 17:37:52	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	27-Nov-2025 17:37:52	    alformats: html/io/fileformats.html
build	27-Nov-2025 17:37:52	    strucprefs: html/features/preferences.html#structure
build	27-Nov-2025 17:37:52	    siftsmapping: html/features/siftsmapping.html
build	27-Nov-2025 17:37:52	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	27-Nov-2025 17:37:52	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	27-Nov-2025 17:37:52	    newkeys: html/features/newkeystrokes.html
build	27-Nov-2025 17:37:52	    importvcf.attribs: html/features/importvcf.html#attribs
build	27-Nov-2025 17:37:52	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	27-Nov-2025 17:37:52	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	27-Nov-2025 17:37:52	    jalarchive: html/features/jalarchive.html
build	27-Nov-2025 17:37:52	    newsreader: html/webServices/newsreader.html
build	27-Nov-2025 17:37:52	    jalviewcltool: html/features/commandline.html#script
build	27-Nov-2025 17:37:52	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	27-Nov-2025 17:37:52	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	27-Nov-2025 17:37:52	    paematrixformat: html/io/paematrixformat.html
build	27-Nov-2025 17:37:52	    overview: html/features/overview.html
build	27-Nov-2025 17:37:52	0 invalid map urls
build	27-Nov-2025 17:37:52	0 invalid image attributes
build	27-Nov-2025 17:37:52	520 internal href links (120 with anchors)
build	27-Nov-2025 17:37:52	0 invalid internal href links
build	27-Nov-2025 17:37:52	0 invalid internal anchor links
build	27-Nov-2025 17:37:52	112 external href links
build	27-Nov-2025 17:37:52	External links not verified as internet not available
build	27-Nov-2025 17:37:52	*** Success ***
build	27-Nov-2025 17:37:53	
build	27-Nov-2025 17:37:53	> Task :jar
build	27-Nov-2025 17:37:53	> Task :syncJars
build	27-Nov-2025 17:37:53	> Task :makeDist
build	27-Nov-2025 17:38:02	> Task :shadowJar
build	27-Nov-2025 17:38:02	
build	27-Nov-2025 17:38:02	> Task :getdownImagesCopy
build	27-Nov-2025 17:38:02	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:38:02	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:02	
build	27-Nov-2025 17:38:02	> Task :getdownImagesProcess
build	27-Nov-2025 17:38:02	> Task :getdownImages
build	27-Nov-2025 17:38:03	> Task :getdownWebsiteBuild
build	27-Nov-2025 17:38:04	
build	27-Nov-2025 17:38:04	> Task :getdownDigest
build	27-Nov-2025 17:38:04	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
build	27-Nov-2025 17:38:04	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	27-Nov-2025 17:38:04	
build	27-Nov-2025 17:38:04	> Task :getdown
build	27-Nov-2025 17:38:04	
build	27-Nov-2025 17:38:04	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	27-Nov-2025 17:38:04	
build	27-Nov-2025 17:38:04	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	27-Nov-2025 17:38:04	
build	27-Nov-2025 17:38:04	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	27-Nov-2025 17:38:04	
build	27-Nov-2025 17:38:04	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	27-Nov-2025 17:38:04	Please consult deprecation warnings for more details.
build	27-Nov-2025 17:38:04	
build	27-Nov-2025 17:38:04	BUILD SUCCESSFUL in 2m 39s
build	27-Nov-2025 17:38:04	22 actionable tasks: 21 executed, 1 up-to-date
error	27-Nov-2025 17:38:04	2025/11/27 17:38:03:089 WARNING Starting without install4j classes
error	27-Nov-2025 17:38:04	2025/11/27 17:38:04:041 WARNING Starting without install4j classes
simple	27-Nov-2025 17:38:05	Finished task 'Jalview distribution for Java 11' with result: Success
command	27-Nov-2025 17:38:05	Substituting variable: ${bamboo.planKey} with JB-GPC654
simple	27-Nov-2025 17:38:05	Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	27-Nov-2025 17:38:05	Bamboo Artifactory Plugin version: 2.6.2
command	27-Nov-2025 17:38:05	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job #1 (JB-GPC654-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-GPC654 shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_dependency_parent_0=JB-GDB729-5\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-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_repository_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC654-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GPC654-JOB1\nbamboo_shortPlanName=bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_46498600_name=Jalview Gitlab\nbamboo_repository_46498600_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC654-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_shortPlanKey=GPC654\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_buildTimeStamp=2025-11-27T17:19:12.535Z\nbamboo_repository_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_buildResultKey=JB-GPC654-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\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-GPC654 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=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_46498600_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_planRepository_1_type=gitv2\nbamboo_repository_46498600_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_planRepository_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\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_repository_46498600_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_plan_storageTag=plan-46302771\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=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1\nbamboo_planKey=JB-GPC654\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498600_git_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	27-Nov-2025 17:38:06	
build	27-Nov-2025 17:38:06	> Configure project :
build	27-Nov-2025 17:38:06	Using properties from file './utils/channels/default/channel_gradle.properties'
build	27-Nov-2025 17:38:06	JALVIEW_VERSION is set to '2.11.5.1'
build	27-Nov-2025 17:38:06	HEADLESS BUILD
build	27-Nov-2025 17:38:06	J2S ENABLED
build	27-Nov-2025 17:38:06	Using a BUILD profile.
build	27-Nov-2025 17:38:06	eclipseDir exists
build	27-Nov-2025 17:38:06	
build	27-Nov-2025 17:38:06	> Task :copyHelp UP-TO-DATE
build	27-Nov-2025 17:38:07	> Task :buildIndices
build	27-Nov-2025 17:38:07	> Task :copyResources UP-TO-DATE
build	27-Nov-2025 17:38:07	> Task :copyChannelResources UP-TO-DATE
build	27-Nov-2025 17:38:07	
build	27-Nov-2025 17:38:07	> Task :createBuildProperties
build	27-Nov-2025 17:38:07	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:38:07	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:07	
build	27-Nov-2025 17:38:07	> Task :buildResources
build	27-Nov-2025 17:38:07	> Task :copyDocs
build	27-Nov-2025 17:38:07	
build	27-Nov-2025 17:38:07	> Task :convertMdFiles
build	27-Nov-2025 17:38:07	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	27-Nov-2025 17:38:07	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	27-Nov-2025 17:38:07	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	27-Nov-2025 17:38:07	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/building.html
build	27-Nov-2025 17:38:07	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	27-Nov-2025 17:38:07	
build	27-Nov-2025 17:38:07	> Task :releasesTemplates
build	27-Nov-2025 17:38:07	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:38:07	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:07	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:07	Stripping rc/test/etc for 2_11_5_1
build	27-Nov-2025 17:38:07	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md
build	27-Nov-2025 17:38:07	
build	27-Nov-2025 17:38:07	> Task :prepare
build	27-Nov-2025 17:38:09	
build	27-Nov-2025 17:38:09	> Task :compileJava
build	27-Nov-2025 17:38:09	Setting target compatibility to 1.8
error	27-Nov-2025 17:38:16	Note: Some input files use or override a deprecated API.
error	27-Nov-2025 17:38:16	Note: Recompile with -Xlint:deprecation for details.
error	27-Nov-2025 17:38:16	Note: Some input files use unchecked or unsafe operations.
error	27-Nov-2025 17:38:16	Note: Recompile with -Xlint:unchecked for details.
build	27-Nov-2025 17:38:20	
build	27-Nov-2025 17:38:20	> Task :processResources
build	27-Nov-2025 17:38:20	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:38:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:20	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:20	
build	27-Nov-2025 17:38:20	> Task :classes
build	27-Nov-2025 17:38:20	> Task :cleanPackageDir
build	27-Nov-2025 17:38:22	
build	27-Nov-2025 17:38:22	> Task :compileLinkCheck
build	27-Nov-2025 17:38:22	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:38:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:38:24	
build	27-Nov-2025 17:38:24	> Task :linkCheck
build	27-Nov-2025 17:38:24	Checking help file links
build	27-Nov-2025 17:40:30	
build	27-Nov-2025 17:40:30	Results:
build	27-Nov-2025 17:40:30	161 distinct help targets
build	27-Nov-2025 17:40:30	161 help mappings
build	27-Nov-2025 17:40:30	0 invalid targets
build	27-Nov-2025 17:40:30	31 unused targets
build	27-Nov-2025 17:40:30	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	27-Nov-2025 17:40:30	    overviewprefs: html/features/preferences.html#overview
build	27-Nov-2025 17:40:30	    cdnafeatures: html/features/codingfeatures.html
build	27-Nov-2025 17:40:30	    startupprefs: html/features/preferences.html#startup
build	27-Nov-2025 17:40:30	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	27-Nov-2025 17:40:30	    io.modellerpir: html/io/modellerpir.html
build	27-Nov-2025 17:40:30	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	27-Nov-2025 17:40:30	    pdbmcviewer: html/features/pdbviewer.html
build	27-Nov-2025 17:40:30	    groovy.colours: html/features/groovy.html#groovyColours
build	27-Nov-2025 17:40:30	    seqmappings: html/features/seqmappings.html
build	27-Nov-2025 17:40:30	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	27-Nov-2025 17:40:30	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	27-Nov-2025 17:40:30	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	27-Nov-2025 17:40:30	    search: html/features/search.html
build	27-Nov-2025 17:40:30	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	27-Nov-2025 17:40:30	    alformats: html/io/fileformats.html
build	27-Nov-2025 17:40:30	    strucprefs: html/features/preferences.html#structure
build	27-Nov-2025 17:40:30	    siftsmapping: html/features/siftsmapping.html
build	27-Nov-2025 17:40:30	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	27-Nov-2025 17:40:30	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	27-Nov-2025 17:40:30	    newkeys: html/features/newkeystrokes.html
build	27-Nov-2025 17:40:30	    importvcf.attribs: html/features/importvcf.html#attribs
build	27-Nov-2025 17:40:30	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	27-Nov-2025 17:40:30	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	27-Nov-2025 17:40:30	    jalarchive: html/features/jalarchive.html
build	27-Nov-2025 17:40:30	    newsreader: html/webServices/newsreader.html
build	27-Nov-2025 17:40:30	    jalviewcltool: html/features/commandline.html#script
build	27-Nov-2025 17:40:30	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	27-Nov-2025 17:40:30	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	27-Nov-2025 17:40:30	    paematrixformat: html/io/paematrixformat.html
build	27-Nov-2025 17:40:30	    overview: html/features/overview.html
build	27-Nov-2025 17:40:30	0 invalid map urls
build	27-Nov-2025 17:40:30	0 invalid image attributes
build	27-Nov-2025 17:40:30	520 internal href links (120 with anchors)
build	27-Nov-2025 17:40:30	0 invalid internal href links
build	27-Nov-2025 17:40:30	0 invalid internal anchor links
build	27-Nov-2025 17:40:30	112 external href links
build	27-Nov-2025 17:40:30	External links not verified as internet not available
build	27-Nov-2025 17:40:30	*** Success ***
build	27-Nov-2025 17:40:30	
build	27-Nov-2025 17:40:30	> Task :jar
build	27-Nov-2025 17:40:31	> Task :syncJars
build	27-Nov-2025 17:40:31	> Task :makeDist
build	27-Nov-2025 17:40:38	> Task :shadowJar
build	27-Nov-2025 17:40:38	
build	27-Nov-2025 17:40:38	> Task :getdownImagesCopy
build	27-Nov-2025 17:40:38	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	27-Nov-2025 17:40:38	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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	27-Nov-2025 17:40:38	
build	27-Nov-2025 17:40:38	> Task :getdownImagesProcess
build	27-Nov-2025 17:40:38	> Task :getdownImages
build	27-Nov-2025 17:40:38	> Task :getdownWebsiteBuild
error	27-Nov-2025 17:40:40	2025/11/27 17:40:38:956 WARNING Starting without install4j classes
error	27-Nov-2025 17:40:40	2025/11/27 17:40:39:448 WARNING Starting without install4j classes
build	27-Nov-2025 17:40:40	
build	27-Nov-2025 17:40:40	> Task :getdownDigest
build	27-Nov-2025 17:40:40	Generating digest file './build/website/docroot/getdown/default/1.8/digest.txt'...
build	27-Nov-2025 17:40:40	Generating digest file './build/website/docroot/getdown/default/1.8/digest2.txt'...
build	27-Nov-2025 17:40:40	
build	27-Nov-2025 17:40:40	> Task :getdown
build	27-Nov-2025 17:40:40	
build	27-Nov-2025 17:40:40	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	27-Nov-2025 17:40:40	
build	27-Nov-2025 17:40:40	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	27-Nov-2025 17:40:40	
build	27-Nov-2025 17:40:40	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	27-Nov-2025 17:40:40	
build	27-Nov-2025 17:40:40	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	27-Nov-2025 17:40:40	Please consult deprecation warnings for more details.
build	27-Nov-2025 17:40:40	
build	27-Nov-2025 17:40:40	BUILD SUCCESSFUL in 2m 35s
build	27-Nov-2025 17:40:40	21 actionable tasks: 18 executed, 3 up-to-date
simple	27-Nov-2025 17:40:40	Finished task 'Jalview distribution for Java 8' with result: Success
simple	27-Nov-2025 17:40:40	Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled
simple	27-Nov-2025 17:40:40	Running post build plugin 'NCover Results Collector'
simple	27-Nov-2025 17:40:40	Running post build plugin 'Artifact Copier'
simple	27-Nov-2025 17:40:40	Publishing an artifact: Jalview executables
simple	27-Nov-2025 17:40:41	Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 216.3 ms
simple	27-Nov-2025 17:40:41	Publishing an artifact: install4j installers
error	27-Nov-2025 17:40:41	Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/install4j does not exist.
simple	27-Nov-2025 17:40:41	The artifact hasn't been successfully published after 4.264 ms
simple	27-Nov-2025 17:40:41	Publishing an artifact: getdown-channel
error	27-Nov-2025 17:40:41	Unable to publish artifact [getdown-channel]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/getdown/website does not exist.
simple	27-Nov-2025 17:40:41	The artifact hasn't been successfully published after 178.9 μs
simple	27-Nov-2025 17:40:41	Publishing an artifact: Jalview getdown launcher
error	27-Nov-2025 17:40:41	Unable to publish artifact [Jalview getdown launcher]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/getdown/files does not exist.
simple	27-Nov-2025 17:40:41	The artifact hasn't been successfully published after 46.39 μs
simple	27-Nov-2025 17:40:41	Publishing an artifact: getdown build for website
simple	27-Nov-2025 17:40:42	Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 1.130 s
simple	27-Nov-2025 17:40:42	Publishing an artifact: getdown build for archive
error	27-Nov-2025 17:40:42	Unable to publish artifact [getdown build for archive]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/website/docroot/old does not exist.
simple	27-Nov-2025 17:40:42	The artifact hasn't been successfully published after 152.2 μs
simple	27-Nov-2025 17:40:42	Running post build plugin 'Artifactory Release Management Staging'
simple	27-Nov-2025 17:40:42	Running post build plugin 'Artifactory Build Info Copier'
simple	27-Nov-2025 17:40:42	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	27-Nov-2025 17:40:42	Running post build plugin 'npm Cache Cleanup'
simple	27-Nov-2025 17:40:42	Running post build plugin 'Clover Results Collector'
simple	27-Nov-2025 17:40:42	Running post build plugin 'Docker Container Cleanup'
simple	27-Nov-2025 17:40:42	Finalising the build...
simple	27-Nov-2025 17:40:42	Stopping timer.
simple	27-Nov-2025 17:40:42	Build JB-GPC654-JOB1-1 completed.
simple	27-Nov-2025 17:40:42	Running on server: post build plugin 'NCover Results Collector'
simple	27-Nov-2025 17:40:42	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	27-Nov-2025 17:40:42	Running on server: post build plugin 'Clover Delta Calculator'
simple	27-Nov-2025 17:40:42	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	27-Nov-2025 17:40:42	All post build plugins have finished
simple	27-Nov-2025 17:40:42	Generating build results summary...
simple	27-Nov-2025 17:40:42	Saving build results to disk...
simple	27-Nov-2025 17:40:42	Logging substituted variables...
simple	27-Nov-2025 17:40:42	Indexing build results...
simple	27-Nov-2025 17:40:42	Finished building JB-GPC654-JOB1-1.