simple	25-Sep-2025 13:17:34	Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence - Default Job #1 (JB-GDL93-JOB1-1) started building on agent Default Agent
simple	25-Sep-2025 13:17:34	
simple	25-Sep-2025 13:17:34	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1
simple	25-Sep-2025 13:17:34	Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence - Default Job #1 (JB-GDL93-JOB1-1)
simple	25-Sep-2025 13:17:34	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	25-Sep-2025 13:17:34	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1
simple	25-Sep-2025 13:17:34	Updating source code to revision: 0ef8e143ad499423fa6af90141b658fb19c976ba
simple	25-Sep-2025 13:17:35	Fetching 'refs/heads/bug/JAL-4603_Export_files_missing_part_of_sequence' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	25-Sep-2025 13:17:35	Checking out revision 0ef8e143ad499423fa6af90141b658fb19c976ba.
simple	25-Sep-2025 13:17:35	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1/.git'.
simple	25-Sep-2025 13:17:35	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1'...
simple	25-Sep-2025 13:17:36	done.
simple	25-Sep-2025 13:17:42	Switched to a new branch 'bug/JAL-4603_Export_files_missing_part_of_sequence'
simple	25-Sep-2025 13:17:42	Branch bug/JAL-4603_Export_files_missing_part_of_sequence set up to track remote branch bug/JAL-4603_Export_files_missing_part_of_sequence from origin.
simple	25-Sep-2025 13:17:42	Updated source code to revision: 0ef8e143ad499423fa6af90141b658fb19c976ba
simple	25-Sep-2025 13:17:42	Finished task 'Checkout Default Repository' with result: Success
simple	25-Sep-2025 13:17:42	Running pre-build action: VCS Version Collector
simple	25-Sep-2025 13:17:42	Running pre-build action: Artifactory Release Staging
command	25-Sep-2025 13:17:42	Substituting variable: ${bamboo.planKey} with JB-GDL93
simple	25-Sep-2025 13:17:42	Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	25-Sep-2025 13:17:42	Bamboo Artifactory Plugin version: 2.6.2
command	25-Sep-2025 13:17:42	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence - Default Job #1 (JB-GDL93-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL93 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_dependency_parent_0=JB-GDB710-2\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=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_repository_revision_number=0ef8e143ad499423fa6af90141b658fb19c976ba\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL93-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-GDL93-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL93-JOB1\nbamboo_shortPlanName=bug-JAL-4603_Export_files_missing_part_of_sequence\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_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL93-JOB1-1\nbamboo_repository_46498486_revision_number=0ef8e143ad499423fa6af90141b658fb19c976ba\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence\nbamboo_shortPlanKey=GDL93\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=0ef8e143ad499423fa6af90141b658fb19c976ba\nbamboo_buildTimeStamp=2025-09-25T13:17:34.890+01:00\nbamboo_repository_git_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_buildResultKey=JB-GDL93-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=0ef8e143ad499423fa6af90141b658fb19c976ba\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498486_git_username=\nbamboo_repository_46498486_branch_name=bug/JAL-4603_Export_files_missing_part_of_sequence\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-4603_Export_files_missing_part_of_sequence\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-4603_Export_files_missing_part_of_sequence\nbamboo_repository_46498486_git_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4603_Export_files_missing_part_of_sequence\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-46302543\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_repository_46498486_name=Jalview Gitlab\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-GDL93-JOB1\nbamboo_planKey=JB-GDL93\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498486_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4603_Export_files_missing_part_of_sequence\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	25-Sep-2025 13:17:44	
build	25-Sep-2025 13:17:44	> Configure project :
build	25-Sep-2025 13:17:44	Using properties from file './utils/channels/default/channel_gradle.properties'
build	25-Sep-2025 13:17:44	JALVIEW_VERSION is set to '2.11.5.0'
build	25-Sep-2025 13:17:44	HEADLESS BUILD
build	25-Sep-2025 13:17:44	J2S ENABLED
build	25-Sep-2025 13:17:44	Using a BUILD profile.
build	25-Sep-2025 13:17:44	eclipseDir exists
build	25-Sep-2025 13:17:44	
build	25-Sep-2025 13:17:44	> Task :clean
build	25-Sep-2025 13:17:44	> Task :cleanPackageDir UP-TO-DATE
build	25-Sep-2025 13:17:45	> Task :getdownImagesCopy
build	25-Sep-2025 13:17:45	> Task :getdownImagesProcess
build	25-Sep-2025 13:17:45	> Task :getdownImages
build	25-Sep-2025 13:17:45	> Task :copyHelp
build	25-Sep-2025 13:17:47	> Task :buildIndices
build	25-Sep-2025 13:17:47	> Task :copyResources
build	25-Sep-2025 13:17:47	> Task :copyChannelResources
build	25-Sep-2025 13:17:48	
build	25-Sep-2025 13:17:48	> Task :createBuildProperties
build	25-Sep-2025 13:17:48	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	25-Sep-2025 13:17:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	25-Sep-2025 13:17:48	
build	25-Sep-2025 13:17:48	> Task :buildResources
build	25-Sep-2025 13:17:48	> Task :copyDocs
build	25-Sep-2025 13:17:48	
build	25-Sep-2025 13:17:48	> Task :convertMdFiles
build	25-Sep-2025 13:17:48	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	25-Sep-2025 13:17:48	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	25-Sep-2025 13:17:48	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	25-Sep-2025 13:17:48	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1/build/resources/doc_build/doc/building.html
build	25-Sep-2025 13:17:48	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	25-Sep-2025 13:17:48	
build	25-Sep-2025 13:17:48	> Task :releasesTemplates
build	25-Sep-2025 13:17:48	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	25-Sep-2025 13:17:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	25-Sep-2025 13:17:48	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	25-Sep-2025 13:17:48	Stripping rc/test/etc for 2_11_5_0
build	25-Sep-2025 13:17:48	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_0.md
build	25-Sep-2025 13:17:48	
build	25-Sep-2025 13:17:48	> Task :prepare
build	25-Sep-2025 13:17:50	
build	25-Sep-2025 13:17:50	> Task :compileJava
build	25-Sep-2025 13:17:50	Setting target compatibility to 11
error	25-Sep-2025 13:17:56	Note: Some input files use or override a deprecated API.
error	25-Sep-2025 13:17:56	Note: Recompile with -Xlint:deprecation for details.
error	25-Sep-2025 13:17:56	Note: Some input files use unchecked or unsafe operations.
error	25-Sep-2025 13:17:56	Note: Recompile with -Xlint:unchecked for details.
build	25-Sep-2025 13:17:58	
build	25-Sep-2025 13:17:58	> Task :processResources
build	25-Sep-2025 13:17:58	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	25-Sep-2025 13:17:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	25-Sep-2025 13:17:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	25-Sep-2025 13:17:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	25-Sep-2025 13:17:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	25-Sep-2025 13:17:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	25-Sep-2025 13:17:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	25-Sep-2025 13:17:58	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	25-Sep-2025 13:17:58	
build	25-Sep-2025 13:17:58	> Task :classes
build	25-Sep-2025 13:17:59	
build	25-Sep-2025 13:17:59	> Task :compileLinkCheck
build	25-Sep-2025 13:17:59	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	25-Sep-2025 13:17:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	25-Sep-2025 13:17:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	25-Sep-2025 13:17:59	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	25-Sep-2025 13:18:02	
build	25-Sep-2025 13:18:02	> Task :linkCheck
build	25-Sep-2025 13:18:02	Checking help file links
build	25-Sep-2025 13:20:09	
build	25-Sep-2025 13:20:09	Results:
build	25-Sep-2025 13:20:09	161 distinct help targets
build	25-Sep-2025 13:20:09	161 help mappings
build	25-Sep-2025 13:20:09	0 invalid targets
build	25-Sep-2025 13:20:09	31 unused targets
build	25-Sep-2025 13:20:09	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	25-Sep-2025 13:20:09	    overviewprefs: html/features/preferences.html#overview
build	25-Sep-2025 13:20:09	    cdnafeatures: html/features/codingfeatures.html
build	25-Sep-2025 13:20:09	    startupprefs: html/features/preferences.html#startup
build	25-Sep-2025 13:20:09	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	25-Sep-2025 13:20:09	    io.modellerpir: html/io/modellerpir.html
build	25-Sep-2025 13:20:09	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	25-Sep-2025 13:20:09	    pdbmcviewer: html/features/pdbviewer.html
build	25-Sep-2025 13:20:09	    groovy.colours: html/features/groovy.html#groovyColours
build	25-Sep-2025 13:20:09	    seqmappings: html/features/seqmappings.html
build	25-Sep-2025 13:20:09	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	25-Sep-2025 13:20:09	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	25-Sep-2025 13:20:09	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	25-Sep-2025 13:20:09	    search: html/features/search.html
build	25-Sep-2025 13:20:09	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	25-Sep-2025 13:20:09	    alformats: html/io/fileformats.html
build	25-Sep-2025 13:20:09	    strucprefs: html/features/preferences.html#structure
build	25-Sep-2025 13:20:09	    siftsmapping: html/features/siftsmapping.html
build	25-Sep-2025 13:20:09	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	25-Sep-2025 13:20:09	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	25-Sep-2025 13:20:09	    newkeys: html/features/newkeystrokes.html
build	25-Sep-2025 13:20:09	    importvcf.attribs: html/features/importvcf.html#attribs
build	25-Sep-2025 13:20:09	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	25-Sep-2025 13:20:09	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	25-Sep-2025 13:20:09	    jalarchive: html/features/jalarchive.html
build	25-Sep-2025 13:20:09	    newsreader: html/webServices/newsreader.html
build	25-Sep-2025 13:20:09	    jalviewcltool: html/features/commandline.html#script
build	25-Sep-2025 13:20:09	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	25-Sep-2025 13:20:09	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	25-Sep-2025 13:20:09	    paematrixformat: html/io/paematrixformat.html
build	25-Sep-2025 13:20:09	    overview: html/features/overview.html
build	25-Sep-2025 13:20:09	0 invalid map urls
build	25-Sep-2025 13:20:09	0 invalid image attributes
build	25-Sep-2025 13:20:09	520 internal href links (120 with anchors)
build	25-Sep-2025 13:20:09	0 invalid internal href links
build	25-Sep-2025 13:20:09	0 invalid internal anchor links
build	25-Sep-2025 13:20:09	112 external href links
build	25-Sep-2025 13:20:09	External links not verified as internet not available
build	25-Sep-2025 13:20:09	*** Success ***
build	25-Sep-2025 13:20:10	
build	25-Sep-2025 13:20:10	> Task :jar
build	25-Sep-2025 13:20:10	> Task :syncJars
build	25-Sep-2025 13:20:10	> Task :makeDist
build	25-Sep-2025 13:20:10	> Task :getdownWebsiteBuild
build	25-Sep-2025 13:20:12	
build	25-Sep-2025 13:20:12	> Task :getdownDigest
build	25-Sep-2025 13:20:12	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
build	25-Sep-2025 13:20:12	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	25-Sep-2025 13:20:12	
build	25-Sep-2025 13:20:12	> Task :getdown
build	25-Sep-2025 13:20:12	
build	25-Sep-2025 13:20:12	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	25-Sep-2025 13:20:12	
build	25-Sep-2025 13:20:12	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	25-Sep-2025 13:20:12	
build	25-Sep-2025 13:20:12	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	25-Sep-2025 13:20:12	
build	25-Sep-2025 13:20:12	Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness.
build	25-Sep-2025 13:20:12	Please consult deprecation warnings for more details.
build	25-Sep-2025 13:20:12	
build	25-Sep-2025 13:20:12	BUILD SUCCESSFUL in 2m 29s
build	25-Sep-2025 13:20:12	21 actionable tasks: 20 executed, 1 up-to-date
error	25-Sep-2025 13:20:12	2025/09/25 13:20:10:996 WARNING Starting without install4j classes
error	25-Sep-2025 13:20:12	2025/09/25 13:20:11:568 WARNING Starting without install4j classes
simple	25-Sep-2025 13:20:12	Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success
simple	25-Sep-2025 13:20:12	Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command	25-Sep-2025 13:20:12	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence - Default Job #1 (JB-GDL93-JOB1-1)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL93-JOB1-1-ScriptBuildTask-1320295979409935417.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_dependency_parent_0=JB-GDB710-2\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_repository_revision_number=0ef8e143ad499423fa6af90141b658fb19c976ba\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL93-JOB1-1\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL93-JOB1\nbamboo_shortPlanName=bug-JAL-4603_Export_files_missing_part_of_sequence\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_buildNumber=1\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-GDL93-JOB1-1\nbamboo_repository_46498486_revision_number=0ef8e143ad499423fa6af90141b658fb19c976ba\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence\nbamboo_shortPlanKey=GDL93\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=0ef8e143ad499423fa6af90141b658fb19c976ba\nbamboo_buildTimeStamp=2025-09-25T13:17:34.890+01:00\nbamboo_repository_git_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_buildResultKey=JB-GDL93-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=0ef8e143ad499423fa6af90141b658fb19c976ba\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498486_git_username=\nbamboo_repository_46498486_branch_name=bug/JAL-4603_Export_files_missing_part_of_sequence\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-GDL93 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\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-4603_Export_files_missing_part_of_sequence\nbamboo_repository_46498486_git_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4603_Export_files_missing_part_of_sequence\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-46302543\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_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_repository_46498486_name=Jalview Gitlab\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-GDL93-JOB1\nbamboo_planKey=JB-GDL93\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498486_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_1_branchName=bug/JAL-4603_Export_files_missing_part_of_sequence\n
simple	25-Sep-2025 13:20:12	Finished task 'Copy JVL file and produce link in HTML' with result: Success
simple	25-Sep-2025 13:20:12	Running post build plugin 'NCover Results Collector'
simple	25-Sep-2025 13:20:12	Running post build plugin 'Artifact Copier'
simple	25-Sep-2025 13:20:12	Publishing an artifact: getdown
simple	25-Sep-2025 13:20:13	Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 811.5 ms
simple	25-Sep-2025 13:20:13	Running post build plugin 'Artifactory Release Management Staging'
simple	25-Sep-2025 13:20:13	Running post build plugin 'Artifactory Build Info Copier'
simple	25-Sep-2025 13:20:13	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	25-Sep-2025 13:20:13	Running post build plugin 'npm Cache Cleanup'
simple	25-Sep-2025 13:20:13	Running post build plugin 'Clover Results Collector'
simple	25-Sep-2025 13:20:13	Running post build plugin 'Docker Container Cleanup'
simple	25-Sep-2025 13:20:13	Finalising the build...
simple	25-Sep-2025 13:20:13	Stopping timer.
simple	25-Sep-2025 13:20:13	Build JB-GDL93-JOB1-1 completed.
simple	25-Sep-2025 13:20:13	Running on server: post build plugin 'NCover Results Collector'
simple	25-Sep-2025 13:20:13	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	25-Sep-2025 13:20:13	Running on server: post build plugin 'Clover Delta Calculator'
simple	25-Sep-2025 13:20:13	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	25-Sep-2025 13:20:13	All post build plugins have finished
simple	25-Sep-2025 13:20:13	Generating build results summary...
simple	25-Sep-2025 13:20:13	Saving build results to disk...
simple	25-Sep-2025 13:20:13	Logging substituted variables...
simple	25-Sep-2025 13:20:13	Indexing build results...
simple	25-Sep-2025 13:20:13	Finished building JB-GDL93-JOB1-1.