simple 17-Feb-2025 17:20:29 Build Jalview Builds - Getdown DEVELOP Launchers - develop - Default Job #3 (JB-GDL52-JOB1-3) started building on agent Default Agent
simple 17-Feb-2025 17:20:29
simple 17-Feb-2025 17:20:29 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-JOB1
simple 17-Feb-2025 17:20:29 Executing build Jalview Builds - Getdown DEVELOP Launchers - develop - Default Job #3 (JB-GDL52-JOB1-3)
simple 17-Feb-2025 17:20:29 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple 17-Feb-2025 17:20:29 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-JOB1
simple 17-Feb-2025 17:20:29 Updating source code to revision: 2bd12a6bc5270ce38fce1e858e02ef060433aa0b
simple 17-Feb-2025 17:20:29 Fetching 'refs/heads/develop' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple 17-Feb-2025 17:20:29 Checking out revision 2bd12a6bc5270ce38fce1e858e02ef060433aa0b.
simple 17-Feb-2025 17:20:29 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple 17-Feb-2025 17:20:29 637f19e..2bd12a6 develop -> origin/develop
simple 17-Feb-2025 17:20:29 cfeef18..dd2df48 releases/Release_2_11_4_Branch -> origin/releases/Release_2_11_4_Branch
simple 17-Feb-2025 17:20:29 Already on 'develop'
simple 17-Feb-2025 17:20:29 Your branch is behind 'origin/develop' by 1 commit, and can be fast-forwarded.
simple 17-Feb-2025 17:20:29 (use "git pull" to update your local branch)
simple 17-Feb-2025 17:20:29 HEAD is now at 2bd12a6 JAL-4490 release notes for JAL-4511
simple 17-Feb-2025 17:20:29 Updated source code to revision: 2bd12a6bc5270ce38fce1e858e02ef060433aa0b
simple 17-Feb-2025 17:20:29 Finished task 'Checkout Default Repository' with result: Success
simple 17-Feb-2025 17:20:29 Running pre-build action: VCS Version Collector
simple 17-Feb-2025 17:20:29 Running pre-build action: Artifactory Release Staging
command 17-Feb-2025 17:20:29 Substituting variable: ${bamboo.planKey} with JB-GDL52
simple 17-Feb-2025 17:20:29 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple 17-Feb-2025 17:20:29 Bamboo Artifactory Plugin version: 2.6.2
command 17-Feb-2025 17:20:29 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - develop - Default Job #3 (JB-GDL52-JOB1-3)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL52 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_repository_46498277_name=Jalview Gitlab\nbamboo_dependency_parent_0=JB-GDB663-3\nbamboo_repository_46498277_git_username=\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=develop\nbamboo_repository_revision_number=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL52-JOB1-3\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-GDL52-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL52-JOB1\nbamboo_shortPlanName=develop\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=3\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-GDL52-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - develop\nbamboo_shortPlanKey=GDL52\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nbamboo_repository_46498277_git_branch=develop\nbamboo_buildTimeStamp=2025-02-17T17:20:29.402Z\nbamboo_repository_previous_revision_number=637f19e96cfb28244fe2adb13e36d0cbe16dbe6c\nbamboo_repository_46498277_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-GDL52-JOB1-3\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - develop - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498277_revision_number=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_46498277_branch_name=develop\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_46498277_previous_revision_number=637f19e96cfb28244fe2adb13e36d0cbe16dbe6c\nbamboo_planRepository_branch=develop\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=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\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-46302139\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-GDL52-JOB1\nbamboo_planKey=JB-GDL52\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build 17-Feb-2025 17:20:31
build 17-Feb-2025 17:20:31 > Configure project :
build 17-Feb-2025 17:20:31 Using properties from file './utils/channels/default/channel_gradle.properties'
build 17-Feb-2025 17:20:31 JALVIEW_VERSION is set to '2.11.4.2'
build 17-Feb-2025 17:20:31 HEADLESS BUILD
build 17-Feb-2025 17:20:31 J2S ENABLED
build 17-Feb-2025 17:20:31 Using a BUILD profile.
build 17-Feb-2025 17:20:31 eclipseDir exists
build 17-Feb-2025 17:20:31
build 17-Feb-2025 17:20:31 > Task :clean
build 17-Feb-2025 17:20:31 > Task :cleanPackageDir
build 17-Feb-2025 17:20:31 > Task :getdownImagesCopy
build 17-Feb-2025 17:20:32 > Task :getdownImagesProcess
build 17-Feb-2025 17:20:32 > Task :getdownImages
build 17-Feb-2025 17:20:32 > Task :copyHelp
build 17-Feb-2025 17:20:34 > Task :buildIndices
build 17-Feb-2025 17:20:34 > Task :copyResources
build 17-Feb-2025 17:20:34 > Task :copyChannelResources
build 17-Feb-2025 17:20:34
build 17-Feb-2025 17:20:34 > Task :createBuildProperties
build 17-Feb-2025 17:20:34 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build 17-Feb-2025 17:20:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:34
build 17-Feb-2025 17:20:34 > Task :buildResources
build 17-Feb-2025 17:20:34 > Task :copyDocs
build 17-Feb-2025 17:20:34
build 17-Feb-2025 17:20:34 > Task :convertMdFiles
build 17-Feb-2025 17:20:34 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build 17-Feb-2025 17:20:34 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-JOB1/build/resources/doc_build/doc/releaseprocess.html
build 17-Feb-2025 17:20:34 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build 17-Feb-2025 17:20:34 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-JOB1/build/resources/doc_build/doc/building.html
build 17-Feb-2025 17:20:34 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-JOB1/build/resources/doc_build/doc/jalview-projects.html
build 17-Feb-2025 17:20:34
build 17-Feb-2025 17:20:34 > Task :releasesTemplates
build 17-Feb-2025 17:20:34 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build 17-Feb-2025 17:20:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:34 Stripping rc/test/etc for 2_11_4_2
build 17-Feb-2025 17:20:34 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_2.md
build 17-Feb-2025 17:20:34
build 17-Feb-2025 17:20:34 > Task :prepare
build 17-Feb-2025 17:20:36
build 17-Feb-2025 17:20:36 > Task :compileJava
build 17-Feb-2025 17:20:36 Setting target compatibility to 11
error 17-Feb-2025 17:20:42 Note: Some input files use or override a deprecated API.
error 17-Feb-2025 17:20:42 Note: Recompile with -Xlint:deprecation for details.
error 17-Feb-2025 17:20:42 Note: Some input files use unchecked or unsafe operations.
error 17-Feb-2025 17:20:42 Note: Recompile with -Xlint:unchecked for details.
build 17-Feb-2025 17:20:42
build 17-Feb-2025 17:20:42 > Task :processResources
build 17-Feb-2025 17:20:42 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build 17-Feb-2025 17:20:42 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:42 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:42 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:42 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:42 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:42 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:42 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:42 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:42
build 17-Feb-2025 17:20:42 > Task :classes
build 17-Feb-2025 17:20:44
build 17-Feb-2025 17:20:44 > Task :compileLinkCheck
build 17-Feb-2025 17:20:44 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build 17-Feb-2025 17:20:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-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 17-Feb-2025 17:20:44
build 17-Feb-2025 17:20:44 > Task :linkCheck
build 17-Feb-2025 17:20:44 Checking help file links
build 17-Feb-2025 17:20:44
build 17-Feb-2025 17:20:44 Results:
build 17-Feb-2025 17:20:44 159 distinct help targets
build 17-Feb-2025 17:20:44 159 help mappings
build 17-Feb-2025 17:20:44 0 invalid targets
build 17-Feb-2025 17:20:44 32 unused targets
build 17-Feb-2025 17:20:44 uniprotfetcher: html/features/uniprotsequencefetcher.html
build 17-Feb-2025 17:20:44 overviewprefs: html/features/preferences.html#overview
build 17-Feb-2025 17:20:44 cdnafeatures: html/features/codingfeatures.html
build 17-Feb-2025 17:20:44 startupprefs: html/features/preferences.html#startup
build 17-Feb-2025 17:20:44 ensemblfetch: html/features/ensemblsequencefetcher.html
build 17-Feb-2025 17:20:44 io.modellerpir: html/io/modellerpir.html
build 17-Feb-2025 17:20:44 structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build 17-Feb-2025 17:20:44 pdbmcviewer: html/features/pdbviewer.html
build 17-Feb-2025 17:20:44 workingwithpae: html/features/paematrices.html
build 17-Feb-2025 17:20:44 groovy.colours: html/features/groovy.html#groovyColours
build 17-Feb-2025 17:20:44 seqmappings: html/features/seqmappings.html
build 17-Feb-2025 17:20:44 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build 17-Feb-2025 17:20:44 splitframe.mirrorfonts: html/features/splitView.html#mirror
build 17-Feb-2025 17:20:44 subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build 17-Feb-2025 17:20:44 search: html/features/search.html
build 17-Feb-2025 17:20:44 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build 17-Feb-2025 17:20:44 alformats: html/io/fileformats.html
build 17-Feb-2025 17:20:44 strucprefs: html/features/preferences.html#structure
build 17-Feb-2025 17:20:44 siftsmapping: html/features/siftsmapping.html
build 17-Feb-2025 17:20:44 chimera.annotxfer: html/features/chimera.html#annotxfer
build 17-Feb-2025 17:20:44 pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build 17-Feb-2025 17:20:44 newkeys: html/features/newkeystrokes.html
build 17-Feb-2025 17:20:44 importvcf.attribs: html/features/importvcf.html#attribs
build 17-Feb-2025 17:20:44 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build 17-Feb-2025 17:20:44 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build 17-Feb-2025 17:20:44 jalarchive: html/features/jalarchive.html
build 17-Feb-2025 17:20:44 newsreader: html/webServices/newsreader.html
build 17-Feb-2025 17:20:44 jalviewcltool: html/features/commandline.html#script
build 17-Feb-2025 17:20:44 popMenuAddref: html/menus/popupMenu.html#addrefannot
build 17-Feb-2025 17:20:44 splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build 17-Feb-2025 17:20:44 paematrixformat: html/io/paematrixformat.html
build 17-Feb-2025 17:20:44 overview: html/features/overview.html
build 17-Feb-2025 17:20:44 0 invalid map urls
build 17-Feb-2025 17:20:44 0 invalid image attributes
build 17-Feb-2025 17:20:44 508 internal href links (110 with anchors)
build 17-Feb-2025 17:20:44 0 invalid internal href links
build 17-Feb-2025 17:20:44 0 invalid internal anchor links
build 17-Feb-2025 17:20:44 113 external href links
build 17-Feb-2025 17:20:44 External links not verified as internet not available
build 17-Feb-2025 17:20:44 *** Success ***
build 17-Feb-2025 17:20:45
build 17-Feb-2025 17:20:45 > Task :jar
build 17-Feb-2025 17:20:46 > Task :syncJars
build 17-Feb-2025 17:20:46 > Task :makeDist
build 17-Feb-2025 17:20:46 > Task :getdownWebsiteBuild
build 17-Feb-2025 17:20:48
build 17-Feb-2025 17:20:48 > Task :getdownDigest
error 17-Feb-2025 17:20:48 2025/02/17 17:20:46:634 WARNING Starting without install4j classes
error 17-Feb-2025 17:20:48 2025/02/17 17:20:47:326 WARNING Starting without install4j classes
build 17-Feb-2025 17:20:48 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
build 17-Feb-2025 17:20:48 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build 17-Feb-2025 17:20:48
build 17-Feb-2025 17:20:48 > Task :getdown
build 17-Feb-2025 17:20:48
build 17-Feb-2025 17:20:48 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build 17-Feb-2025 17:20:48
build 17-Feb-2025 17:20:48 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build 17-Feb-2025 17:20:48
build 17-Feb-2025 17:20:48 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build 17-Feb-2025 17:20:48
build 17-Feb-2025 17:20:48 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness.
build 17-Feb-2025 17:20:48 Please consult deprecation warnings for more details.
build 17-Feb-2025 17:20:48
build 17-Feb-2025 17:20:48 BUILD SUCCESSFUL in 17s
build 17-Feb-2025 17:20:48 21 actionable tasks: 21 executed
simple 17-Feb-2025 17:20:48 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success
simple 17-Feb-2025 17:20:48 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command 17-Feb-2025 17:20:48 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - develop - Default Job #3 (JB-GDL52-JOB1-3)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL52-JOB1-3-ScriptBuildTask-1218734085536429663.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_repository_46498277_name=Jalview Gitlab\nbamboo_dependency_parent_0=JB-GDB663-3\nbamboo_repository_46498277_git_username=\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL52-JOB1-3\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL52-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL52-JOB1\nbamboo_shortPlanName=develop\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_buildNumber=3\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-GDL52-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - develop\nbamboo_shortPlanKey=GDL52\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nbamboo_repository_46498277_git_branch=develop\nbamboo_buildTimeStamp=2025-02-17T17:20:29.402Z\nbamboo_repository_previous_revision_number=637f19e96cfb28244fe2adb13e36d0cbe16dbe6c\nbamboo_repository_46498277_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-GDL52-JOB1-3\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - develop - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498277_revision_number=2bd12a6bc5270ce38fce1e858e02ef060433aa0b\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-GDL52 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_repository_46498277_branch_name=develop\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46498277_previous_revision_number=637f19e96cfb28244fe2adb13e36d0cbe16dbe6c\nbamboo_planRepository_branch=develop\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=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\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-46302139\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_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-GDL52-JOB1\nbamboo_planKey=JB-GDL52\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=develop\n
simple 17-Feb-2025 17:20:48 Finished task 'Copy JVL file and produce link in HTML' with result: Success
simple 17-Feb-2025 17:20:48 Running post build plugin 'NCover Results Collector'
simple 17-Feb-2025 17:20:48 Running post build plugin 'Artifact Copier'
simple 17-Feb-2025 17:20:48 Publishing an artifact: getdown
simple 17-Feb-2025 17:20:48 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 109.9 ms
simple 17-Feb-2025 17:20:48 Running post build plugin 'Artifactory Release Management Staging'
simple 17-Feb-2025 17:20:48 Running post build plugin 'Artifactory Build Info Copier'
simple 17-Feb-2025 17:20:48 Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple 17-Feb-2025 17:20:48 Running post build plugin 'npm Cache Cleanup'
simple 17-Feb-2025 17:20:48 Running post build plugin 'Clover Results Collector'
simple 17-Feb-2025 17:20:48 Running post build plugin 'Docker Container Cleanup'
simple 17-Feb-2025 17:20:48 Finalising the build...
simple 17-Feb-2025 17:20:48 Stopping timer.
simple 17-Feb-2025 17:20:48 Build JB-GDL52-JOB1-3 completed.
simple 17-Feb-2025 17:20:48 Running on server: post build plugin 'NCover Results Collector'
simple 17-Feb-2025 17:20:48 Running on server: post build plugin 'Build Hanging Detection Configuration'
simple 17-Feb-2025 17:20:48 Running on server: post build plugin 'Clover Delta Calculator'
simple 17-Feb-2025 17:20:48 Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple 17-Feb-2025 17:20:48 All post build plugins have finished
simple 17-Feb-2025 17:20:48 Generating build results summary...
simple 17-Feb-2025 17:20:48 Saving build results to disk...
simple 17-Feb-2025 17:20:48 Logging substituted variables...
simple 17-Feb-2025 17:20:48 Indexing build results...
simple 17-Feb-2025 17:20:48 Finished building JB-GDL52-JOB1-3.