simple 26-Feb-2025 18:36:48 Build Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #5 (JB-GDL51-JOB1-5) started building on agent Default Agent
simple 26-Feb-2025 18:36:48
simple 26-Feb-2025 18:36:48 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1
simple 26-Feb-2025 18:36:48 Executing build Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #5 (JB-GDL51-JOB1-5)
simple 26-Feb-2025 18:36:48 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple 26-Feb-2025 18:36:48 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1
simple 26-Feb-2025 18:36:48 Updating source code to revision: d9b10917dcf53abeb15fd632531e699905025179
simple 26-Feb-2025 18:36:48 Fetching 'refs/heads/feature/JAL-4386_JAL-4435_reformat_node_labels' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple 26-Feb-2025 18:36:49 Checking out revision d9b10917dcf53abeb15fd632531e699905025179.
simple 26-Feb-2025 18:36:49 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple 26-Feb-2025 18:36:49 23ebbc3..d9b1091 feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels
simple 26-Feb-2025 18:36:49 Already on 'feature/JAL-4386_JAL-4435_reformat_node_labels'
simple 26-Feb-2025 18:36:49 Your branch is behind 'origin/feature/JAL-4386_JAL-4435_reformat_node_labels' by 1 commit, and can be fast-forwarded.
simple 26-Feb-2025 18:36:49 (use "git pull" to update your local branch)
simple 26-Feb-2025 18:36:49 HEAD is now at d9b1091 JAL-4515 Add Coloured Backgrounds for Grouped Nodes in Similarity Tree
simple 26-Feb-2025 18:36:49 Updated source code to revision: d9b10917dcf53abeb15fd632531e699905025179
simple 26-Feb-2025 18:36:49 Finished task 'Checkout Default Repository' with result: Success
simple 26-Feb-2025 18:36:49 Running pre-build action: VCS Version Collector
simple 26-Feb-2025 18:36:49 Running pre-build action: Artifactory Release Staging
command 26-Feb-2025 18:36:49 Substituting variable: ${bamboo.planKey} with JB-GDL51
simple 26-Feb-2025 18:36:49 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple 26-Feb-2025 18:36:49 Bamboo Artifactory Plugin version: 2.6.2
command 26-Feb-2025 18:36:49 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #5 (JB-GDL51-JOB1-5)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL51 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_dependency_parent_0=JB-GDB661-7\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_revision_number=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL51-JOB1-5\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-GDL51-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL51-JOB1\nbamboo_shortPlanName=feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_46498276_previous_revision_number=23ebbc38fce7bf2abc5b1129e0f3592e3b792e2e\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=5\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-GDL51-JOB1-5\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498276_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_shortPlanKey=GDL51\nbamboo_repository_46498276_revision_number=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_buildTimeStamp=2025-02-26T18:34:52.853Z\nbamboo_repository_previous_revision_number=23ebbc38fce7bf2abc5b1129e0f3592e3b792e2e\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDL51-JOB1-5\nbamboo_repository_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=d9b10917dcf53abeb15fd632531e699905025179\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498276_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_name=Jalview Gitlab\nbamboo_repository_46498276_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_repository_46498276_git_username=\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\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=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels\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_46498276_name=Jalview Gitlab\nbamboo_plan_storageTag=plan-46302137\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-GDL51-JOB1\nbamboo_planKey=JB-GDL51\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build 26-Feb-2025 18:36:51
build 26-Feb-2025 18:36:51 > Configure project :
build 26-Feb-2025 18:36:51 Using properties from file './utils/channels/default/channel_gradle.properties'
build 26-Feb-2025 18:36:51 JALVIEW_VERSION is set to '2.11.4.0'
build 26-Feb-2025 18:36:51 HEADLESS BUILD
build 26-Feb-2025 18:36:51 J2S ENABLED
build 26-Feb-2025 18:36:51 Using a BUILD profile.
build 26-Feb-2025 18:36:51 eclipseDir exists
build 26-Feb-2025 18:36:51
build 26-Feb-2025 18:36:51 > Task :clean
build 26-Feb-2025 18:36:51 > Task :cleanPackageDir
build 26-Feb-2025 18:36:51 > Task :getdownImagesCopy
build 26-Feb-2025 18:36:51 > Task :getdownImagesProcess
build 26-Feb-2025 18:36:51 > Task :getdownImages
build 26-Feb-2025 18:36:52 > Task :copyHelp
build 26-Feb-2025 18:36:54 > Task :buildIndices
build 26-Feb-2025 18:36:55 > Task :copyResources
build 26-Feb-2025 18:36:55 > Task :copyChannelResources
build 26-Feb-2025 18:36:55
build 26-Feb-2025 18:36:55 > Task :createBuildProperties
build 26-Feb-2025 18:36:55 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build 26-Feb-2025 18:36:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:36:55
build 26-Feb-2025 18:36:55 > Task :buildResources
build 26-Feb-2025 18:36:55 > Task :copyDocs
build 26-Feb-2025 18:36:55
build 26-Feb-2025 18:36:55 > Task :convertMdFiles
build 26-Feb-2025 18:36:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build 26-Feb-2025 18:36:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/build/resources/doc_build/doc/releaseprocess.html
build 26-Feb-2025 18:36:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build 26-Feb-2025 18:36:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/build/resources/doc_build/doc/building.html
build 26-Feb-2025 18:36:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/build/resources/doc_build/doc/jalview-projects.html
build 26-Feb-2025 18:36:56
build 26-Feb-2025 18:36:56 > Task :releasesTemplates
build 26-Feb-2025 18:36:56 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build 26-Feb-2025 18:36:56 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:36:56 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:36:56 Stripping rc/test/etc for 2_11_4_0
build 26-Feb-2025 18:36:56 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_0.md
build 26-Feb-2025 18:36:56
build 26-Feb-2025 18:36:56 > Task :prepare
build 26-Feb-2025 18:36:58
build 26-Feb-2025 18:36:58 > Task :compileJava
build 26-Feb-2025 18:36:58 Setting target compatibility to 11
error 26-Feb-2025 18:37:05 Note: Some input files use or override a deprecated API.
error 26-Feb-2025 18:37:05 Note: Recompile with -Xlint:deprecation for details.
error 26-Feb-2025 18:37:05 Note: Some input files use unchecked or unsafe operations.
error 26-Feb-2025 18:37:05 Note: Recompile with -Xlint:unchecked for details.
build 26-Feb-2025 18:37:05
build 26-Feb-2025 18:37:05 > Task :processResources
build 26-Feb-2025 18:37:05 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build 26-Feb-2025 18:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:37:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:37:05
build 26-Feb-2025 18:37:05 > Task :classes
build 26-Feb-2025 18:37:07
build 26-Feb-2025 18:37:07 > Task :compileLinkCheck
build 26-Feb-2025 18:37:07 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build 26-Feb-2025 18:37:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:37:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:37:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-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 26-Feb-2025 18:37:08
build 26-Feb-2025 18:37:08 > Task :linkCheck
build 26-Feb-2025 18:37:08 Checking help file links
build 26-Feb-2025 18:37:08
build 26-Feb-2025 18:37:08 Results:
build 26-Feb-2025 18:37:08 159 distinct help targets
build 26-Feb-2025 18:37:08 159 help mappings
build 26-Feb-2025 18:37:08 0 invalid targets
build 26-Feb-2025 18:37:08 32 unused targets
build 26-Feb-2025 18:37:08 uniprotfetcher: html/features/uniprotsequencefetcher.html
build 26-Feb-2025 18:37:08 overviewprefs: html/features/preferences.html#overview
build 26-Feb-2025 18:37:08 cdnafeatures: html/features/codingfeatures.html
build 26-Feb-2025 18:37:08 startupprefs: html/features/preferences.html#startup
build 26-Feb-2025 18:37:08 ensemblfetch: html/features/ensemblsequencefetcher.html
build 26-Feb-2025 18:37:08 io.modellerpir: html/io/modellerpir.html
build 26-Feb-2025 18:37:08 structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build 26-Feb-2025 18:37:08 pdbmcviewer: html/features/pdbviewer.html
build 26-Feb-2025 18:37:08 workingwithpae: html/features/paematrices.html
build 26-Feb-2025 18:37:08 groovy.colours: html/features/groovy.html#groovyColours
build 26-Feb-2025 18:37:08 seqmappings: html/features/seqmappings.html
build 26-Feb-2025 18:37:08 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build 26-Feb-2025 18:37:08 splitframe.mirrorfonts: html/features/splitView.html#mirror
build 26-Feb-2025 18:37:08 subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build 26-Feb-2025 18:37:08 search: html/features/search.html
build 26-Feb-2025 18:37:08 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build 26-Feb-2025 18:37:08 alformats: html/io/fileformats.html
build 26-Feb-2025 18:37:08 strucprefs: html/features/preferences.html#structure
build 26-Feb-2025 18:37:08 siftsmapping: html/features/siftsmapping.html
build 26-Feb-2025 18:37:08 chimera.annotxfer: html/features/chimera.html#annotxfer
build 26-Feb-2025 18:37:08 pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build 26-Feb-2025 18:37:08 newkeys: html/features/newkeystrokes.html
build 26-Feb-2025 18:37:08 importvcf.attribs: html/features/importvcf.html#attribs
build 26-Feb-2025 18:37:08 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build 26-Feb-2025 18:37:08 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build 26-Feb-2025 18:37:08 jalarchive: html/features/jalarchive.html
build 26-Feb-2025 18:37:08 newsreader: html/webServices/newsreader.html
build 26-Feb-2025 18:37:08 jalviewcltool: html/features/commandline.html#script
build 26-Feb-2025 18:37:08 popMenuAddref: html/menus/popupMenu.html#addrefannot
build 26-Feb-2025 18:37:08 splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build 26-Feb-2025 18:37:08 paematrixformat: html/io/paematrixformat.html
build 26-Feb-2025 18:37:08 overview: html/features/overview.html
build 26-Feb-2025 18:37:08 0 invalid map urls
build 26-Feb-2025 18:37:08 0 invalid image attributes
build 26-Feb-2025 18:37:08 500 internal href links (107 with anchors)
build 26-Feb-2025 18:37:08 0 invalid internal href links
build 26-Feb-2025 18:37:08 0 invalid internal anchor links
build 26-Feb-2025 18:37:08 113 external href links
build 26-Feb-2025 18:37:08 External links not verified as internet not available
build 26-Feb-2025 18:37:08 *** Success ***
build 26-Feb-2025 18:37:09
build 26-Feb-2025 18:37:09 > Task :jar
build 26-Feb-2025 18:37:10 > Task :syncJars
build 26-Feb-2025 18:37:10 > Task :makeDist
build 26-Feb-2025 18:37:10 > Task :getdownWebsiteBuild
error 26-Feb-2025 18:37:12 2025/02/26 18:37:10:860 WARNING Starting without install4j classes
error 26-Feb-2025 18:37:12 2025/02/26 18:37:11:476 WARNING Starting without install4j classes
build 26-Feb-2025 18:37:12
build 26-Feb-2025 18:37:12 > Task :getdownDigest
build 26-Feb-2025 18:37:12 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
build 26-Feb-2025 18:37:12 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build 26-Feb-2025 18:37:12
build 26-Feb-2025 18:37:12 > Task :getdown
build 26-Feb-2025 18:37:12
build 26-Feb-2025 18:37:12 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build 26-Feb-2025 18:37:12
build 26-Feb-2025 18:37:12 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build 26-Feb-2025 18:37:12
build 26-Feb-2025 18:37:12 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build 26-Feb-2025 18:37:12
build 26-Feb-2025 18:37:12 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness.
build 26-Feb-2025 18:37:12 Please consult deprecation warnings for more details.
build 26-Feb-2025 18:37:12
build 26-Feb-2025 18:37:12 BUILD SUCCESSFUL in 22s
build 26-Feb-2025 18:37:12 21 actionable tasks: 21 executed
simple 26-Feb-2025 18:37:12 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success
simple 26-Feb-2025 18:37:12 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command 26-Feb-2025 18:37:12 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #5 (JB-GDL51-JOB1-5)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL51-JOB1-5-ScriptBuildTask-1999292762846485992.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_dependency_parent_0=JB-GDB661-7\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_revision_number=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL51-JOB1-5\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL51-JOB1\nbamboo_shortPlanName=feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_46498276_previous_revision_number=23ebbc38fce7bf2abc5b1129e0f3592e3b792e2e\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_buildNumber=5\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-GDL51-JOB1-5\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498276_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_shortPlanKey=GDL51\nbamboo_repository_46498276_revision_number=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_buildTimeStamp=2025-02-26T18:34:52.853Z\nbamboo_repository_previous_revision_number=23ebbc38fce7bf2abc5b1129e0f3592e3b792e2e\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDL51-JOB1-5\nbamboo_repository_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498276_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\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-GDL51 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_repository_46498276_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_46498276_git_username=\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\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=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_repository_46498276_name=Jalview Gitlab\nbamboo_plan_storageTag=plan-46302137\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-GDL51-JOB1\nbamboo_planKey=JB-GDL51\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels\n
simple 26-Feb-2025 18:37:12 Finished task 'Copy JVL file and produce link in HTML' with result: Success
simple 26-Feb-2025 18:37:12 Running post build plugin 'NCover Results Collector'
simple 26-Feb-2025 18:37:12 Running post build plugin 'Artifact Copier'
simple 26-Feb-2025 18:37:12 Publishing an artifact: getdown
simple 26-Feb-2025 18:37:12 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 99.27 ms
simple 26-Feb-2025 18:37:12 Running post build plugin 'Artifactory Release Management Staging'
simple 26-Feb-2025 18:37:12 Running post build plugin 'Artifactory Build Info Copier'
simple 26-Feb-2025 18:37:12 Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple 26-Feb-2025 18:37:12 Running post build plugin 'npm Cache Cleanup'
simple 26-Feb-2025 18:37:12 Running post build plugin 'Clover Results Collector'
simple 26-Feb-2025 18:37:12 Running post build plugin 'Docker Container Cleanup'
simple 26-Feb-2025 18:37:12 Finalising the build...
simple 26-Feb-2025 18:37:12 Stopping timer.
simple 26-Feb-2025 18:37:12 Build JB-GDL51-JOB1-5 completed.
simple 26-Feb-2025 18:37:12 Running on server: post build plugin 'NCover Results Collector'
simple 26-Feb-2025 18:37:12 Running on server: post build plugin 'Build Hanging Detection Configuration'
simple 26-Feb-2025 18:37:12 Running on server: post build plugin 'Clover Delta Calculator'
simple 26-Feb-2025 18:37:12 Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple 26-Feb-2025 18:37:12 All post build plugins have finished
simple 26-Feb-2025 18:37:12 Generating build results summary...
simple 26-Feb-2025 18:37:12 Saving build results to disk...
simple 26-Feb-2025 18:37:12 Logging substituted variables...
simple 26-Feb-2025 18:37:12 Indexing build results...
simple 26-Feb-2025 18:37:12 Finished building JB-GDL51-JOB1-5.