simple 07-Mar-2025 09:52:24 Build Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #6 (JB-GDL51-JOB1-6) started building on agent Default Agent
simple 07-Mar-2025 09:52:24
simple 07-Mar-2025 09:52:24 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1
simple 07-Mar-2025 09:52:24 Executing build Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #6 (JB-GDL51-JOB1-6)
simple 07-Mar-2025 09:52:24 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple 07-Mar-2025 09:52:24 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1
simple 07-Mar-2025 09:52:24 Updating source code to revision: fbda4585b2681eea8794f267dc30b6e98bfad030
simple 07-Mar-2025 09:52:24 Fetching 'refs/heads/feature/JAL-4386_JAL-4435_reformat_node_labels' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple 07-Mar-2025 09:52:25 Checking out revision fbda4585b2681eea8794f267dc30b6e98bfad030.
simple 07-Mar-2025 09:52:25 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple 07-Mar-2025 09:52:25 d9b1091..fbda458 feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels
simple 07-Mar-2025 09:52:25 * [new branch] jims_2_12/JAL-4519_error_reporting_and_slivka -> origin/jims_2_12/JAL-4519_error_reporting_and_slivka
simple 07-Mar-2025 09:52:25 * [new branch] spike/JAL-4517_customNodenamesInNewick -> origin/spike/JAL-4517_customNodenamesInNewick
simple 07-Mar-2025 09:52:25 Already on 'feature/JAL-4386_JAL-4435_reformat_node_labels'
simple 07-Mar-2025 09:52:25 Your branch is behind 'origin/feature/JAL-4386_JAL-4435_reformat_node_labels' by 3 commits, and can be fast-forwarded.
simple 07-Mar-2025 09:52:25 (use "git pull" to update your local branch)
simple 07-Mar-2025 09:52:25 HEAD is now at fbda458 Merge branch 'spike/JAL-4517_customNodenamesInNewick' into 'feature/JAL-4386_JAL-4435_reformat_node_labels'
simple 07-Mar-2025 09:52:25 Updated source code to revision: fbda4585b2681eea8794f267dc30b6e98bfad030
simple 07-Mar-2025 09:52:25 Finished task 'Checkout Default Repository' with result: Success
simple 07-Mar-2025 09:52:25 Running pre-build action: VCS Version Collector
simple 07-Mar-2025 09:52:25 Running pre-build action: Artifactory Release Staging
command 07-Mar-2025 09:52:25 Substituting variable: ${bamboo.planKey} with JB-GDL51
simple 07-Mar-2025 09:52:25 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple 07-Mar-2025 09:52:25 Bamboo Artifactory Plugin version: 2.6.2
command 07-Mar-2025 09:52:25 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #6 (JB-GDL51-JOB1-6)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL51 -Pbamboo_buildResultsUrl=${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-GDB661-8\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=fbda4585b2681eea8794f267dc30b6e98bfad030\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL51-JOB1-6\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=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=6\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-JOB1-6\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=fbda4585b2681eea8794f267dc30b6e98bfad030\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=fbda4585b2681eea8794f267dc30b6e98bfad030\nbamboo_buildTimeStamp=2025-03-07T09:50:26.728Z\nbamboo_repository_previous_revision_number=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDL51-JOB1-6\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=fbda4585b2681eea8794f267dc30b6e98bfad030\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 07-Mar-2025 09:52:27
build 07-Mar-2025 09:52:27 > Configure project :
build 07-Mar-2025 09:52:27 Using properties from file './utils/channels/default/channel_gradle.properties'
build 07-Mar-2025 09:52:27 JALVIEW_VERSION is set to '2.11.4.0'
build 07-Mar-2025 09:52:27 HEADLESS BUILD
build 07-Mar-2025 09:52:27 J2S ENABLED
build 07-Mar-2025 09:52:27 Using a BUILD profile.
build 07-Mar-2025 09:52:27 eclipseDir exists
build 07-Mar-2025 09:52:27
build 07-Mar-2025 09:52:27 > Task :clean
build 07-Mar-2025 09:52:27 > Task :cleanPackageDir
build 07-Mar-2025 09:52:27 > Task :getdownImagesCopy
build 07-Mar-2025 09:52:28 > Task :getdownImagesProcess
build 07-Mar-2025 09:52:28 > Task :getdownImages
build 07-Mar-2025 09:52:28 > Task :copyHelp
build 07-Mar-2025 09:52:30 > Task :buildIndices
build 07-Mar-2025 09:52:31 > Task :copyResources
build 07-Mar-2025 09:52:31 > Task :copyChannelResources
build 07-Mar-2025 09:52:31
build 07-Mar-2025 09:52:31 > Task :createBuildProperties
build 07-Mar-2025 09:52:31 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build 07-Mar-2025 09:52:31 - 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 07-Mar-2025 09:52:31
build 07-Mar-2025 09:52:31 > Task :buildResources
build 07-Mar-2025 09:52:31 > Task :copyDocs
build 07-Mar-2025 09:52:31
build 07-Mar-2025 09:52:31 > Task :convertMdFiles
build 07-Mar-2025 09:52:31 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build 07-Mar-2025 09:52:31 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/build/resources/doc_build/doc/releaseprocess.html
build 07-Mar-2025 09:52:31 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 07-Mar-2025 09:52:31 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/build/resources/doc_build/doc/building.html
build 07-Mar-2025 09:52:31 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/build/resources/doc_build/doc/jalview-projects.html
build 07-Mar-2025 09:52:32
build 07-Mar-2025 09:52:32 > Task :releasesTemplates
build 07-Mar-2025 09:52:32 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build 07-Mar-2025 09:52:32 - 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 07-Mar-2025 09:52:32 - 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 07-Mar-2025 09:52:32 Stripping rc/test/etc for 2_11_4_0
build 07-Mar-2025 09:52:32 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_0.md
build 07-Mar-2025 09:52:32
build 07-Mar-2025 09:52:32 > Task :prepare
build 07-Mar-2025 09:52:34
build 07-Mar-2025 09:52:34 > Task :compileJava
build 07-Mar-2025 09:52:34 Setting target compatibility to 11
error 07-Mar-2025 09:52:41 Note: Some input files use or override a deprecated API.
error 07-Mar-2025 09:52:41 Note: Recompile with -Xlint:deprecation for details.
error 07-Mar-2025 09:52:41 Note: Some input files use unchecked or unsafe operations.
error 07-Mar-2025 09:52:41 Note: Recompile with -Xlint:unchecked for details.
build 07-Mar-2025 09:52:42
build 07-Mar-2025 09:52:42 > Task :processResources
build 07-Mar-2025 09:52:42 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build 07-Mar-2025 09:52:42 - 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 07-Mar-2025 09:52:42 - 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 07-Mar-2025 09:52:42 - 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 07-Mar-2025 09:52:42 - 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 07-Mar-2025 09:52:42 - 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 07-Mar-2025 09:52:42 - 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 07-Mar-2025 09:52:42 - 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 07-Mar-2025 09:52:42 - 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 07-Mar-2025 09:52:42
build 07-Mar-2025 09:52:42 > Task :classes
build 07-Mar-2025 09:52:44
build 07-Mar-2025 09:52:44 > Task :compileLinkCheck
build 07-Mar-2025 09:52:44 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build 07-Mar-2025 09:52:44 - 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 07-Mar-2025 09:52:44 - 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 07-Mar-2025 09:52:44 - 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 07-Mar-2025 09:52:44
build 07-Mar-2025 09:52:44 > Task :linkCheck
build 07-Mar-2025 09:52:44 Checking help file links
build 07-Mar-2025 09:52:44
build 07-Mar-2025 09:52:44 Results:
build 07-Mar-2025 09:52:44 159 distinct help targets
build 07-Mar-2025 09:52:44 159 help mappings
build 07-Mar-2025 09:52:44 0 invalid targets
build 07-Mar-2025 09:52:44 32 unused targets
build 07-Mar-2025 09:52:44 uniprotfetcher: html/features/uniprotsequencefetcher.html
build 07-Mar-2025 09:52:44 overviewprefs: html/features/preferences.html#overview
build 07-Mar-2025 09:52:44 cdnafeatures: html/features/codingfeatures.html
build 07-Mar-2025 09:52:44 startupprefs: html/features/preferences.html#startup
build 07-Mar-2025 09:52:44 ensemblfetch: html/features/ensemblsequencefetcher.html
build 07-Mar-2025 09:52:44 io.modellerpir: html/io/modellerpir.html
build 07-Mar-2025 09:52:44 structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build 07-Mar-2025 09:52:44 pdbmcviewer: html/features/pdbviewer.html
build 07-Mar-2025 09:52:44 workingwithpae: html/features/paematrices.html
build 07-Mar-2025 09:52:44 groovy.colours: html/features/groovy.html#groovyColours
build 07-Mar-2025 09:52:44 seqmappings: html/features/seqmappings.html
build 07-Mar-2025 09:52:44 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build 07-Mar-2025 09:52:44 splitframe.mirrorfonts: html/features/splitView.html#mirror
build 07-Mar-2025 09:52:44 subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build 07-Mar-2025 09:52:44 search: html/features/search.html
build 07-Mar-2025 09:52:44 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build 07-Mar-2025 09:52:44 alformats: html/io/fileformats.html
build 07-Mar-2025 09:52:44 strucprefs: html/features/preferences.html#structure
build 07-Mar-2025 09:52:44 siftsmapping: html/features/siftsmapping.html
build 07-Mar-2025 09:52:44 chimera.annotxfer: html/features/chimera.html#annotxfer
build 07-Mar-2025 09:52:44 pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build 07-Mar-2025 09:52:44 newkeys: html/features/newkeystrokes.html
build 07-Mar-2025 09:52:44 importvcf.attribs: html/features/importvcf.html#attribs
build 07-Mar-2025 09:52:44 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build 07-Mar-2025 09:52:44 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build 07-Mar-2025 09:52:44 jalarchive: html/features/jalarchive.html
build 07-Mar-2025 09:52:44 newsreader: html/webServices/newsreader.html
build 07-Mar-2025 09:52:44 jalviewcltool: html/features/commandline.html#script
build 07-Mar-2025 09:52:44 popMenuAddref: html/menus/popupMenu.html#addrefannot
build 07-Mar-2025 09:52:44 splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build 07-Mar-2025 09:52:44 paematrixformat: html/io/paematrixformat.html
build 07-Mar-2025 09:52:44 overview: html/features/overview.html
build 07-Mar-2025 09:52:44 0 invalid map urls
build 07-Mar-2025 09:52:44 0 invalid image attributes
build 07-Mar-2025 09:52:44 500 internal href links (107 with anchors)
build 07-Mar-2025 09:52:44 0 invalid internal href links
build 07-Mar-2025 09:52:44 0 invalid internal anchor links
build 07-Mar-2025 09:52:44 113 external href links
build 07-Mar-2025 09:52:44 External links not verified as internet not available
build 07-Mar-2025 09:52:44 *** Success ***
build 07-Mar-2025 09:52:45
build 07-Mar-2025 09:52:45 > Task :jar
build 07-Mar-2025 09:52:46 > Task :syncJars
build 07-Mar-2025 09:52:46 > Task :makeDist
build 07-Mar-2025 09:52:47 > Task :getdownWebsiteBuild
build 07-Mar-2025 09:52:48
build 07-Mar-2025 09:52:48 > Task :getdownDigest
build 07-Mar-2025 09:52:48 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
build 07-Mar-2025 09:52:48 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build 07-Mar-2025 09:52:48
error 07-Mar-2025 09:52:48 2025/03/07 09:52:47:434 WARNING Starting without install4j classes
error 07-Mar-2025 09:52:48 2025/03/07 09:52:47:996 WARNING Starting without install4j classes
build 07-Mar-2025 09:52:48 > Task :getdown
build 07-Mar-2025 09:52:48
build 07-Mar-2025 09:52:48 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build 07-Mar-2025 09:52:48
build 07-Mar-2025 09:52:48 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build 07-Mar-2025 09:52:48
build 07-Mar-2025 09:52:48 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build 07-Mar-2025 09:52:48
build 07-Mar-2025 09:52:48 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness.
build 07-Mar-2025 09:52:48 Please consult deprecation warnings for more details.
build 07-Mar-2025 09:52:48
build 07-Mar-2025 09:52:48 BUILD SUCCESSFUL in 22s
build 07-Mar-2025 09:52:48 21 actionable tasks: 21 executed
simple 07-Mar-2025 09:52:48 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success
simple 07-Mar-2025 09:52:48 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command 07-Mar-2025 09:52:48 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #6 (JB-GDL51-JOB1-6)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL51-JOB1-6-ScriptBuildTask-467823855975058594.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-GDB661-8\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=fbda4585b2681eea8794f267dc30b6e98bfad030\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL51-JOB1-6\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=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_buildNumber=6\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-JOB1-6\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=fbda4585b2681eea8794f267dc30b6e98bfad030\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=fbda4585b2681eea8794f267dc30b6e98bfad030\nbamboo_buildTimeStamp=2025-03-07T09:50:26.728Z\nbamboo_repository_previous_revision_number=d9b10917dcf53abeb15fd632531e699905025179\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDL51-JOB1-6\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=fbda4585b2681eea8794f267dc30b6e98bfad030\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 07-Mar-2025 09:52:49 Finished task 'Copy JVL file and produce link in HTML' with result: Success
simple 07-Mar-2025 09:52:49 Running post build plugin 'NCover Results Collector'
simple 07-Mar-2025 09:52:49 Running post build plugin 'Artifact Copier'
simple 07-Mar-2025 09:52:49 Publishing an artifact: getdown
simple 07-Mar-2025 09:52:49 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 92.32 ms
simple 07-Mar-2025 09:52:49 Running post build plugin 'Artifactory Release Management Staging'
simple 07-Mar-2025 09:52:49 Running post build plugin 'Artifactory Build Info Copier'
simple 07-Mar-2025 09:52:49 Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple 07-Mar-2025 09:52:49 Running post build plugin 'npm Cache Cleanup'
simple 07-Mar-2025 09:52:49 Running post build plugin 'Clover Results Collector'
simple 07-Mar-2025 09:52:49 Running post build plugin 'Docker Container Cleanup'
simple 07-Mar-2025 09:52:49 Finalising the build...
simple 07-Mar-2025 09:52:49 Stopping timer.
simple 07-Mar-2025 09:52:49 Build JB-GDL51-JOB1-6 completed.
simple 07-Mar-2025 09:52:49 Running on server: post build plugin 'NCover Results Collector'
simple 07-Mar-2025 09:52:49 Running on server: post build plugin 'Build Hanging Detection Configuration'
simple 07-Mar-2025 09:52:49 Running on server: post build plugin 'Clover Delta Calculator'
simple 07-Mar-2025 09:52:49 Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple 07-Mar-2025 09:52:49 All post build plugins have finished
simple 07-Mar-2025 09:52:49 Generating build results summary...
simple 07-Mar-2025 09:52:49 Saving build results to disk...
simple 07-Mar-2025 09:52:49 Logging substituted variables...
simple 07-Mar-2025 09:52:49 Indexing build results...
simple 07-Mar-2025 09:52:49 Finished building JB-GDL51-JOB1-6.