simple 18-Oct-2024 13:31:58 Build Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #5 (JB-GDL32-JOB1-5) started building on agent Default Agent simple 18-Oct-2024 13:31:58 simple 18-Oct-2024 13:31:58 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1 simple 18-Oct-2024 13:31:58 Executing build Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #5 (JB-GDL32-JOB1-5) simple 18-Oct-2024 13:31:58 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 18-Oct-2024 13:31:58 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1 simple 18-Oct-2024 13:31:58 Updating source code to revision: e1ff67badd0334881d8f07bbcac4262e16e5a709 simple 18-Oct-2024 13:31:58 Fetching 'refs/heads/feature/JAL-4386_JAL-4435_reformat_node_labels' from 'http://source.jalview.org/git/jalview.git'. simple 18-Oct-2024 13:31:59 Checking out revision e1ff67badd0334881d8f07bbcac4262e16e5a709. simple 18-Oct-2024 13:31:59 Previous HEAD position was 87ad046... Merge branch 'feature/JAL-4386_JAL-4435_coloured_lines_for_providers' into feature/JAL-4386_JAL-4435_reformat_node_labels simple 18-Oct-2024 13:31:59 Your branch is behind 'origin/feature/JAL-4386_JAL-4435_reformat_node_labels' by 4 commits, and can be fast-forwarded. simple 18-Oct-2024 13:31:59 (use "git pull" to update your local branch) simple 18-Oct-2024 13:31:59 Switched to branch 'feature/JAL-4386_JAL-4435_reformat_node_labels' simple 18-Oct-2024 13:31:59 HEAD is now at e1ff67b Merge branch 'feature/JAL-4476_reformat_ss_consensus_annotation_labels' into feature/JAL-4386_JAL-4435_reformat_node_labels simple 18-Oct-2024 13:31:59 Updated source code to revision: e1ff67badd0334881d8f07bbcac4262e16e5a709 simple 18-Oct-2024 13:31:59 Finished task 'Checkout Default Repository' with result: Success simple 18-Oct-2024 13:31:59 Running pre-build action: VCS Version Collector simple 18-Oct-2024 13:31:59 Running pre-build action: Artifactory Release Staging command 18-Oct-2024 13:31:59 Substituting variable: ${bamboo.planKey} with JB-GDL32 simple 18-Oct-2024 13:31:59 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 18-Oct-2024 13:31:59 Bamboo Artifactory Plugin version: 2.6.2 command 18-Oct-2024 13:31:59 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #5 (JB-GDL32-JOB1-5)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL32 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_dependency_parent_0=JB-GDB633-5\nbamboo_repository_46498138_name=Jalview Git\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=e1ff67badd0334881d8f07bbcac4262e16e5a709\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL32-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-GDL32-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL32-JOB1\nbamboo_shortPlanName=feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_planRepository_name=Jalview Git\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-GDL32-JOB1-5\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_shortPlanKey=GDL32\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=e1ff67badd0334881d8f07bbcac4262e16e5a709\nbamboo_buildTimeStamp=2024-10-18T13:26:53.353+01:00\nbamboo_repository_previous_revision_number=87ad04639b5b83d8c9e32c38ec75c481530dda3b\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDL32-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=e1ff67badd0334881d8f07bbcac4262e16e5a709\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_repository_46498138_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_46498138_revision_number=e1ff67badd0334881d8f07bbcac4262e16e5a709\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=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_46498138_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_git_username=\nbamboo_repository_46498138_previous_revision_number=87ad04639b5b83d8c9e32c38ec75c481530dda3b\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_repository_46498138_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301875\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=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_repository_46498138_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1\nbamboo_planKey=JB-GDL32\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/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 18-Oct-2024 13:32:00 build 18-Oct-2024 13:32:00 > Configure project : build 18-Oct-2024 13:32:00 Using properties from file './utils/channels/default/channel_gradle.properties' build 18-Oct-2024 13:32:00 JALVIEW_VERSION is set to '2.11.4.0' build 18-Oct-2024 13:32:00 HEADLESS BUILD build 18-Oct-2024 13:32:00 J2S ENABLED build 18-Oct-2024 13:32:00 Using a BUILD profile. build 18-Oct-2024 13:32:00 eclipseDir exists build 18-Oct-2024 13:32:00 build 18-Oct-2024 13:32:00 > Task :clean build 18-Oct-2024 13:32:00 > Task :cleanPackageDir build 18-Oct-2024 13:32:00 > Task :getdownImagesCopy build 18-Oct-2024 13:32:00 > Task :getdownImagesProcess build 18-Oct-2024 13:32:00 > Task :getdownImages build 18-Oct-2024 13:32:01 > Task :copyHelp build 18-Oct-2024 13:32:02 > Task :buildIndices build 18-Oct-2024 13:32:02 > Task :copyResources build 18-Oct-2024 13:32:02 > Task :copyChannelResources build 18-Oct-2024 13:32:02 build 18-Oct-2024 13:32:02 > Task :createBuildProperties build 18-Oct-2024 13:32:02 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 18-Oct-2024 13:32:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:02 build 18-Oct-2024 13:32:02 > Task :buildResources build 18-Oct-2024 13:32:02 > Task :copyDocs build 18-Oct-2024 13:32:02 build 18-Oct-2024 13:32:02 > Task :convertMdFiles build 18-Oct-2024 13:32:02 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 18-Oct-2024 13:32:02 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1/build/resources/doc_build/doc/releaseprocess.html build 18-Oct-2024 13:32:02 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 18-Oct-2024 13:32:02 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1/build/resources/doc_build/doc/building.html build 18-Oct-2024 13:32:02 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1/build/resources/doc_build/doc/jalview-projects.html build 18-Oct-2024 13:32:02 build 18-Oct-2024 13:32:02 > Task :releasesTemplates build 18-Oct-2024 13:32:02 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 18-Oct-2024 13:32:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:02 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:02 Stripping rc/test/etc for 2_11_4_0 build 18-Oct-2024 13:32:02 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_0.md build 18-Oct-2024 13:32:02 build 18-Oct-2024 13:32:02 > Task :prepare build 18-Oct-2024 13:32:04 build 18-Oct-2024 13:32:04 > Task :compileJava build 18-Oct-2024 13:32:04 Setting target compatibility to 11 error 18-Oct-2024 13:32:10 Note: Some input files use or override a deprecated API. error 18-Oct-2024 13:32:10 Note: Recompile with -Xlint:deprecation for details. error 18-Oct-2024 13:32:10 Note: Some input files use unchecked or unsafe operations. error 18-Oct-2024 13:32:10 Note: Recompile with -Xlint:unchecked for details. build 18-Oct-2024 13:32:10 build 18-Oct-2024 13:32:10 > Task :processResources build 18-Oct-2024 13:32:10 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 18-Oct-2024 13:32:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:10 build 18-Oct-2024 13:32:10 > Task :classes build 18-Oct-2024 13:32:11 build 18-Oct-2024 13:32:11 > Task :compileLinkCheck build 18-Oct-2024 13:32:11 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 18-Oct-2024 13:32:11 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:11 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:11 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-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 18-Oct-2024 13:32:13 build 18-Oct-2024 13:32:13 > Task :linkCheck build 18-Oct-2024 13:32:13 Checking help file links build 18-Oct-2024 13:34:19 build 18-Oct-2024 13:34:19 Results: build 18-Oct-2024 13:34:19 159 distinct help targets build 18-Oct-2024 13:34:19 159 help mappings build 18-Oct-2024 13:34:19 0 invalid targets build 18-Oct-2024 13:34:19 32 unused targets build 18-Oct-2024 13:34:19 uniprotfetcher: html/features/uniprotsequencefetcher.html build 18-Oct-2024 13:34:19 overviewprefs: html/features/preferences.html#overview build 18-Oct-2024 13:34:19 cdnafeatures: html/features/codingfeatures.html build 18-Oct-2024 13:34:19 startupprefs: html/features/preferences.html#startup build 18-Oct-2024 13:34:19 ensemblfetch: html/features/ensemblsequencefetcher.html build 18-Oct-2024 13:34:19 io.modellerpir: html/io/modellerpir.html build 18-Oct-2024 13:34:19 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 18-Oct-2024 13:34:19 pdbmcviewer: html/features/pdbviewer.html build 18-Oct-2024 13:34:19 workingwithpae: html/features/paematrices.html build 18-Oct-2024 13:34:19 groovy.colours: html/features/groovy.html#groovyColours build 18-Oct-2024 13:34:19 seqmappings: html/features/seqmappings.html build 18-Oct-2024 13:34:19 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 18-Oct-2024 13:34:19 splitframe.mirrorfonts: html/features/splitView.html#mirror build 18-Oct-2024 13:34:19 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 18-Oct-2024 13:34:19 search: html/features/search.html build 18-Oct-2024 13:34:19 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 18-Oct-2024 13:34:19 alformats: html/io/fileformats.html build 18-Oct-2024 13:34:19 strucprefs: html/features/preferences.html#structure build 18-Oct-2024 13:34:19 siftsmapping: html/features/siftsmapping.html build 18-Oct-2024 13:34:19 chimera.annotxfer: html/features/chimera.html#annotxfer build 18-Oct-2024 13:34:19 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 18-Oct-2024 13:34:19 newkeys: html/features/newkeystrokes.html build 18-Oct-2024 13:34:19 importvcf.attribs: html/features/importvcf.html#attribs build 18-Oct-2024 13:34:19 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 18-Oct-2024 13:34:19 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 18-Oct-2024 13:34:19 jalarchive: html/features/jalarchive.html build 18-Oct-2024 13:34:19 newsreader: html/webServices/newsreader.html build 18-Oct-2024 13:34:19 jalviewcltool: html/features/commandline.html#script build 18-Oct-2024 13:34:19 popMenuAddref: html/menus/popupMenu.html#addrefannot build 18-Oct-2024 13:34:19 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 18-Oct-2024 13:34:19 paematrixformat: html/io/paematrixformat.html build 18-Oct-2024 13:34:19 overview: html/features/overview.html build 18-Oct-2024 13:34:19 0 invalid map urls build 18-Oct-2024 13:34:19 0 invalid image attributes build 18-Oct-2024 13:34:19 500 internal href links (107 with anchors) build 18-Oct-2024 13:34:19 0 invalid internal href links build 18-Oct-2024 13:34:19 0 invalid internal anchor links build 18-Oct-2024 13:34:19 113 external href links build 18-Oct-2024 13:34:19 External links not verified as internet not available build 18-Oct-2024 13:34:19 *** Success *** build 18-Oct-2024 13:34:20 build 18-Oct-2024 13:34:20 > Task :jar build 18-Oct-2024 13:34:20 > Task :syncJars build 18-Oct-2024 13:34:20 > Task :makeDist build 18-Oct-2024 13:34:20 > Task :getdownWebsiteBuild build 18-Oct-2024 13:34:22 build 18-Oct-2024 13:34:22 > Task :getdownDigest build 18-Oct-2024 13:34:22 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 18-Oct-2024 13:34:22 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... error 18-Oct-2024 13:34:22 2024/10/18 13:34:21:031 WARNING Starting without install4j classes error 18-Oct-2024 13:34:22 2024/10/18 13:34:21:607 WARNING Starting without install4j classes build 18-Oct-2024 13:34:22 build 18-Oct-2024 13:34:22 > Task :getdown build 18-Oct-2024 13:34:22 build 18-Oct-2024 13:34:22 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 18-Oct-2024 13:34:22 build 18-Oct-2024 13:34:22 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 18-Oct-2024 13:34:22 build 18-Oct-2024 13:34:22 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 18-Oct-2024 13:34:22 build 18-Oct-2024 13:34:22 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 18-Oct-2024 13:34:22 Please consult deprecation warnings for more details. build 18-Oct-2024 13:34:22 build 18-Oct-2024 13:34:22 BUILD SUCCESSFUL in 2m 22s build 18-Oct-2024 13:34:22 21 actionable tasks: 21 executed simple 18-Oct-2024 13:34:22 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 18-Oct-2024 13:34:22 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 18-Oct-2024 13:34:22 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #5 (JB-GDL32-JOB1-5)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL32-JOB1-5-ScriptBuildTask-596360067966008268.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_dependency_parent_0=JB-GDB633-5\nbamboo_repository_46498138_name=Jalview Git\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=e1ff67badd0334881d8f07bbcac4262e16e5a709\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL32-JOB1-5\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL32-JOB1\nbamboo_shortPlanName=feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_planRepository_name=Jalview Git\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-GDL32-JOB1-5\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels\nbamboo_shortPlanKey=GDL32\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=e1ff67badd0334881d8f07bbcac4262e16e5a709\nbamboo_buildTimeStamp=2024-10-18T13:26:53.353+01:00\nbamboo_repository_previous_revision_number=87ad04639b5b83d8c9e32c38ec75c481530dda3b\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDL32-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=e1ff67badd0334881d8f07bbcac4262e16e5a709\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_repository_46498138_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\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-GDL32 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_repository_46498138_revision_number=e1ff67badd0334881d8f07bbcac4262e16e5a709\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_46498138_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_repository_git_username=\nbamboo_repository_46498138_previous_revision_number=87ad04639b5b83d8c9e32c38ec75c481530dda3b\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_repository_46498138_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301875\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=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_repository_46498138_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1\nbamboo_planKey=JB-GDL32\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels\n simple 18-Oct-2024 13:34:22 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 18-Oct-2024 13:34:22 Running post build plugin 'NCover Results Collector' simple 18-Oct-2024 13:34:22 Running post build plugin 'Artifact Copier' simple 18-Oct-2024 13:34:22 Publishing an artifact: getdown simple 18-Oct-2024 13:34:22 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 93.60 ms simple 18-Oct-2024 13:34:22 Running post build plugin 'Artifactory Release Management Staging' simple 18-Oct-2024 13:34:22 Running post build plugin 'Artifactory Build Info Copier' simple 18-Oct-2024 13:34:22 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 18-Oct-2024 13:34:22 Running post build plugin 'npm Cache Cleanup' simple 18-Oct-2024 13:34:22 Running post build plugin 'Clover Results Collector' simple 18-Oct-2024 13:34:22 Running post build plugin 'Docker Container Cleanup' simple 18-Oct-2024 13:34:22 Finalising the build... simple 18-Oct-2024 13:34:22 Stopping timer. simple 18-Oct-2024 13:34:22 Build JB-GDL32-JOB1-5 completed. simple 18-Oct-2024 13:34:22 Running on server: post build plugin 'NCover Results Collector' simple 18-Oct-2024 13:34:22 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 18-Oct-2024 13:34:22 Running on server: post build plugin 'Clover Delta Calculator' simple 18-Oct-2024 13:34:22 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 18-Oct-2024 13:34:22 All post build plugins have finished simple 18-Oct-2024 13:34:22 Generating build results summary... simple 18-Oct-2024 13:34:22 Saving build results to disk... simple 18-Oct-2024 13:34:22 Logging substituted variables... simple 18-Oct-2024 13:34:22 Indexing build results... simple 18-Oct-2024 13:34:22 Finished building JB-GDL32-JOB1-5.