simple 06-Dec-2024 10:38:15 Build Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #7 (JB-GDL32-JOB1-7) started building on agent Default Agent simple 06-Dec-2024 10:38:15 simple 06-Dec-2024 10:38:15 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1 simple 06-Dec-2024 10:38:15 Executing build Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #7 (JB-GDL32-JOB1-7) simple 06-Dec-2024 10:38:15 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 06-Dec-2024 10:38:15 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1 simple 06-Dec-2024 10:38:15 Updating source code to revision: b01e34e4193f67114db140e6aa32eb1ef7e5b38f simple 06-Dec-2024 10:38:16 Fetching 'refs/heads/feature/JAL-4386_JAL-4435_reformat_node_labels' from 'http://source.jalview.org/git/jalview.git'. simple 06-Dec-2024 10:38:16 Checking out revision b01e34e4193f67114db140e6aa32eb1ef7e5b38f. simple 06-Dec-2024 10:38:17 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 06-Dec-2024 10:38:17 1c79fdc..b01e34e feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels simple 06-Dec-2024 10:38:17 1da3b80..5275010 JAL-4474_jalview.ps1_not_working -> origin/JAL-4474_jalview.ps1_not_working simple 06-Dec-2024 10:38:17 946589c..72a0f1e bug/JAL-4477_unmapped_filename_characters -> origin/bug/JAL-4477_unmapped_filename_characters simple 06-Dec-2024 10:38:17 * [new branch] bug/JAL-4482_gradle_task_linkCheck_fails -> origin/bug/JAL-4482_gradle_task_linkCheck_fails simple 06-Dec-2024 10:38:17 * [new branch] bug/JAL-4492_gradle_build_not_excluding_classes -> origin/bug/JAL-4492_gradle_build_not_excluding_classes simple 06-Dec-2024 10:38:17 9fb123c..544bd63 develop -> origin/develop simple 06-Dec-2024 10:38:17 * [new branch] experiment/JAL-4386_JAL-4435_with_HSB_colours -> origin/experiment/JAL-4386_JAL-4435_with_HSB_colours simple 06-Dec-2024 10:38:17 503c832..cfb9738 experiment/JAL-4386_experimental_string_to_colour_scheme_methods -> origin/experiment/JAL-4386_experimental_string_to_colour_scheme_methods simple 06-Dec-2024 10:38:17 * [new branch] features/JAL-3914_modelqualityscores_v2115 -> origin/features/JAL-3914_modelqualityscores_v2115 simple 06-Dec-2024 10:38:17 * [new branch] features/JAL-4489_cluster_pca_and_pasimap -> origin/features/JAL-4489_cluster_pca_and_pasimap simple 06-Dec-2024 10:38:17 * [new branch] features/JAL-4489_clustering_and_pca_pasimap_views -> origin/features/JAL-4489_clustering_and_pca_pasimap_views simple 06-Dec-2024 10:38:17 * [new branch] patch/JAL-4077_jmolsaveloadwindows -> origin/patch/JAL-4077_jmolsaveloadwindows simple 06-Dec-2024 10:38:17 * [new branch] patch/JAL-4333_translatecodonexception -> origin/patch/JAL-4333_translatecodonexception simple 06-Dec-2024 10:38:17 * [new branch] spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure -> origin/spike/JAL-4366_JAL-4386_JAL-4435_expandedmsafromstructure simple 06-Dec-2024 10:38:18 Already on 'feature/JAL-4386_JAL-4435_reformat_node_labels' simple 06-Dec-2024 10:38:18 Your branch is behind 'origin/feature/JAL-4386_JAL-4435_reformat_node_labels' by 1 commit, and can be fast-forwarded. simple 06-Dec-2024 10:38:18 (use "git pull" to update your local branch) simple 06-Dec-2024 10:38:18 HEAD is now at b01e34e JAL-4435 Map annotation row to tree node simple 06-Dec-2024 10:38:18 Updated source code to revision: b01e34e4193f67114db140e6aa32eb1ef7e5b38f simple 06-Dec-2024 10:38:18 Finished task 'Checkout Default Repository' with result: Success simple 06-Dec-2024 10:38:18 Running pre-build action: VCS Version Collector simple 06-Dec-2024 10:38:18 Running pre-build action: Artifactory Release Staging command 06-Dec-2024 10:38:18 Substituting variable: ${bamboo.planKey} with JB-GDL32 simple 06-Dec-2024 10:38:18 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 06-Dec-2024 10:38:18 Bamboo Artifactory Plugin version: 2.6.2 command 06-Dec-2024 10:38:18 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #7 (JB-GDL32-JOB1-7)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL32 -Pbamboo_buildResultsUrl=${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-GDB633-7\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=b01e34e4193f67114db140e6aa32eb1ef7e5b38f\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL32-JOB1-7\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=7\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-JOB1-7\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=b01e34e4193f67114db140e6aa32eb1ef7e5b38f\nbamboo_buildTimeStamp=2024-12-06T10:38:15.867Z\nbamboo_repository_previous_revision_number=1c79fdcc0d6c6c934767a6a04e192b262ec78de3\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDL32-JOB1-7\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=b01e34e4193f67114db140e6aa32eb1ef7e5b38f\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=b01e34e4193f67114db140e6aa32eb1ef7e5b38f\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=1c79fdcc0d6c6c934767a6a04e192b262ec78de3\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 06-Dec-2024 10:38:21 build 06-Dec-2024 10:38:21 > Configure project : build 06-Dec-2024 10:38:21 Using properties from file './utils/channels/default/channel_gradle.properties' build 06-Dec-2024 10:38:21 JALVIEW_VERSION is set to '2.11.4.0' build 06-Dec-2024 10:38:21 HEADLESS BUILD build 06-Dec-2024 10:38:21 J2S ENABLED build 06-Dec-2024 10:38:21 Using a BUILD profile. build 06-Dec-2024 10:38:21 eclipseDir exists build 06-Dec-2024 10:38:22 build 06-Dec-2024 10:38:22 > Task :clean build 06-Dec-2024 10:38:22 > Task :cleanPackageDir build 06-Dec-2024 10:38:22 > Task :getdownImagesCopy build 06-Dec-2024 10:38:22 > Task :getdownImagesProcess build 06-Dec-2024 10:38:22 > Task :getdownImages build 06-Dec-2024 10:38:24 > Task :copyHelp build 06-Dec-2024 10:38:27 > Task :buildIndices build 06-Dec-2024 10:38:27 > Task :copyResources build 06-Dec-2024 10:38:27 > Task :copyChannelResources build 06-Dec-2024 10:38:27 build 06-Dec-2024 10:38:27 > Task :createBuildProperties build 06-Dec-2024 10:38:27 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 06-Dec-2024 10:38:27 - 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 06-Dec-2024 10:38:27 build 06-Dec-2024 10:38:27 > Task :buildResources build 06-Dec-2024 10:38:28 > Task :copyDocs build 06-Dec-2024 10:38:28 build 06-Dec-2024 10:38:28 > Task :convertMdFiles build 06-Dec-2024 10:38:28 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 06-Dec-2024 10:38:28 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1/build/resources/doc_build/doc/releaseprocess.html build 06-Dec-2024 10:38:28 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 06-Dec-2024 10:38:28 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1/build/resources/doc_build/doc/building.html build 06-Dec-2024 10:38:28 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1/build/resources/doc_build/doc/jalview-projects.html build 06-Dec-2024 10:38:28 build 06-Dec-2024 10:38:28 > Task :releasesTemplates build 06-Dec-2024 10:38:28 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 06-Dec-2024 10:38:28 - 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 06-Dec-2024 10:38:28 - 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 06-Dec-2024 10:38:28 Stripping rc/test/etc for 2_11_4_0 build 06-Dec-2024 10:38:28 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL32-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_0.md build 06-Dec-2024 10:38:28 build 06-Dec-2024 10:38:28 > Task :prepare build 06-Dec-2024 10:38:30 build 06-Dec-2024 10:38:30 > Task :compileJava build 06-Dec-2024 10:38:30 Setting target compatibility to 11 error 06-Dec-2024 10:38:40 Note: Some input files use or override a deprecated API. error 06-Dec-2024 10:38:40 Note: Recompile with -Xlint:deprecation for details. error 06-Dec-2024 10:38:40 Note: Some input files use unchecked or unsafe operations. error 06-Dec-2024 10:38:40 Note: Recompile with -Xlint:unchecked for details. build 06-Dec-2024 10:38:41 build 06-Dec-2024 10:38:41 > Task :processResources build 06-Dec-2024 10:38:41 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 06-Dec-2024 10:38:41 - 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 06-Dec-2024 10:38:41 - 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 06-Dec-2024 10:38:41 - 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 06-Dec-2024 10:38:41 - 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 06-Dec-2024 10:38:41 - 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 06-Dec-2024 10:38:41 - 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 06-Dec-2024 10:38:41 - 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 06-Dec-2024 10:38:41 - 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 06-Dec-2024 10:38:41 build 06-Dec-2024 10:38:41 > Task :classes build 06-Dec-2024 10:38:42 build 06-Dec-2024 10:38:42 > Task :compileLinkCheck build 06-Dec-2024 10:38:42 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 06-Dec-2024 10:38:42 - 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 06-Dec-2024 10:38:42 - 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 06-Dec-2024 10:38:42 - 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 06-Dec-2024 10:38:44 build 06-Dec-2024 10:38:44 > Task :linkCheck build 06-Dec-2024 10:38:44 Checking help file links build 06-Dec-2024 10:40:50 build 06-Dec-2024 10:40:50 Results: build 06-Dec-2024 10:40:50 159 distinct help targets build 06-Dec-2024 10:40:50 159 help mappings build 06-Dec-2024 10:40:50 0 invalid targets build 06-Dec-2024 10:40:50 32 unused targets build 06-Dec-2024 10:40:50 uniprotfetcher: html/features/uniprotsequencefetcher.html build 06-Dec-2024 10:40:50 overviewprefs: html/features/preferences.html#overview build 06-Dec-2024 10:40:50 cdnafeatures: html/features/codingfeatures.html build 06-Dec-2024 10:40:50 startupprefs: html/features/preferences.html#startup build 06-Dec-2024 10:40:50 ensemblfetch: html/features/ensemblsequencefetcher.html build 06-Dec-2024 10:40:50 io.modellerpir: html/io/modellerpir.html build 06-Dec-2024 10:40:50 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 06-Dec-2024 10:40:50 pdbmcviewer: html/features/pdbviewer.html build 06-Dec-2024 10:40:50 workingwithpae: html/features/paematrices.html build 06-Dec-2024 10:40:50 groovy.colours: html/features/groovy.html#groovyColours build 06-Dec-2024 10:40:50 seqmappings: html/features/seqmappings.html build 06-Dec-2024 10:40:50 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 06-Dec-2024 10:40:50 splitframe.mirrorfonts: html/features/splitView.html#mirror build 06-Dec-2024 10:40:50 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 06-Dec-2024 10:40:50 search: html/features/search.html build 06-Dec-2024 10:40:50 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 06-Dec-2024 10:40:50 alformats: html/io/fileformats.html build 06-Dec-2024 10:40:50 strucprefs: html/features/preferences.html#structure build 06-Dec-2024 10:40:50 siftsmapping: html/features/siftsmapping.html build 06-Dec-2024 10:40:50 chimera.annotxfer: html/features/chimera.html#annotxfer build 06-Dec-2024 10:40:50 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 06-Dec-2024 10:40:50 newkeys: html/features/newkeystrokes.html build 06-Dec-2024 10:40:50 importvcf.attribs: html/features/importvcf.html#attribs build 06-Dec-2024 10:40:50 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 06-Dec-2024 10:40:50 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 06-Dec-2024 10:40:50 jalarchive: html/features/jalarchive.html build 06-Dec-2024 10:40:50 newsreader: html/webServices/newsreader.html build 06-Dec-2024 10:40:50 jalviewcltool: html/features/commandline.html#script build 06-Dec-2024 10:40:50 popMenuAddref: html/menus/popupMenu.html#addrefannot build 06-Dec-2024 10:40:50 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 06-Dec-2024 10:40:50 paematrixformat: html/io/paematrixformat.html build 06-Dec-2024 10:40:50 overview: html/features/overview.html build 06-Dec-2024 10:40:50 0 invalid map urls build 06-Dec-2024 10:40:50 0 invalid image attributes build 06-Dec-2024 10:40:50 500 internal href links (107 with anchors) build 06-Dec-2024 10:40:50 0 invalid internal href links build 06-Dec-2024 10:40:50 0 invalid internal anchor links build 06-Dec-2024 10:40:50 113 external href links build 06-Dec-2024 10:40:50 External links not verified as internet not available build 06-Dec-2024 10:40:50 *** Success *** build 06-Dec-2024 10:40:51 build 06-Dec-2024 10:40:51 > Task :jar build 06-Dec-2024 10:40:52 > Task :syncJars build 06-Dec-2024 10:40:52 > Task :makeDist build 06-Dec-2024 10:40:52 > Task :getdownWebsiteBuild build 06-Dec-2024 10:40:54 build 06-Dec-2024 10:40:54 > Task :getdownDigest build 06-Dec-2024 10:40:54 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 06-Dec-2024 10:40:54 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 06-Dec-2024 10:40:54 build 06-Dec-2024 10:40:54 > Task :getdown build 06-Dec-2024 10:40:54 build 06-Dec-2024 10:40:54 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 06-Dec-2024 10:40:54 build 06-Dec-2024 10:40:54 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 06-Dec-2024 10:40:54 build 06-Dec-2024 10:40:54 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 06-Dec-2024 10:40:54 build 06-Dec-2024 10:40:54 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 06-Dec-2024 10:40:54 Please consult deprecation warnings for more details. build 06-Dec-2024 10:40:54 build 06-Dec-2024 10:40:54 BUILD SUCCESSFUL in 2m 35s build 06-Dec-2024 10:40:54 21 actionable tasks: 21 executed error 06-Dec-2024 10:40:54 2024/12/06 10:40:52:908 WARNING Starting without install4j classes error 06-Dec-2024 10:40:54 2024/12/06 10:40:53:496 WARNING Starting without install4j classes simple 06-Dec-2024 10:40:54 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 06-Dec-2024 10:40:54 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 06-Dec-2024 10:40:54 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #7 (JB-GDL32-JOB1-7)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL32-JOB1-7-ScriptBuildTask-7373130175540571583.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-GDB633-7\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=b01e34e4193f67114db140e6aa32eb1ef7e5b38f\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL32-JOB1-7\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=7\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-JOB1-7\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=b01e34e4193f67114db140e6aa32eb1ef7e5b38f\nbamboo_buildTimeStamp=2024-12-06T10:38:15.867Z\nbamboo_repository_previous_revision_number=1c79fdcc0d6c6c934767a6a04e192b262ec78de3\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDL32-JOB1-7\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=b01e34e4193f67114db140e6aa32eb1ef7e5b38f\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=b01e34e4193f67114db140e6aa32eb1ef7e5b38f\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=1c79fdcc0d6c6c934767a6a04e192b262ec78de3\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 06-Dec-2024 10:40:54 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 06-Dec-2024 10:40:54 Running post build plugin 'NCover Results Collector' simple 06-Dec-2024 10:40:54 Running post build plugin 'Artifact Copier' simple 06-Dec-2024 10:40:54 Publishing an artifact: getdown simple 06-Dec-2024 10:40:54 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 109.5 ms simple 06-Dec-2024 10:40:54 Running post build plugin 'Artifactory Release Management Staging' simple 06-Dec-2024 10:40:54 Running post build plugin 'Artifactory Build Info Copier' simple 06-Dec-2024 10:40:54 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 06-Dec-2024 10:40:54 Running post build plugin 'npm Cache Cleanup' simple 06-Dec-2024 10:40:54 Running post build plugin 'Clover Results Collector' simple 06-Dec-2024 10:40:54 Running post build plugin 'Docker Container Cleanup' simple 06-Dec-2024 10:40:54 Finalising the build... simple 06-Dec-2024 10:40:54 Stopping timer. simple 06-Dec-2024 10:40:54 Build JB-GDL32-JOB1-7 completed. simple 06-Dec-2024 10:40:54 Running on server: post build plugin 'NCover Results Collector' simple 06-Dec-2024 10:40:54 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 06-Dec-2024 10:40:54 Running on server: post build plugin 'Clover Delta Calculator' simple 06-Dec-2024 10:40:54 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 06-Dec-2024 10:40:54 All post build plugins have finished simple 06-Dec-2024 10:40:54 Generating build results summary... simple 06-Dec-2024 10:40:54 Saving build results to disk... simple 06-Dec-2024 10:40:54 Logging substituted variables... simple 06-Dec-2024 10:40:54 Indexing build results... simple 06-Dec-2024 10:40:54 Finished building JB-GDL32-JOB1-7.