simple 14-May-2025 09:53:33 Build Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #13 (JB-GDL51-JOB1-13) started building on agent Default Agent simple 14-May-2025 09:53:33 simple 14-May-2025 09:53:33 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1 simple 14-May-2025 09:53:33 Executing build Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #13 (JB-GDL51-JOB1-13) simple 14-May-2025 09:53:33 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 14-May-2025 09:53:33 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1 simple 14-May-2025 09:53:33 Updating source code to revision: 9f675c0d4465b2153c770f08755afe6f499d30c7 simple 14-May-2025 09:53:33 Fetching 'refs/heads/feature/JAL-4386_JAL-4435_reformat_node_labels' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 14-May-2025 09:53:33 Checking out revision 9f675c0d4465b2153c770f08755afe6f499d30c7. simple 14-May-2025 09:53:33 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 14-May-2025 09:53:33 4ad40bb..9f675c0 feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels simple 14-May-2025 09:53:33 * [new branch] improvement/JAL-4541_slight_increase_in_robustness_of_analytics_from_jalview_desktop -> origin/improvement/JAL-4541_slight_increase_in_robustness_of_analytics_from_jalview_desktop simple 14-May-2025 09:53:34 Already on 'feature/JAL-4386_JAL-4435_reformat_node_labels' simple 14-May-2025 09:53:34 Your branch is behind 'origin/feature/JAL-4386_JAL-4435_reformat_node_labels' by 1 commit, and can be fast-forwarded. simple 14-May-2025 09:53:34 (use "git pull" to update your local branch) simple 14-May-2025 09:53:34 HEAD is now at 9f675c0 JAL-4542 simple 14-May-2025 09:53:34 Updated source code to revision: 9f675c0d4465b2153c770f08755afe6f499d30c7 simple 14-May-2025 09:53:34 Finished task 'Checkout Default Repository' with result: Success simple 14-May-2025 09:53:34 Running pre-build action: VCS Version Collector simple 14-May-2025 09:53:34 Running pre-build action: Artifactory Release Staging command 14-May-2025 09:53:34 Substituting variable: ${bamboo.planKey} with JB-GDL51 simple 14-May-2025 09:53:34 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 14-May-2025 09:53:34 Bamboo Artifactory Plugin version: 2.6.2 command 14-May-2025 09:53:34 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #13 (JB-GDL51-JOB1-13)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL51 -Pbamboo_buildResultsUrl=${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-GDB661-17\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=9f675c0d4465b2153c770f08755afe6f499d30c7\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL51-JOB1-13\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=4ad40bb8c71aba1791b98ec8e1a6087f013c7766\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=13\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-JOB1-13\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=9f675c0d4465b2153c770f08755afe6f499d30c7\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=9f675c0d4465b2153c770f08755afe6f499d30c7\nbamboo_buildTimeStamp=2025-05-14T09:53:33.153+01:00\nbamboo_repository_previous_revision_number=4ad40bb8c71aba1791b98ec8e1a6087f013c7766\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDL51-JOB1-13\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=9f675c0d4465b2153c770f08755afe6f499d30c7\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 14-May-2025 09:53:35 build 14-May-2025 09:53:35 > Configure project : build 14-May-2025 09:53:35 Using properties from file './utils/channels/default/channel_gradle.properties' build 14-May-2025 09:53:35 JALVIEW_VERSION is set to '2.11.4.2' build 14-May-2025 09:53:35 HEADLESS BUILD build 14-May-2025 09:53:35 J2S ENABLED build 14-May-2025 09:53:35 Using a BUILD profile. build 14-May-2025 09:53:35 eclipseDir exists build 14-May-2025 09:53:36 build 14-May-2025 09:53:36 > Task :clean build 14-May-2025 09:53:36 > Task :cleanPackageDir build 14-May-2025 09:53:36 > Task :getdownImagesCopy build 14-May-2025 09:53:36 > Task :getdownImagesProcess build 14-May-2025 09:53:36 > Task :getdownImages build 14-May-2025 09:53:36 > Task :copyHelp build 14-May-2025 09:53:37 > Task :buildIndices build 14-May-2025 09:53:37 > Task :copyResources build 14-May-2025 09:53:37 > Task :copyChannelResources build 14-May-2025 09:53:37 build 14-May-2025 09:53:37 > Task :createBuildProperties build 14-May-2025 09:53:37 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 14-May-2025 09:53:37 - 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 14-May-2025 09:53:37 build 14-May-2025 09:53:37 > Task :buildResources build 14-May-2025 09:53:37 > Task :copyDocs build 14-May-2025 09:53:37 build 14-May-2025 09:53:37 > Task :convertMdFiles build 14-May-2025 09:53:37 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 14-May-2025 09:53:37 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/build/resources/doc_build/doc/releaseprocess.html build 14-May-2025 09:53:37 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 14-May-2025 09:53:37 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/build/resources/doc_build/doc/building.html build 14-May-2025 09:53:37 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/build/resources/doc_build/doc/jalview-projects.html build 14-May-2025 09:53:38 build 14-May-2025 09:53:38 > Task :releasesTemplates build 14-May-2025 09:53:38 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 14-May-2025 09:53:38 - 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 14-May-2025 09:53:38 - 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 14-May-2025 09:53:38 Stripping rc/test/etc for 2_11_4_2 build 14-May-2025 09:53:38 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL51-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_2.md build 14-May-2025 09:53:38 build 14-May-2025 09:53:38 > Task :prepare build 14-May-2025 09:53:40 build 14-May-2025 09:53:40 > Task :compileJava build 14-May-2025 09:53:40 Setting target compatibility to 11 error 14-May-2025 09:53:45 Note: Some input files use or override a deprecated API. error 14-May-2025 09:53:45 Note: Recompile with -Xlint:deprecation for details. error 14-May-2025 09:53:45 Note: Some input files use unchecked or unsafe operations. error 14-May-2025 09:53:45 Note: Recompile with -Xlint:unchecked for details. build 14-May-2025 09:53:45 build 14-May-2025 09:53:45 > Task :processResources build 14-May-2025 09:53:45 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 14-May-2025 09:53:45 - 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 14-May-2025 09:53:45 - 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 14-May-2025 09:53:45 - 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 14-May-2025 09:53:45 - 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 14-May-2025 09:53:45 - 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 14-May-2025 09:53:45 - 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 14-May-2025 09:53:45 - 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 14-May-2025 09:53:45 - 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 14-May-2025 09:53:45 build 14-May-2025 09:53:45 > Task :classes build 14-May-2025 09:53:47 build 14-May-2025 09:53:47 > Task :compileLinkCheck build 14-May-2025 09:53:47 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 14-May-2025 09:53:47 - 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 14-May-2025 09:53:47 - 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 14-May-2025 09:53:47 - 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 14-May-2025 09:53:47 build 14-May-2025 09:53:47 > Task :linkCheck build 14-May-2025 09:53:47 Checking help file links build 14-May-2025 09:53:47 build 14-May-2025 09:53:47 Results: build 14-May-2025 09:53:47 159 distinct help targets build 14-May-2025 09:53:47 159 help mappings build 14-May-2025 09:53:47 0 invalid targets build 14-May-2025 09:53:47 32 unused targets build 14-May-2025 09:53:47 uniprotfetcher: html/features/uniprotsequencefetcher.html build 14-May-2025 09:53:47 overviewprefs: html/features/preferences.html#overview build 14-May-2025 09:53:47 cdnafeatures: html/features/codingfeatures.html build 14-May-2025 09:53:47 startupprefs: html/features/preferences.html#startup build 14-May-2025 09:53:47 ensemblfetch: html/features/ensemblsequencefetcher.html build 14-May-2025 09:53:47 io.modellerpir: html/io/modellerpir.html build 14-May-2025 09:53:47 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 14-May-2025 09:53:47 pdbmcviewer: html/features/pdbviewer.html build 14-May-2025 09:53:47 workingwithpae: html/features/paematrices.html build 14-May-2025 09:53:47 groovy.colours: html/features/groovy.html#groovyColours build 14-May-2025 09:53:47 seqmappings: html/features/seqmappings.html build 14-May-2025 09:53:47 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 14-May-2025 09:53:47 splitframe.mirrorfonts: html/features/splitView.html#mirror build 14-May-2025 09:53:47 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 14-May-2025 09:53:47 search: html/features/search.html build 14-May-2025 09:53:47 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 14-May-2025 09:53:47 alformats: html/io/fileformats.html build 14-May-2025 09:53:47 strucprefs: html/features/preferences.html#structure build 14-May-2025 09:53:47 siftsmapping: html/features/siftsmapping.html build 14-May-2025 09:53:47 chimera.annotxfer: html/features/chimera.html#annotxfer build 14-May-2025 09:53:47 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 14-May-2025 09:53:47 newkeys: html/features/newkeystrokes.html build 14-May-2025 09:53:47 importvcf.attribs: html/features/importvcf.html#attribs build 14-May-2025 09:53:47 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 14-May-2025 09:53:47 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 14-May-2025 09:53:47 jalarchive: html/features/jalarchive.html build 14-May-2025 09:53:47 newsreader: html/webServices/newsreader.html build 14-May-2025 09:53:47 jalviewcltool: html/features/commandline.html#script build 14-May-2025 09:53:47 popMenuAddref: html/menus/popupMenu.html#addrefannot build 14-May-2025 09:53:47 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 14-May-2025 09:53:47 paematrixformat: html/io/paematrixformat.html build 14-May-2025 09:53:47 overview: html/features/overview.html build 14-May-2025 09:53:47 0 invalid map urls build 14-May-2025 09:53:47 0 invalid image attributes build 14-May-2025 09:53:47 508 internal href links (110 with anchors) build 14-May-2025 09:53:47 0 invalid internal href links build 14-May-2025 09:53:47 0 invalid internal anchor links build 14-May-2025 09:53:47 113 external href links build 14-May-2025 09:53:47 External links not verified as internet not available build 14-May-2025 09:53:47 *** Success *** build 14-May-2025 09:53:48 build 14-May-2025 09:53:48 > Task :jar build 14-May-2025 09:53:48 > Task :syncJars build 14-May-2025 09:53:48 > Task :makeDist build 14-May-2025 09:53:48 > Task :getdownWebsiteBuild build 14-May-2025 09:53:50 build 14-May-2025 09:53:50 > Task :getdownDigest build 14-May-2025 09:53:50 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 14-May-2025 09:53:50 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 14-May-2025 09:53:50 build 14-May-2025 09:53:50 > Task :getdown build 14-May-2025 09:53:50 error 14-May-2025 09:53:50 2025/05/14 09:53:48:954 WARNING Starting without install4j classes error 14-May-2025 09:53:50 2025/05/14 09:53:49:493 WARNING Starting without install4j classes build 14-May-2025 09:53:50 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 14-May-2025 09:53:50 build 14-May-2025 09:53:50 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 14-May-2025 09:53:50 build 14-May-2025 09:53:50 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 14-May-2025 09:53:50 build 14-May-2025 09:53:50 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 14-May-2025 09:53:50 Please consult deprecation warnings for more details. build 14-May-2025 09:53:50 build 14-May-2025 09:53:50 BUILD SUCCESSFUL in 15s build 14-May-2025 09:53:50 21 actionable tasks: 21 executed simple 14-May-2025 09:53:50 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 14-May-2025 09:53:50 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 14-May-2025 09:53:50 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - feature-JAL-4386_JAL-4435_reformat_node_labels - Default Job #13 (JB-GDL51-JOB1-13)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL51-JOB1-13-ScriptBuildTask-8845271342305831404.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-GDB661-17\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=9f675c0d4465b2153c770f08755afe6f499d30c7\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL51-JOB1-13\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=4ad40bb8c71aba1791b98ec8e1a6087f013c7766\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_buildNumber=13\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-JOB1-13\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=9f675c0d4465b2153c770f08755afe6f499d30c7\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=9f675c0d4465b2153c770f08755afe6f499d30c7\nbamboo_buildTimeStamp=2025-05-14T09:53:33.153+01:00\nbamboo_repository_previous_revision_number=4ad40bb8c71aba1791b98ec8e1a6087f013c7766\nbamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels\nbamboo_buildResultKey=JB-GDL51-JOB1-13\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=9f675c0d4465b2153c770f08755afe6f499d30c7\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 14-May-2025 09:53:50 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 14-May-2025 09:53:50 Running post build plugin 'NCover Results Collector' simple 14-May-2025 09:53:50 Running post build plugin 'Artifact Copier' simple 14-May-2025 09:53:50 Publishing an artifact: getdown simple 14-May-2025 09:53:51 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 773.4 ms simple 14-May-2025 09:53:51 Running post build plugin 'Artifactory Release Management Staging' simple 14-May-2025 09:53:51 Running post build plugin 'Artifactory Build Info Copier' simple 14-May-2025 09:53:51 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 14-May-2025 09:53:51 Running post build plugin 'npm Cache Cleanup' simple 14-May-2025 09:53:51 Running post build plugin 'Clover Results Collector' simple 14-May-2025 09:53:51 Running post build plugin 'Docker Container Cleanup' simple 14-May-2025 09:53:51 Finalising the build... simple 14-May-2025 09:53:51 Stopping timer. simple 14-May-2025 09:53:51 Build JB-GDL51-JOB1-13 completed. simple 14-May-2025 09:53:51 Running on server: post build plugin 'NCover Results Collector' simple 14-May-2025 09:53:51 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 14-May-2025 09:53:51 Running on server: post build plugin 'Clover Delta Calculator' simple 14-May-2025 09:53:51 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 14-May-2025 09:53:51 All post build plugins have finished simple 14-May-2025 09:53:51 Generating build results summary... simple 14-May-2025 09:53:51 Saving build results to disk... simple 14-May-2025 09:53:51 Logging substituted variables... simple 14-May-2025 09:53:51 Indexing build results... simple 14-May-2025 09:53:51 Finished building JB-GDL51-JOB1-13.