simple 05-Jan-2026 05:21:18 Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job #4 (JB-GDL113-JOB1-4) started building on agent Default Agent simple 05-Jan-2026 05:21:18 simple 05-Jan-2026 05:21:18 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1 simple 05-Jan-2026 05:21:18 Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job #4 (JB-GDL113-JOB1-4) simple 05-Jan-2026 05:21:18 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 05-Jan-2026 05:21:18 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1 simple 05-Jan-2026 05:21:18 Updating source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 simple 05-Jan-2026 05:21:18 Fetching 'refs/heads/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 05-Jan-2026 05:21:19 Checking out revision b6ff7e553d3ba8b32e1d2650df7860706b2a37d5. simple 05-Jan-2026 05:21:19 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 05-Jan-2026 05:21:19 5857fe7..b6ff7e5 bug/JAL-4107_jalviewjs_fixes_on_2_12_branch -> origin/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch simple 05-Jan-2026 05:21:19 Already on 'bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' simple 05-Jan-2026 05:21:19 Your branch is behind 'origin/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' by 1 commit, and can be fast-forwarded. simple 05-Jan-2026 05:21:19 (use "git pull" to update your local branch) simple 05-Jan-2026 05:21:19 HEAD is now at b6ff7e5 JAL-4107 reinstate Console output of DESKTOP CREATED so jalviewjsHeadlessTest passes simple 05-Jan-2026 05:21:19 Updated source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5 simple 05-Jan-2026 05:21:19 Finished task 'Checkout Default Repository' with result: Success simple 05-Jan-2026 05:21:19 Running pre-build action: VCS Version Collector simple 05-Jan-2026 05:21:19 Running pre-build action: Artifactory Release Staging command 05-Jan-2026 05:21:19 Substituting variable: ${bamboo.planKey} with JB-GDL113 simple 05-Jan-2026 05:21:19 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 05-Jan-2026 05:21:19 Bamboo Artifactory Plugin version: 2.6.2 command 05-Jan-2026 05:21:19 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job #4 (JB-GDL113-JOB1-4)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL113 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_dependency_parent_0=JB-GDB734-7\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_46498617_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL113-JOB1-4\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-GDL113-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL113-JOB1\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=4\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-GDL113-JOB1-4\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_46498617_name=Jalview Gitlab\nbamboo_shortPlanKey=GDL113\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_buildTimeStamp=2026-01-05T05:21:18.481Z\nbamboo_repository_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GDL113-JOB1-4\nbamboo_repository_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_repository_46498617_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\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=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\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=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\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_plan_storageTag=plan-46302803\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46498617_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7\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_repository_46498617_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\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-GDL113-JOB1\nbamboo_planKey=JB-GDL113\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498617_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_repository_46498617_git_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 05-Jan-2026 05:21:21 build 05-Jan-2026 05:21:21 > Configure project : build 05-Jan-2026 05:21:21 Using properties from file './utils/channels/default/channel_gradle.properties' build 05-Jan-2026 05:21:21 JALVIEW_VERSION is set to '2.12.0' build 05-Jan-2026 05:21:21 HEADLESS BUILD build 05-Jan-2026 05:21:21 J2S ENABLED build 05-Jan-2026 05:21:21 Using a BUILD profile. build 05-Jan-2026 05:21:21 eclipseDir exists build 05-Jan-2026 05:21:21 build 05-Jan-2026 05:21:21 > Task :clean build 05-Jan-2026 05:21:21 > Task :cleanPackageDir build 05-Jan-2026 05:21:21 > Task :getdownImagesCopy build 05-Jan-2026 05:21:21 > Task :getdownImagesProcess build 05-Jan-2026 05:21:21 > Task :getdownImages build 05-Jan-2026 05:21:21 > Task :copyHelp build 05-Jan-2026 05:21:22 > Task :buildIndices build 05-Jan-2026 05:21:22 > Task :copyResources build 05-Jan-2026 05:21:22 > Task :copyChannelResources build 05-Jan-2026 05:21:22 build 05-Jan-2026 05:21:22 > Task :createBuildProperties build 05-Jan-2026 05:21:22 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 05-Jan-2026 05:21:22 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:22 build 05-Jan-2026 05:21:22 > Task :buildResources build 05-Jan-2026 05:21:23 > Task :copyDocs build 05-Jan-2026 05:21:23 build 05-Jan-2026 05:21:23 > Task :convertMdFiles build 05-Jan-2026 05:21:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 05-Jan-2026 05:21:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/releaseprocess.html build 05-Jan-2026 05:21:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 05-Jan-2026 05:21:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/JalviewJS-API.html build 05-Jan-2026 05:21:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/building.html build 05-Jan-2026 05:21:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/addingWebClient.html build 05-Jan-2026 05:21:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/jalview-projects.html build 05-Jan-2026 05:21:23 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html build 05-Jan-2026 05:21:23 build 05-Jan-2026 05:21:23 > Task :releasesTemplates build 05-Jan-2026 05:21:23 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 05-Jan-2026 05:21:23 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:23 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:23 Stripping rc/test/etc for 2_12_0 build 05-Jan-2026 05:21:23 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/help/markdown/whatsnew/whatsnew-2_12_0.md build 05-Jan-2026 05:21:23 build 05-Jan-2026 05:21:23 > Task :prepare build 05-Jan-2026 05:21:25 build 05-Jan-2026 05:21:25 > Task :compileJava build 05-Jan-2026 05:21:25 Setting target compatibility to 11 error 05-Jan-2026 05:21:31 Note: Some input files use or override a deprecated API. error 05-Jan-2026 05:21:31 Note: Recompile with -Xlint:deprecation for details. error 05-Jan-2026 05:21:31 Note: Some input files use unchecked or unsafe operations. error 05-Jan-2026 05:21:31 Note: Recompile with -Xlint:unchecked for details. build 05-Jan-2026 05:21:31 build 05-Jan-2026 05:21:31 > Task :processResources build 05-Jan-2026 05:21:31 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 05-Jan-2026 05:21:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:31 build 05-Jan-2026 05:21:31 > Task :classes build 05-Jan-2026 05:21:32 build 05-Jan-2026 05:21:32 > Task :compileLinkCheck build 05-Jan-2026 05:21:32 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 05-Jan-2026 05:21:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-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 05-Jan-2026 05:21:34 build 05-Jan-2026 05:21:34 > Task :linkCheck build 05-Jan-2026 05:21:34 Checking help file links build 05-Jan-2026 05:23:40 build 05-Jan-2026 05:23:40 Results: build 05-Jan-2026 05:23:40 162 distinct help targets build 05-Jan-2026 05:23:40 162 help mappings build 05-Jan-2026 05:23:40 0 invalid targets build 05-Jan-2026 05:23:40 31 unused targets build 05-Jan-2026 05:23:40 uniprotfetcher: html/features/uniprotsequencefetcher.html build 05-Jan-2026 05:23:40 overviewprefs: html/features/preferences.html#overview build 05-Jan-2026 05:23:40 cdnafeatures: html/features/codingfeatures.html build 05-Jan-2026 05:23:40 startupprefs: html/features/preferences.html#startup build 05-Jan-2026 05:23:40 ensemblfetch: html/features/ensemblsequencefetcher.html build 05-Jan-2026 05:23:40 io.modellerpir: html/io/modellerpir.html build 05-Jan-2026 05:23:40 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 05-Jan-2026 05:23:40 pdbmcviewer: html/features/pdbviewer.html build 05-Jan-2026 05:23:40 groovy.colours: html/features/groovy.html#groovyColours build 05-Jan-2026 05:23:40 seqmappings: html/features/seqmappings.html build 05-Jan-2026 05:23:40 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 05-Jan-2026 05:23:40 splitframe.mirrorfonts: html/features/splitView.html#mirror build 05-Jan-2026 05:23:40 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 05-Jan-2026 05:23:40 search: html/features/search.html build 05-Jan-2026 05:23:40 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 05-Jan-2026 05:23:40 alformats: html/io/fileformats.html build 05-Jan-2026 05:23:40 strucprefs: html/features/preferences.html#structure build 05-Jan-2026 05:23:40 siftsmapping: html/features/siftsmapping.html build 05-Jan-2026 05:23:40 chimera.annotxfer: html/features/chimera.html#annotxfer build 05-Jan-2026 05:23:40 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 05-Jan-2026 05:23:40 newkeys: html/features/newkeystrokes.html build 05-Jan-2026 05:23:40 importvcf.attribs: html/features/importvcf.html#attribs build 05-Jan-2026 05:23:40 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 05-Jan-2026 05:23:40 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 05-Jan-2026 05:23:40 jalarchive: html/features/jalarchive.html build 05-Jan-2026 05:23:40 newsreader: html/webServices/newsreader.html build 05-Jan-2026 05:23:40 jalviewcltool: html/features/commandline.html#script build 05-Jan-2026 05:23:40 popMenuAddref: html/menus/popupMenu.html#addrefannot build 05-Jan-2026 05:23:40 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 05-Jan-2026 05:23:40 paematrixformat: html/io/paematrixformat.html build 05-Jan-2026 05:23:40 overview: html/features/overview.html build 05-Jan-2026 05:23:40 0 invalid map urls build 05-Jan-2026 05:23:40 0 invalid image attributes build 05-Jan-2026 05:23:40 520 internal href links (119 with anchors) build 05-Jan-2026 05:23:40 0 invalid internal href links build 05-Jan-2026 05:23:40 0 invalid internal anchor links build 05-Jan-2026 05:23:40 113 external href links build 05-Jan-2026 05:23:40 External links not verified as internet not available build 05-Jan-2026 05:23:40 *** Success *** build 05-Jan-2026 05:23:41 build 05-Jan-2026 05:23:41 > Task :jar build 05-Jan-2026 05:23:41 > Task :syncJars build 05-Jan-2026 05:23:41 > Task :makeDist build 05-Jan-2026 05:23:41 > Task :getdownWebsiteBuild error 05-Jan-2026 05:23:43 2026/01/05 05:23:41:878 WARNING Starting without install4j classes build 05-Jan-2026 05:23:43 build 05-Jan-2026 05:23:43 > Task :getdownDigest build 05-Jan-2026 05:23:43 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 05-Jan-2026 05:23:43 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 05-Jan-2026 05:23:43 build 05-Jan-2026 05:23:43 > Task :getdown error 05-Jan-2026 05:23:43 2026/01/05 05:23:42:464 WARNING Starting without install4j classes build 05-Jan-2026 05:23:43 build 05-Jan-2026 05:23:43 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 05-Jan-2026 05:23:43 build 05-Jan-2026 05:23:43 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 05-Jan-2026 05:23:43 build 05-Jan-2026 05:23:43 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 05-Jan-2026 05:23:43 build 05-Jan-2026 05:23:43 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 05-Jan-2026 05:23:43 Please consult deprecation warnings for more details. build 05-Jan-2026 05:23:43 build 05-Jan-2026 05:23:43 BUILD SUCCESSFUL in 2m 23s build 05-Jan-2026 05:23:43 21 actionable tasks: 21 executed simple 05-Jan-2026 05:23:43 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 05-Jan-2026 05:23:43 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 05-Jan-2026 05:23:43 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job #4 (JB-GDL113-JOB1-4)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL113-JOB1-4-ScriptBuildTask-7629770546900925241.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_dependency_parent_0=JB-GDB734-7\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_46498617_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL113-JOB1-4\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL113-JOB1\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_buildNumber=4\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-GDL113-JOB1-4\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_46498617_name=Jalview Gitlab\nbamboo_shortPlanKey=GDL113\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_buildTimeStamp=2026-01-05T05:21:18.481Z\nbamboo_repository_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GDL113-JOB1-4\nbamboo_repository_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_repository_46498617_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\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-GDL113 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\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=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302803\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_46498617_previous_revision_number=5857fe763e55a89397fc3bb157f282726c22b1a7\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_repository_46498617_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\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-GDL113-JOB1\nbamboo_planKey=JB-GDL113\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498617_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_repository_46498617_git_username=\nbamboo_planRepository_1_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\n simple 05-Jan-2026 05:23:43 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 05-Jan-2026 05:23:43 Running post build plugin 'NCover Results Collector' simple 05-Jan-2026 05:23:43 Running post build plugin 'Artifact Copier' simple 05-Jan-2026 05:23:43 Publishing an artifact: getdown simple 05-Jan-2026 05:23:43 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 194.2 ms simple 05-Jan-2026 05:23:43 Running post build plugin 'Artifactory Release Management Staging' simple 05-Jan-2026 05:23:43 Running post build plugin 'Artifactory Build Info Copier' simple 05-Jan-2026 05:23:43 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 05-Jan-2026 05:23:43 Running post build plugin 'npm Cache Cleanup' simple 05-Jan-2026 05:23:43 Running post build plugin 'Clover Results Collector' simple 05-Jan-2026 05:23:43 Running post build plugin 'Docker Container Cleanup' simple 05-Jan-2026 05:23:43 Finalising the build... simple 05-Jan-2026 05:23:43 Stopping timer. simple 05-Jan-2026 05:23:43 Build JB-GDL113-JOB1-4 completed. simple 05-Jan-2026 05:23:43 Running on server: post build plugin 'NCover Results Collector' simple 05-Jan-2026 05:23:43 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 05-Jan-2026 05:23:43 Running on server: post build plugin 'Clover Delta Calculator' simple 05-Jan-2026 05:23:43 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 05-Jan-2026 05:23:43 All post build plugins have finished simple 05-Jan-2026 05:23:43 Generating build results summary... simple 05-Jan-2026 05:23:43 Saving build results to disk... simple 05-Jan-2026 05:23:43 Logging substituted variables... simple 05-Jan-2026 05:23:43 Indexing build results... simple 05-Jan-2026 05:23:43 Finished building JB-GDL113-JOB1-4.