simple 11-Feb-2026 11:32:11 Build Jalview Builds - Getdown DEVELOP Launchers - citation.cff - Default Job #2 (JB-GDL119-JOB1-2) started building on agent Default Agent simple 11-Feb-2026 11:32:11 simple 11-Feb-2026 11:32:11 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-JOB1 simple 11-Feb-2026 11:32:11 Executing build Jalview Builds - Getdown DEVELOP Launchers - citation.cff - Default Job #2 (JB-GDL119-JOB1-2) simple 11-Feb-2026 11:32:11 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 11-Feb-2026 11:32:11 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-JOB1 simple 11-Feb-2026 11:32:11 Updating source code to revision: 1617d0ed323d507874712592b848e1ffdcec2883 simple 11-Feb-2026 11:32:11 Fetching 'refs/heads/citation.cff' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 11-Feb-2026 11:32:11 Checking out revision 1617d0ed323d507874712592b848e1ffdcec2883. simple 11-Feb-2026 11:32:12 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 11-Feb-2026 11:32:12 ab2dfae..1617d0e citation.cff -> origin/citation.cff simple 11-Feb-2026 11:32:12 * [new branch] bug/JAL-4624_JAL-4623_Mul_SS_in_PCA -> origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA simple 11-Feb-2026 11:32:12 * [new branch] bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch -> origin/bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch simple 11-Feb-2026 11:32:12 * [new branch] epic/JAL-3907_jalview_running_under_java_17 -> origin/epic/JAL-3907_jalview_running_under_java_17 simple 11-Feb-2026 11:32:12 * [new branch] epic/JAL-4320_gradle_upgrade_to_gradle9 -> origin/epic/JAL-4320_gradle_upgrade_to_gradle9 simple 11-Feb-2026 11:32:12 * [new branch] task/JAL-4645_JAL-4320_add_gradle_wrapper -> origin/task/JAL-4645_JAL-4320_add_gradle_wrapper simple 11-Feb-2026 11:32:13 Already on 'citation.cff' simple 11-Feb-2026 11:32:13 Your branch is behind 'origin/citation.cff' by 4 commits, and can be fast-forwarded. simple 11-Feb-2026 11:32:13 (use "git pull" to update your local branch) simple 11-Feb-2026 11:32:13 HEAD is now at 1617d0e JAL-4651 make it all valid simple 11-Feb-2026 11:32:13 Updated source code to revision: 1617d0ed323d507874712592b848e1ffdcec2883 simple 11-Feb-2026 11:32:13 Finished task 'Checkout Default Repository' with result: Success simple 11-Feb-2026 11:32:13 Running pre-build action: VCS Version Collector simple 11-Feb-2026 11:32:13 Running pre-build action: Artifactory Release Staging command 11-Feb-2026 11:32:13 Substituting variable: ${bamboo.planKey} with JB-GDL119 simple 11-Feb-2026 11:32:13 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 11-Feb-2026 11:32:13 Bamboo Artifactory Plugin version: 2.6.2 command 11-Feb-2026 11:32:13 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - citation.cff - Default Job #2 (JB-GDL119-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL119 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=citation.cff\nbamboo_dependency_parent_0=JB-GDB740-4\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=citation.cff\nbamboo_repository_revision_number=1617d0ed323d507874712592b848e1ffdcec2883\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL119-JOB1-2\nbamboo_repository_48168991_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\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-GDL119-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL119-JOB1\nbamboo_repository_48168991_revision_number=1617d0ed323d507874712592b848e1ffdcec2883\nbamboo_shortPlanName=citation.cff\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=2\nbamboo_repository_48168991_branch_name=citation.cff\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-GDL119-JOB1-2\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - citation.cff\nbamboo_shortPlanKey=GDL119\nbamboo_shortJobKey=JOB1\nbamboo_repository_48168991_name=Jalview Gitlab\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1617d0ed323d507874712592b848e1ffdcec2883\nbamboo_buildTimeStamp=2026-02-11T11:32:11.481Z\nbamboo_repository_previous_revision_number=ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25\nbamboo_repository_git_branch=citation.cff\nbamboo_buildResultKey=JB-GDL119-JOB1-2\nbamboo_repository_branch_name=citation.cff\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - citation.cff - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=1617d0ed323d507874712592b848e1ffdcec2883\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_48168991_git_branch=citation.cff\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=citation.cff\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=citation.cff\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=citation.cff\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-47972413\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_repository_48168991_previous_revision_number=ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25\nbamboo_repository_48168991_git_username=\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-GDL119-JOB1\nbamboo_planKey=JB-GDL119\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=citation.cff\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 11-Feb-2026 11:32:15 build 11-Feb-2026 11:32:15 > Configure project : build 11-Feb-2026 11:32:15 Using properties from file './utils/channels/default/channel_gradle.properties' build 11-Feb-2026 11:32:15 JALVIEW_VERSION is set to '2.11.5.1' build 11-Feb-2026 11:32:15 HEADLESS BUILD build 11-Feb-2026 11:32:15 J2S ENABLED build 11-Feb-2026 11:32:15 Using a BUILD profile. build 11-Feb-2026 11:32:15 eclipseDir exists build 11-Feb-2026 11:32:15 build 11-Feb-2026 11:32:15 > Task :clean build 11-Feb-2026 11:32:15 > Task :cleanPackageDir build 11-Feb-2026 11:32:15 > Task :getdownImagesCopy build 11-Feb-2026 11:32:15 > Task :getdownImagesProcess build 11-Feb-2026 11:32:15 > Task :getdownImages build 11-Feb-2026 11:32:15 > Task :copyHelp build 11-Feb-2026 11:32:17 > Task :buildIndices build 11-Feb-2026 11:32:17 > Task :copyResources build 11-Feb-2026 11:32:17 > Task :copyChannelResources build 11-Feb-2026 11:32:17 build 11-Feb-2026 11:32:17 > Task :createBuildProperties build 11-Feb-2026 11:32:17 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 11-Feb-2026 11:32:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:17 build 11-Feb-2026 11:32:17 > Task :buildResources build 11-Feb-2026 11:32:17 > Task :copyDocs build 11-Feb-2026 11:32:17 build 11-Feb-2026 11:32:17 > Task :convertMdFiles build 11-Feb-2026 11:32:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 11-Feb-2026 11:32:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-JOB1/build/resources/doc_build/doc/releaseprocess.html build 11-Feb-2026 11:32:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 11-Feb-2026 11:32:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-JOB1/build/resources/doc_build/doc/building.html build 11-Feb-2026 11:32:17 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-JOB1/build/resources/doc_build/doc/jalview-projects.html build 11-Feb-2026 11:32:17 build 11-Feb-2026 11:32:17 > Task :releasesTemplates build 11-Feb-2026 11:32:17 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 11-Feb-2026 11:32:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:17 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:17 Stripping rc/test/etc for 2_11_5_1 build 11-Feb-2026 11:32:17 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md build 11-Feb-2026 11:32:17 build 11-Feb-2026 11:32:17 > Task :prepare build 11-Feb-2026 11:32:19 build 11-Feb-2026 11:32:19 > Task :compileJava build 11-Feb-2026 11:32:19 Setting target compatibility to 11 error 11-Feb-2026 11:32:24 Note: Some input files use or override a deprecated API. error 11-Feb-2026 11:32:24 Note: Recompile with -Xlint:deprecation for details. error 11-Feb-2026 11:32:24 Note: Some input files use unchecked or unsafe operations. error 11-Feb-2026 11:32:24 Note: Recompile with -Xlint:unchecked for details. build 11-Feb-2026 11:32:25 build 11-Feb-2026 11:32:25 > Task :processResources build 11-Feb-2026 11:32:25 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 11-Feb-2026 11:32:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:25 build 11-Feb-2026 11:32:25 > Task :classes build 11-Feb-2026 11:32:26 build 11-Feb-2026 11:32:26 > Task :compileLinkCheck build 11-Feb-2026 11:32:26 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 11-Feb-2026 11:32:26 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:26 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:26 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-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 11-Feb-2026 11:32:26 build 11-Feb-2026 11:32:26 > Task :linkCheck build 11-Feb-2026 11:32:26 Checking help file links build 11-Feb-2026 11:32:26 build 11-Feb-2026 11:32:26 Results: build 11-Feb-2026 11:32:26 161 distinct help targets build 11-Feb-2026 11:32:26 161 help mappings build 11-Feb-2026 11:32:26 0 invalid targets build 11-Feb-2026 11:32:26 31 unused targets build 11-Feb-2026 11:32:26 uniprotfetcher: html/features/uniprotsequencefetcher.html build 11-Feb-2026 11:32:26 overviewprefs: html/features/preferences.html#overview build 11-Feb-2026 11:32:26 cdnafeatures: html/features/codingfeatures.html build 11-Feb-2026 11:32:26 startupprefs: html/features/preferences.html#startup build 11-Feb-2026 11:32:26 ensemblfetch: html/features/ensemblsequencefetcher.html build 11-Feb-2026 11:32:26 io.modellerpir: html/io/modellerpir.html build 11-Feb-2026 11:32:26 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 11-Feb-2026 11:32:26 pdbmcviewer: html/features/pdbviewer.html build 11-Feb-2026 11:32:26 groovy.colours: html/features/groovy.html#groovyColours build 11-Feb-2026 11:32:26 seqmappings: html/features/seqmappings.html build 11-Feb-2026 11:32:26 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 11-Feb-2026 11:32:26 splitframe.mirrorfonts: html/features/splitView.html#mirror build 11-Feb-2026 11:32:26 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 11-Feb-2026 11:32:26 search: html/features/search.html build 11-Feb-2026 11:32:26 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 11-Feb-2026 11:32:26 alformats: html/io/fileformats.html build 11-Feb-2026 11:32:26 strucprefs: html/features/preferences.html#structure build 11-Feb-2026 11:32:26 siftsmapping: html/features/siftsmapping.html build 11-Feb-2026 11:32:26 chimera.annotxfer: html/features/chimera.html#annotxfer build 11-Feb-2026 11:32:26 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 11-Feb-2026 11:32:26 newkeys: html/features/newkeystrokes.html build 11-Feb-2026 11:32:26 importvcf.attribs: html/features/importvcf.html#attribs build 11-Feb-2026 11:32:26 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 11-Feb-2026 11:32:26 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 11-Feb-2026 11:32:26 jalarchive: html/features/jalarchive.html build 11-Feb-2026 11:32:26 newsreader: html/webServices/newsreader.html build 11-Feb-2026 11:32:26 jalviewcltool: html/features/commandline.html#script build 11-Feb-2026 11:32:26 popMenuAddref: html/menus/popupMenu.html#addrefannot build 11-Feb-2026 11:32:26 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 11-Feb-2026 11:32:26 paematrixformat: html/io/paematrixformat.html build 11-Feb-2026 11:32:26 overview: html/features/overview.html build 11-Feb-2026 11:32:26 0 invalid map urls build 11-Feb-2026 11:32:26 0 invalid image attributes build 11-Feb-2026 11:32:26 520 internal href links (120 with anchors) build 11-Feb-2026 11:32:26 0 invalid internal href links build 11-Feb-2026 11:32:26 0 invalid internal anchor links build 11-Feb-2026 11:32:26 112 external href links build 11-Feb-2026 11:32:26 External links not verified as internet not available build 11-Feb-2026 11:32:26 *** Success *** build 11-Feb-2026 11:32:27 build 11-Feb-2026 11:32:27 > Task :jar build 11-Feb-2026 11:32:28 > Task :syncJars build 11-Feb-2026 11:32:28 > Task :makeDist build 11-Feb-2026 11:32:28 > Task :getdownWebsiteBuild build 11-Feb-2026 11:32:29 build 11-Feb-2026 11:32:29 > Task :getdownDigest build 11-Feb-2026 11:32:29 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... error 11-Feb-2026 11:32:29 2026/02/11 11:32:28:531 WARNING Starting without install4j classes build 11-Feb-2026 11:32:29 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... error 11-Feb-2026 11:32:29 2026/02/11 11:32:29:183 WARNING Starting without install4j classes build 11-Feb-2026 11:32:29 build 11-Feb-2026 11:32:29 > Task :getdown build 11-Feb-2026 11:32:29 build 11-Feb-2026 11:32:29 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 11-Feb-2026 11:32:29 build 11-Feb-2026 11:32:29 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 11-Feb-2026 11:32:29 build 11-Feb-2026 11:32:29 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 11-Feb-2026 11:32:29 build 11-Feb-2026 11:32:29 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 11-Feb-2026 11:32:29 Please consult deprecation warnings for more details. build 11-Feb-2026 11:32:29 build 11-Feb-2026 11:32:29 BUILD SUCCESSFUL in 16s build 11-Feb-2026 11:32:29 21 actionable tasks: 21 executed simple 11-Feb-2026 11:32:30 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 11-Feb-2026 11:32:30 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 11-Feb-2026 11:32:30 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - citation.cff - Default Job #2 (JB-GDL119-JOB1-2)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL119-JOB1-2-ScriptBuildTask-2273657762384016700.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=citation.cff\nbamboo_dependency_parent_0=JB-GDB740-4\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=citation.cff\nbamboo_repository_revision_number=1617d0ed323d507874712592b848e1ffdcec2883\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL119-JOB1-2\nbamboo_repository_48168991_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL119-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL119-JOB1\nbamboo_repository_48168991_revision_number=1617d0ed323d507874712592b848e1ffdcec2883\nbamboo_shortPlanName=citation.cff\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_buildNumber=2\nbamboo_repository_48168991_branch_name=citation.cff\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-GDL119-JOB1-2\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - citation.cff\nbamboo_shortPlanKey=GDL119\nbamboo_shortJobKey=JOB1\nbamboo_repository_48168991_name=Jalview Gitlab\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=1617d0ed323d507874712592b848e1ffdcec2883\nbamboo_buildTimeStamp=2026-02-11T11:32:11.481Z\nbamboo_repository_previous_revision_number=ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25\nbamboo_repository_git_branch=citation.cff\nbamboo_buildResultKey=JB-GDL119-JOB1-2\nbamboo_repository_branch_name=citation.cff\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - citation.cff - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=1617d0ed323d507874712592b848e1ffdcec2883\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\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-GDL119 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_repository_48168991_git_branch=citation.cff\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=citation.cff\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=citation.cff\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=citation.cff\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-47972413\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_repository_48168991_previous_revision_number=ab2dfae0e6d0eb6d8823eeefa656e7c44419fa25\nbamboo_repository_48168991_git_username=\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-GDL119-JOB1\nbamboo_planKey=JB-GDL119\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=citation.cff\n simple 11-Feb-2026 11:32:30 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 11-Feb-2026 11:32:30 Running post build plugin 'NCover Results Collector' simple 11-Feb-2026 11:32:30 Running post build plugin 'Artifact Copier' simple 11-Feb-2026 11:32:30 Publishing an artifact: getdown simple 11-Feb-2026 11:32:30 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 154.6 ms simple 11-Feb-2026 11:32:30 Running post build plugin 'Artifactory Release Management Staging' simple 11-Feb-2026 11:32:30 Running post build plugin 'Artifactory Build Info Copier' simple 11-Feb-2026 11:32:30 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 11-Feb-2026 11:32:30 Running post build plugin 'npm Cache Cleanup' simple 11-Feb-2026 11:32:30 Running post build plugin 'Clover Results Collector' simple 11-Feb-2026 11:32:30 Running post build plugin 'Docker Container Cleanup' simple 11-Feb-2026 11:32:30 Finalising the build... simple 11-Feb-2026 11:32:30 Stopping timer. simple 11-Feb-2026 11:32:30 Build JB-GDL119-JOB1-2 completed. simple 11-Feb-2026 11:32:30 Running on server: post build plugin 'NCover Results Collector' simple 11-Feb-2026 11:32:30 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 11-Feb-2026 11:32:30 Running on server: post build plugin 'Clover Delta Calculator' simple 11-Feb-2026 11:32:30 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 11-Feb-2026 11:32:30 All post build plugins have finished simple 11-Feb-2026 11:32:30 Generating build results summary... simple 11-Feb-2026 11:32:30 Saving build results to disk... simple 11-Feb-2026 11:32:30 Logging substituted variables... simple 11-Feb-2026 11:32:30 Indexing build results... simple 11-Feb-2026 11:32:30 Finished building JB-GDL119-JOB1-2.