simple 10-Dec-2025 18:18:49 Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job #2 (JB-GDL113-JOB1-2) started building on agent Default Agent simple 10-Dec-2025 18:18:49 simple 10-Dec-2025 18:18:49 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1 simple 10-Dec-2025 18:18:49 Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job #2 (JB-GDL113-JOB1-2) simple 10-Dec-2025 18:18:49 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 10-Dec-2025 18:18:49 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1 simple 10-Dec-2025 18:18:49 Updating source code to revision: b80719bcafaf18f88875dd6956bb3bd47ff21bed simple 10-Dec-2025 18:18:49 Fetching 'refs/heads/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 10-Dec-2025 18:18:50 Checking out revision b80719bcafaf18f88875dd6956bb3bd47ff21bed. simple 10-Dec-2025 18:18:50 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 10-Dec-2025 18:18:50 e087526..b80719b bug/JAL-4107_jalviewjs_fixes_on_2_12_branch -> origin/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch simple 10-Dec-2025 18:18:50 * [new branch] bug/JAL-4559_old_cli_args_in_JVL_docs -> origin/bug/JAL-4559_old_cli_args_in_JVL_docs simple 10-Dec-2025 18:18:50 4d0c90d..5a35253 development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch simple 10-Dec-2025 18:18:50 * [new branch] patch/JAL-4606_again_and_again -> origin/patch/JAL-4606_again_and_again simple 10-Dec-2025 18:18:50 c586364..9e8107e releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch simple 10-Dec-2025 18:18:52 Already on 'bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' simple 10-Dec-2025 18:18:52 Your branch is behind 'origin/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' by 2 commits, and can be fast-forwarded. simple 10-Dec-2025 18:18:52 (use "git pull" to update your local branch) simple 10-Dec-2025 18:18:52 HEAD is now at b80719b JAL-4107 Add an instanceExists() non-instantiating check to ApplicationSingletonProvider and use for Jalview class. Change all tests for Jalview.getInstance() == null to Jalview.instanceExists(). Some Eclipse formatting has also happened in AlignExportOptions.java and Console.java. simple 10-Dec-2025 18:18:52 Updated source code to revision: b80719bcafaf18f88875dd6956bb3bd47ff21bed simple 10-Dec-2025 18:18:52 Finished task 'Checkout Default Repository' with result: Success simple 10-Dec-2025 18:18:52 Running pre-build action: VCS Version Collector simple 10-Dec-2025 18:18:52 Running pre-build action: Artifactory Release Staging command 10-Dec-2025 18:18:52 Substituting variable: ${bamboo.planKey} with JB-GDL113 simple 10-Dec-2025 18:18:52 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 10-Dec-2025 18:18:52 Bamboo Artifactory Plugin version: 2.6.2 command 10-Dec-2025 18:18:52 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job #2 (JB-GDL113-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL113 -Pbamboo_buildResultsUrl=${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-GDB734-3\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=b80719bcafaf18f88875dd6956bb3bd47ff21bed\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL113-JOB1-2\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=2\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-JOB1-2\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=b80719bcafaf18f88875dd6956bb3bd47ff21bed\nbamboo_buildTimeStamp=2025-12-10T18:18:49.847Z\nbamboo_repository_previous_revision_number=e0875267ed4b699db969bf10b30bafe83a1cbd7d\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GDL113-JOB1-2\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=b80719bcafaf18f88875dd6956bb3bd47ff21bed\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=e0875267ed4b699db969bf10b30bafe83a1cbd7d\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=b80719bcafaf18f88875dd6956bb3bd47ff21bed\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 10-Dec-2025 18:18:53 build 10-Dec-2025 18:18:53 > Configure project : build 10-Dec-2025 18:18:53 Using properties from file './utils/channels/default/channel_gradle.properties' build 10-Dec-2025 18:18:53 JALVIEW_VERSION is set to '2.12.0' build 10-Dec-2025 18:18:53 HEADLESS BUILD build 10-Dec-2025 18:18:53 J2S ENABLED build 10-Dec-2025 18:18:53 Using a BUILD profile. build 10-Dec-2025 18:18:53 eclipseDir exists build 10-Dec-2025 18:18:53 build 10-Dec-2025 18:18:53 > Task :clean build 10-Dec-2025 18:18:53 > Task :cleanPackageDir build 10-Dec-2025 18:18:53 > Task :getdownImagesCopy build 10-Dec-2025 18:18:54 > Task :getdownImagesProcess build 10-Dec-2025 18:18:54 > Task :getdownImages build 10-Dec-2025 18:18:54 > Task :copyHelp build 10-Dec-2025 18:18:55 > Task :buildIndices build 10-Dec-2025 18:18:55 > Task :copyResources build 10-Dec-2025 18:18:55 > Task :copyChannelResources build 10-Dec-2025 18:18:55 build 10-Dec-2025 18:18:55 > Task :createBuildProperties build 10-Dec-2025 18:18:55 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 10-Dec-2025 18:18:55 - 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 10-Dec-2025 18:18:55 build 10-Dec-2025 18:18:55 > Task :buildResources build 10-Dec-2025 18:18:55 > Task :copyDocs build 10-Dec-2025 18:18:55 build 10-Dec-2025 18:18:55 > Task :convertMdFiles build 10-Dec-2025 18:18:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 10-Dec-2025 18:18:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/releaseprocess.html build 10-Dec-2025 18:18:55 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 10-Dec-2025 18:18:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/JalviewJS-API.html build 10-Dec-2025 18:18:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/building.html build 10-Dec-2025 18:18:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/addingWebClient.html build 10-Dec-2025 18:18:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/jalview-projects.html build 10-Dec-2025 18:18:55 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html build 10-Dec-2025 18:18:56 build 10-Dec-2025 18:18:56 > Task :releasesTemplates build 10-Dec-2025 18:18:56 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 10-Dec-2025 18:18:56 - 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 10-Dec-2025 18:18:56 - 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 10-Dec-2025 18:18:56 Stripping rc/test/etc for 2_12_0 build 10-Dec-2025 18:18:56 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL113-JOB1/help/markdown/whatsnew/whatsnew-2_12_0.md build 10-Dec-2025 18:18:56 build 10-Dec-2025 18:18:56 > Task :prepare build 10-Dec-2025 18:18:58 build 10-Dec-2025 18:18:58 > Task :compileJava build 10-Dec-2025 18:18:58 Setting target compatibility to 11 error 10-Dec-2025 18:19:04 Note: Some input files use or override a deprecated API. error 10-Dec-2025 18:19:04 Note: Recompile with -Xlint:deprecation for details. error 10-Dec-2025 18:19:04 Note: Some input files use unchecked or unsafe operations. error 10-Dec-2025 18:19:04 Note: Recompile with -Xlint:unchecked for details. build 10-Dec-2025 18:19:04 build 10-Dec-2025 18:19:04 > Task :processResources build 10-Dec-2025 18:19:04 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 10-Dec-2025 18:19:04 - 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 10-Dec-2025 18:19:04 - 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 10-Dec-2025 18:19:04 - 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 10-Dec-2025 18:19:04 - 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 10-Dec-2025 18:19:04 - 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 10-Dec-2025 18:19:04 - 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 10-Dec-2025 18:19:04 - 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 10-Dec-2025 18:19:04 - 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 10-Dec-2025 18:19:04 build 10-Dec-2025 18:19:04 > Task :classes build 10-Dec-2025 18:19:05 build 10-Dec-2025 18:19:05 > Task :compileLinkCheck build 10-Dec-2025 18:19:05 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 10-Dec-2025 18:19:05 - 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 10-Dec-2025 18:19:05 - 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 10-Dec-2025 18:19:05 - 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 10-Dec-2025 18:19:07 build 10-Dec-2025 18:19:07 > Task :linkCheck build 10-Dec-2025 18:19:07 Checking help file links build 10-Dec-2025 18:21:13 build 10-Dec-2025 18:21:13 Results: build 10-Dec-2025 18:21:13 162 distinct help targets build 10-Dec-2025 18:21:13 162 help mappings build 10-Dec-2025 18:21:13 0 invalid targets build 10-Dec-2025 18:21:13 31 unused targets build 10-Dec-2025 18:21:13 uniprotfetcher: html/features/uniprotsequencefetcher.html build 10-Dec-2025 18:21:13 overviewprefs: html/features/preferences.html#overview build 10-Dec-2025 18:21:13 cdnafeatures: html/features/codingfeatures.html build 10-Dec-2025 18:21:13 startupprefs: html/features/preferences.html#startup build 10-Dec-2025 18:21:13 ensemblfetch: html/features/ensemblsequencefetcher.html build 10-Dec-2025 18:21:13 io.modellerpir: html/io/modellerpir.html build 10-Dec-2025 18:21:13 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 10-Dec-2025 18:21:13 pdbmcviewer: html/features/pdbviewer.html build 10-Dec-2025 18:21:13 groovy.colours: html/features/groovy.html#groovyColours build 10-Dec-2025 18:21:13 seqmappings: html/features/seqmappings.html build 10-Dec-2025 18:21:13 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 10-Dec-2025 18:21:13 splitframe.mirrorfonts: html/features/splitView.html#mirror build 10-Dec-2025 18:21:13 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 10-Dec-2025 18:21:13 search: html/features/search.html build 10-Dec-2025 18:21:13 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 10-Dec-2025 18:21:13 alformats: html/io/fileformats.html build 10-Dec-2025 18:21:13 strucprefs: html/features/preferences.html#structure build 10-Dec-2025 18:21:13 siftsmapping: html/features/siftsmapping.html build 10-Dec-2025 18:21:13 chimera.annotxfer: html/features/chimera.html#annotxfer build 10-Dec-2025 18:21:13 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 10-Dec-2025 18:21:13 newkeys: html/features/newkeystrokes.html build 10-Dec-2025 18:21:13 importvcf.attribs: html/features/importvcf.html#attribs build 10-Dec-2025 18:21:13 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 10-Dec-2025 18:21:13 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 10-Dec-2025 18:21:13 jalarchive: html/features/jalarchive.html build 10-Dec-2025 18:21:13 newsreader: html/webServices/newsreader.html build 10-Dec-2025 18:21:13 jalviewcltool: html/features/commandline.html#script build 10-Dec-2025 18:21:13 popMenuAddref: html/menus/popupMenu.html#addrefannot build 10-Dec-2025 18:21:13 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 10-Dec-2025 18:21:13 paematrixformat: html/io/paematrixformat.html build 10-Dec-2025 18:21:13 overview: html/features/overview.html build 10-Dec-2025 18:21:13 0 invalid map urls build 10-Dec-2025 18:21:13 0 invalid image attributes build 10-Dec-2025 18:21:13 520 internal href links (119 with anchors) build 10-Dec-2025 18:21:13 0 invalid internal href links build 10-Dec-2025 18:21:13 0 invalid internal anchor links build 10-Dec-2025 18:21:13 113 external href links build 10-Dec-2025 18:21:13 External links not verified as internet not available build 10-Dec-2025 18:21:13 *** Success *** build 10-Dec-2025 18:21:14 build 10-Dec-2025 18:21:14 > Task :jar build 10-Dec-2025 18:21:14 > Task :syncJars build 10-Dec-2025 18:21:14 > Task :makeDist build 10-Dec-2025 18:21:14 > Task :getdownWebsiteBuild build 10-Dec-2025 18:21:16 build 10-Dec-2025 18:21:16 > Task :getdownDigest build 10-Dec-2025 18:21:16 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 10-Dec-2025 18:21:16 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... error 10-Dec-2025 18:21:16 2025/12/10 18:21:15:055 WARNING Starting without install4j classes build 10-Dec-2025 18:21:16 build 10-Dec-2025 18:21:16 > Task :getdown build 10-Dec-2025 18:21:16 build 10-Dec-2025 18:21:16 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 10-Dec-2025 18:21:16 build 10-Dec-2025 18:21:16 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 10-Dec-2025 18:21:16 build 10-Dec-2025 18:21:16 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 10-Dec-2025 18:21:16 error 10-Dec-2025 18:21:16 2025/12/10 18:21:15:609 WARNING Starting without install4j classes build 10-Dec-2025 18:21:16 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 10-Dec-2025 18:21:16 Please consult deprecation warnings for more details. build 10-Dec-2025 18:21:16 build 10-Dec-2025 18:21:16 BUILD SUCCESSFUL in 2m 23s build 10-Dec-2025 18:21:16 21 actionable tasks: 21 executed simple 10-Dec-2025 18:21:16 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 10-Dec-2025 18:21:16 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 10-Dec-2025 18:21:16 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job #2 (JB-GDL113-JOB1-2)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL113-JOB1-2-ScriptBuildTask-2321413543662366342.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-GDB734-3\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=b80719bcafaf18f88875dd6956bb3bd47ff21bed\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL113-JOB1-2\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=2\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-JOB1-2\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=b80719bcafaf18f88875dd6956bb3bd47ff21bed\nbamboo_buildTimeStamp=2025-12-10T18:18:49.847Z\nbamboo_repository_previous_revision_number=e0875267ed4b699db969bf10b30bafe83a1cbd7d\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GDL113-JOB1-2\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=b80719bcafaf18f88875dd6956bb3bd47ff21bed\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=e0875267ed4b699db969bf10b30bafe83a1cbd7d\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=b80719bcafaf18f88875dd6956bb3bd47ff21bed\nbamboo_repository_46498617_git_username=\nbamboo_planRepository_1_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\n simple 10-Dec-2025 18:21:16 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 10-Dec-2025 18:21:16 Running post build plugin 'NCover Results Collector' simple 10-Dec-2025 18:21:16 Running post build plugin 'Artifact Copier' simple 10-Dec-2025 18:21:16 Publishing an artifact: getdown simple 10-Dec-2025 18:21:16 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 184.9 ms simple 10-Dec-2025 18:21:16 Running post build plugin 'Artifactory Release Management Staging' simple 10-Dec-2025 18:21:16 Running post build plugin 'Artifactory Build Info Copier' simple 10-Dec-2025 18:21:16 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 10-Dec-2025 18:21:16 Running post build plugin 'npm Cache Cleanup' simple 10-Dec-2025 18:21:16 Running post build plugin 'Clover Results Collector' simple 10-Dec-2025 18:21:16 Running post build plugin 'Docker Container Cleanup' simple 10-Dec-2025 18:21:16 Finalising the build... simple 10-Dec-2025 18:21:16 Stopping timer. simple 10-Dec-2025 18:21:16 Build JB-GDL113-JOB1-2 completed. simple 10-Dec-2025 18:21:16 Running on server: post build plugin 'NCover Results Collector' simple 10-Dec-2025 18:21:16 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 10-Dec-2025 18:21:16 Running on server: post build plugin 'Clover Delta Calculator' simple 10-Dec-2025 18:21:16 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 10-Dec-2025 18:21:16 All post build plugins have finished simple 10-Dec-2025 18:21:16 Generating build results summary... simple 10-Dec-2025 18:21:16 Saving build results to disk... simple 10-Dec-2025 18:21:16 Logging substituted variables... simple 10-Dec-2025 18:21:16 Indexing build results... simple 10-Dec-2025 18:21:16 Finished building JB-GDL113-JOB1-2.