simple 04-Mar-2026 12:11:20 Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Default Job #4 (JB-GDL123-JOB1-4) started building on agent Default Agent simple 04-Mar-2026 12:11:20 simple 04-Mar-2026 12:11:20 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1 simple 04-Mar-2026 12:11:20 Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Default Job #4 (JB-GDL123-JOB1-4) simple 04-Mar-2026 12:11:20 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 04-Mar-2026 12:11:20 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1 simple 04-Mar-2026 12:11:20 Updating source code to revision: c36b1d121eaf5e74db628f810d4ee72164870015 simple 04-Mar-2026 12:11:20 Fetching 'refs/heads/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 04-Mar-2026 12:11:20 Checking out revision c36b1d121eaf5e74db628f810d4ee72164870015. simple 04-Mar-2026 12:11:21 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 04-Mar-2026 12:11:21 944aa49..c36b1d1 bug/JAL-4624_JAL-4623_Mul_SS_in_PCA -> origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA simple 04-Mar-2026 12:11:21 * [new branch] epic/JAL-4320_JAL-4644_refactor_directory_structure -> origin/epic/JAL-4320_JAL-4644_refactor_directory_structure simple 04-Mar-2026 12:11:21 9efd725..b443e47 epic/JAL-4320_gradle_upgrade_to_gradle9 -> origin/epic/JAL-4320_gradle_upgrade_to_gradle9 simple 04-Mar-2026 12:11:21 Already on 'bug/JAL-4624_JAL-4623_Mul_SS_in_PCA' simple 04-Mar-2026 12:11:21 Your branch is behind 'origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA' by 1 commit, and can be fast-forwarded. simple 04-Mar-2026 12:11:21 (use "git pull" to update your local branch) simple 04-Mar-2026 12:11:21 HEAD is now at c36b1d1 JAL-4623 Changes for labels in output points file simple 04-Mar-2026 12:11:21 Updated source code to revision: c36b1d121eaf5e74db628f810d4ee72164870015 simple 04-Mar-2026 12:11:21 Finished task 'Checkout Default Repository' with result: Success simple 04-Mar-2026 12:11:21 Running pre-build action: VCS Version Collector simple 04-Mar-2026 12:11:21 Running pre-build action: Artifactory Release Staging command 04-Mar-2026 12:11:21 Substituting variable: ${bamboo.planKey} with JB-GDL123 simple 04-Mar-2026 12:11:21 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 04-Mar-2026 12:11:21 Bamboo Artifactory Plugin version: 2.6.2 command 04-Mar-2026 12:11:21 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Default Job #4 (JB-GDL123-JOB1-4)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL123 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_dependency_parent_0=JB-GDB744-5\nbamboo_repository_48169016_previous_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_dependency_parent_total=1\nbamboo_repository_48169016_name=Jalview Gitlab\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_repository_revision_number=c36b1d121eaf5e74db628f810d4ee72164870015\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL123-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-GDL123-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL123-JOB1\nbamboo_shortPlanName=bug-JAL-4624_JAL-4623_Mul_SS_in_PCA\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_repository_48169016_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL123-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-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_shortPlanKey=GDL123\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=c36b1d121eaf5e74db628f810d4ee72164870015\nbamboo_buildTimeStamp=2026-03-04T12:11:20.378Z\nbamboo_repository_previous_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_repository_48169016_git_username=\nbamboo_repository_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildResultKey=JB-GDL123-JOB1-4\nbamboo_repository_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_48169016_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_planRepository_1_revision=c36b1d121eaf5e74db628f810d4ee72164870015\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169016_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_repository_name=Jalview Gitlab\nbamboo_repository_48169016_revision_number=c36b1d121eaf5e74db628f810d4ee72164870015\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-4624_JAL-4623_Mul_SS_in_PCA\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-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\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-47972463\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1\nbamboo_planKey=JB-GDL123\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 04-Mar-2026 12:11:23 build 04-Mar-2026 12:11:23 > Configure project : build 04-Mar-2026 12:11:23 Using properties from file './utils/channels/default/channel_gradle.properties' build 04-Mar-2026 12:11:23 JALVIEW_VERSION is set to '2.12.0' build 04-Mar-2026 12:11:23 HEADLESS BUILD build 04-Mar-2026 12:11:23 J2S ENABLED build 04-Mar-2026 12:11:23 Using a BUILD profile. build 04-Mar-2026 12:11:23 eclipseDir exists build 04-Mar-2026 12:11:23 build 04-Mar-2026 12:11:23 > Task :clean build 04-Mar-2026 12:11:23 > Task :cleanPackageDir build 04-Mar-2026 12:11:23 > Task :getdownImagesCopy build 04-Mar-2026 12:11:23 > Task :getdownImagesProcess build 04-Mar-2026 12:11:23 > Task :getdownImages build 04-Mar-2026 12:11:24 > Task :copyHelp build 04-Mar-2026 12:11:25 > Task :buildIndices build 04-Mar-2026 12:11:25 > Task :copyResources build 04-Mar-2026 12:11:25 > Task :copyChannelResources build 04-Mar-2026 12:11:25 build 04-Mar-2026 12:11:25 > Task :createBuildProperties build 04-Mar-2026 12:11:25 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 04-Mar-2026 12:11:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:25 build 04-Mar-2026 12:11:25 > Task :buildResources build 04-Mar-2026 12:11:25 > Task :copyDocs build 04-Mar-2026 12:11:25 build 04-Mar-2026 12:11:25 > Task :convertMdFiles build 04-Mar-2026 12:11:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 04-Mar-2026 12:11:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/releaseprocess.html build 04-Mar-2026 12:11:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 04-Mar-2026 12:11:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/JalviewJS-API.html build 04-Mar-2026 12:11:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/building.html build 04-Mar-2026 12:11:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/addingWebClient.html build 04-Mar-2026 12:11:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/jalview-projects.html build 04-Mar-2026 12:11:25 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html build 04-Mar-2026 12:11:25 build 04-Mar-2026 12:11:25 > Task :releasesTemplates build 04-Mar-2026 12:11:25 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 04-Mar-2026 12:11:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:25 Stripping rc/test/etc for 2_12_0 build 04-Mar-2026 12:11:25 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/help/markdown/whatsnew/whatsnew-2_12_0.md build 04-Mar-2026 12:11:25 build 04-Mar-2026 12:11:25 > Task :prepare build 04-Mar-2026 12:11:27 build 04-Mar-2026 12:11:27 > Task :compileJava build 04-Mar-2026 12:11:27 Setting target compatibility to 11 error 04-Mar-2026 12:11:34 Note: Some input files use or override a deprecated API. error 04-Mar-2026 12:11:34 Note: Recompile with -Xlint:deprecation for details. error 04-Mar-2026 12:11:34 Note: Some input files use unchecked or unsafe operations. error 04-Mar-2026 12:11:34 Note: Recompile with -Xlint:unchecked for details. build 04-Mar-2026 12:11:35 build 04-Mar-2026 12:11:35 > Task :processResources build 04-Mar-2026 12:11:35 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 04-Mar-2026 12:11:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:35 build 04-Mar-2026 12:11:35 > Task :classes build 04-Mar-2026 12:11:36 build 04-Mar-2026 12:11:36 > Task :compileLinkCheck build 04-Mar-2026 12:11:36 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 04-Mar-2026 12:11:36 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:36 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:36 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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 04-Mar-2026 12:11:36 build 04-Mar-2026 12:11:36 > Task :linkCheck build 04-Mar-2026 12:11:36 Checking help file links build 04-Mar-2026 12:11:36 build 04-Mar-2026 12:11:36 Results: build 04-Mar-2026 12:11:36 162 distinct help targets build 04-Mar-2026 12:11:36 162 help mappings build 04-Mar-2026 12:11:36 0 invalid targets build 04-Mar-2026 12:11:36 31 unused targets build 04-Mar-2026 12:11:36 uniprotfetcher: html/features/uniprotsequencefetcher.html build 04-Mar-2026 12:11:36 overviewprefs: html/features/preferences.html#overview build 04-Mar-2026 12:11:36 cdnafeatures: html/features/codingfeatures.html build 04-Mar-2026 12:11:36 startupprefs: html/features/preferences.html#startup build 04-Mar-2026 12:11:36 ensemblfetch: html/features/ensemblsequencefetcher.html build 04-Mar-2026 12:11:36 io.modellerpir: html/io/modellerpir.html build 04-Mar-2026 12:11:36 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 04-Mar-2026 12:11:36 pdbmcviewer: html/features/pdbviewer.html build 04-Mar-2026 12:11:36 groovy.colours: html/features/groovy.html#groovyColours build 04-Mar-2026 12:11:36 seqmappings: html/features/seqmappings.html build 04-Mar-2026 12:11:36 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 04-Mar-2026 12:11:36 splitframe.mirrorfonts: html/features/splitView.html#mirror build 04-Mar-2026 12:11:36 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 04-Mar-2026 12:11:36 search: html/features/search.html build 04-Mar-2026 12:11:36 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 04-Mar-2026 12:11:36 alformats: html/io/fileformats.html build 04-Mar-2026 12:11:36 strucprefs: html/features/preferences.html#structure build 04-Mar-2026 12:11:36 siftsmapping: html/features/siftsmapping.html build 04-Mar-2026 12:11:36 chimera.annotxfer: html/features/chimera.html#annotxfer build 04-Mar-2026 12:11:36 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 04-Mar-2026 12:11:36 newkeys: html/features/newkeystrokes.html build 04-Mar-2026 12:11:36 importvcf.attribs: html/features/importvcf.html#attribs build 04-Mar-2026 12:11:36 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 04-Mar-2026 12:11:36 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 04-Mar-2026 12:11:36 jalarchive: html/features/jalarchive.html build 04-Mar-2026 12:11:36 newsreader: html/webServices/newsreader.html build 04-Mar-2026 12:11:36 jalviewcltool: html/features/commandline.html#script build 04-Mar-2026 12:11:36 popMenuAddref: html/menus/popupMenu.html#addrefannot build 04-Mar-2026 12:11:36 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 04-Mar-2026 12:11:36 paematrixformat: html/io/paematrixformat.html build 04-Mar-2026 12:11:36 overview: html/features/overview.html build 04-Mar-2026 12:11:36 0 invalid map urls build 04-Mar-2026 12:11:36 0 invalid image attributes build 04-Mar-2026 12:11:36 520 internal href links (119 with anchors) build 04-Mar-2026 12:11:36 0 invalid internal href links build 04-Mar-2026 12:11:36 0 invalid internal anchor links build 04-Mar-2026 12:11:36 113 external href links build 04-Mar-2026 12:11:36 External links not verified as internet not available build 04-Mar-2026 12:11:36 *** Success *** build 04-Mar-2026 12:11:37 build 04-Mar-2026 12:11:37 > Task :jar build 04-Mar-2026 12:11:37 > Task :syncJars build 04-Mar-2026 12:11:37 > Task :makeDist build 04-Mar-2026 12:11:38 > Task :getdownWebsiteBuild error 04-Mar-2026 12:11:39 2026/03/04 12:11:38:376 WARNING Starting without install4j classes error 04-Mar-2026 12:11:39 2026/03/04 12:11:38:961 WARNING Starting without install4j classes build 04-Mar-2026 12:11:39 build 04-Mar-2026 12:11:39 > Task :getdownDigest build 04-Mar-2026 12:11:39 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 04-Mar-2026 12:11:39 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 04-Mar-2026 12:11:39 build 04-Mar-2026 12:11:39 > Task :getdown build 04-Mar-2026 12:11:39 build 04-Mar-2026 12:11:39 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 04-Mar-2026 12:11:39 build 04-Mar-2026 12:11:39 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 04-Mar-2026 12:11:39 build 04-Mar-2026 12:11:39 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 04-Mar-2026 12:11:39 build 04-Mar-2026 12:11:39 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 04-Mar-2026 12:11:39 Please consult deprecation warnings for more details. build 04-Mar-2026 12:11:39 build 04-Mar-2026 12:11:39 BUILD SUCCESSFUL in 18s build 04-Mar-2026 12:11:39 21 actionable tasks: 21 executed simple 04-Mar-2026 12:11:39 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 04-Mar-2026 12:11:39 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 04-Mar-2026 12:11:39 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Default Job #4 (JB-GDL123-JOB1-4)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL123-JOB1-4-ScriptBuildTask-3935082437222462212.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_dependency_parent_0=JB-GDB744-5\nbamboo_repository_48169016_previous_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_repository_48169016_name=Jalview Gitlab\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_repository_revision_number=c36b1d121eaf5e74db628f810d4ee72164870015\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL123-JOB1-4\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL123-JOB1\nbamboo_shortPlanName=bug-JAL-4624_JAL-4623_Mul_SS_in_PCA\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_repository_48169016_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL123-JOB1-4\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_shortPlanKey=GDL123\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=c36b1d121eaf5e74db628f810d4ee72164870015\nbamboo_buildTimeStamp=2026-03-04T12:11:20.378Z\nbamboo_repository_previous_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df\nbamboo_repository_48169016_git_username=\nbamboo_repository_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildResultKey=JB-GDL123-JOB1-4\nbamboo_repository_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_48169016_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_planRepository_1_revision=c36b1d121eaf5e74db628f810d4ee72164870015\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_48169016_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_repository_name=Jalview Gitlab\nbamboo_repository_48169016_revision_number=c36b1d121eaf5e74db628f810d4ee72164870015\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-GDL123 -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-4624_JAL-4623_Mul_SS_in_PCA\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-4624_JAL-4623_Mul_SS_in_PCA\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\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-47972463\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1\nbamboo_planKey=JB-GDL123\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA\n simple 04-Mar-2026 12:11:39 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 04-Mar-2026 12:11:39 Running post build plugin 'NCover Results Collector' simple 04-Mar-2026 12:11:39 Running post build plugin 'Artifact Copier' simple 04-Mar-2026 12:11:39 Publishing an artifact: getdown simple 04-Mar-2026 12:11:40 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 136.0 ms simple 04-Mar-2026 12:11:40 Running post build plugin 'Artifactory Release Management Staging' simple 04-Mar-2026 12:11:40 Running post build plugin 'Artifactory Build Info Copier' simple 04-Mar-2026 12:11:40 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 04-Mar-2026 12:11:40 Running post build plugin 'npm Cache Cleanup' simple 04-Mar-2026 12:11:40 Running post build plugin 'Clover Results Collector' simple 04-Mar-2026 12:11:40 Running post build plugin 'Docker Container Cleanup' simple 04-Mar-2026 12:11:40 Finalising the build... simple 04-Mar-2026 12:11:40 Stopping timer. simple 04-Mar-2026 12:11:40 Build JB-GDL123-JOB1-4 completed. simple 04-Mar-2026 12:11:40 Running on server: post build plugin 'NCover Results Collector' simple 04-Mar-2026 12:11:40 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 04-Mar-2026 12:11:40 Running on server: post build plugin 'Clover Delta Calculator' simple 04-Mar-2026 12:11:40 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 04-Mar-2026 12:11:40 All post build plugins have finished simple 04-Mar-2026 12:11:40 Generating build results summary... simple 04-Mar-2026 12:11:40 Saving build results to disk... simple 04-Mar-2026 12:11:40 Logging substituted variables... simple 04-Mar-2026 12:11:40 Indexing build results... simple 04-Mar-2026 12:11:40 Finished building JB-GDL123-JOB1-4.