simple 27-Nov-2025 17:32:33 Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job #1 (JB-GDL111-JOB1-1) started building on agent Default Agent simple 27-Nov-2025 17:32:33 simple 27-Nov-2025 17:32:33 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1 simple 27-Nov-2025 17:32:33 Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job #1 (JB-GDL111-JOB1-1) simple 27-Nov-2025 17:32:33 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 27-Nov-2025 17:32:33 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1 simple 27-Nov-2025 17:32:33 Updating source code to revision: acbb7d39481e53918a63f69cd008b4f6bbd7a588 simple 27-Nov-2025 17:32:33 Fetching 'refs/heads/bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 27-Nov-2025 17:32:34 Checking out revision acbb7d39481e53918a63f69cd008b4f6bbd7a588. simple 27-Nov-2025 17:32:34 Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1/.git'. simple 27-Nov-2025 17:32:35 Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1'... simple 27-Nov-2025 17:32:35 done. simple 27-Nov-2025 17:32:42 Switched to a new branch 'bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus' simple 27-Nov-2025 17:32:42 Branch bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus set up to track remote branch bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus from origin. simple 27-Nov-2025 17:32:42 Updated source code to revision: acbb7d39481e53918a63f69cd008b4f6bbd7a588 simple 27-Nov-2025 17:32:42 Finished task 'Checkout Default Repository' with result: Success simple 27-Nov-2025 17:32:42 Running pre-build action: VCS Version Collector simple 27-Nov-2025 17:32:42 Running pre-build action: Artifactory Release Staging command 27-Nov-2025 17:32:42 Substituting variable: ${bamboo.planKey} with JB-GDL111 simple 27-Nov-2025 17:32:42 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 27-Nov-2025 17:32:42 Bamboo Artifactory Plugin version: 2.6.2 command 27-Nov-2025 17:32:42 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job #1 (JB-GDL111-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL111 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_dependency_parent_0=JB-GDB729-5\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=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_repository_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL111-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_46498603_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL111-JOB1\nbamboo_shortPlanName=bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_repository_46498603_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\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-GDL111-JOB1-1\nbamboo_repository_46498603_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588\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-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_shortPlanKey=GDL111\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_repository_46498603_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_buildTimeStamp=2025-11-27T17:19:11.296Z\nbamboo_repository_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_buildResultKey=JB-GDL111-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588\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/\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-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46498603_name=Jalview Gitlab\nbamboo_planRepository_branchDisplayName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\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-46302777\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-GDL111-JOB1\nbamboo_repository_46498603_git_username=\nbamboo_planKey=JB-GDL111\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 27-Nov-2025 17:32:45 build 27-Nov-2025 17:32:45 > Configure project : build 27-Nov-2025 17:32:45 Using properties from file './utils/channels/default/channel_gradle.properties' build 27-Nov-2025 17:32:45 JALVIEW_VERSION is set to '2.11.5.1' build 27-Nov-2025 17:32:45 HEADLESS BUILD build 27-Nov-2025 17:32:45 J2S ENABLED build 27-Nov-2025 17:32:45 Using a BUILD profile. build 27-Nov-2025 17:32:45 eclipseDir exists build 27-Nov-2025 17:32:45 build 27-Nov-2025 17:32:45 > Task :clean build 27-Nov-2025 17:32:45 > Task :cleanPackageDir UP-TO-DATE build 27-Nov-2025 17:32:45 > Task :getdownImagesCopy build 27-Nov-2025 17:32:45 > Task :getdownImagesProcess build 27-Nov-2025 17:32:45 > Task :getdownImages build 27-Nov-2025 17:32:46 > Task :copyHelp build 27-Nov-2025 17:32:48 > Task :buildIndices build 27-Nov-2025 17:32:48 > Task :copyResources build 27-Nov-2025 17:32:48 > Task :copyChannelResources build 27-Nov-2025 17:32:48 build 27-Nov-2025 17:32:48 > Task :createBuildProperties build 27-Nov-2025 17:32:48 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 27-Nov-2025 17:32:48 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-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 27-Nov-2025 17:32:48 build 27-Nov-2025 17:32:48 > Task :buildResources build 27-Nov-2025 17:32:48 > Task :copyDocs build 27-Nov-2025 17:32:48 build 27-Nov-2025 17:32:48 > Task :convertMdFiles build 27-Nov-2025 17:32:48 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 27-Nov-2025 17:32:48 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1/build/resources/doc_build/doc/releaseprocess.html build 27-Nov-2025 17:32:48 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 27-Nov-2025 17:32:48 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1/build/resources/doc_build/doc/building.html build 27-Nov-2025 17:32:48 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1/build/resources/doc_build/doc/jalview-projects.html build 27-Nov-2025 17:32:48 build 27-Nov-2025 17:32:48 > Task :releasesTemplates build 27-Nov-2025 17:32:48 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 27-Nov-2025 17:32:48 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-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 27-Nov-2025 17:32:48 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-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 27-Nov-2025 17:32:48 Stripping rc/test/etc for 2_11_5_1 build 27-Nov-2025 17:32:48 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md build 27-Nov-2025 17:32:48 build 27-Nov-2025 17:32:48 > Task :prepare build 27-Nov-2025 17:32:51 build 27-Nov-2025 17:32:51 > Task :compileJava build 27-Nov-2025 17:32:51 Setting target compatibility to 11 error 27-Nov-2025 17:32:59 Note: Some input files use or override a deprecated API. error 27-Nov-2025 17:32:59 Note: Recompile with -Xlint:deprecation for details. error 27-Nov-2025 17:32:59 Note: Some input files use unchecked or unsafe operations. error 27-Nov-2025 17:32:59 Note: Recompile with -Xlint:unchecked for details. build 27-Nov-2025 17:32:59 build 27-Nov-2025 17:32:59 > Task :processResources build 27-Nov-2025 17:32:59 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 27-Nov-2025 17:32:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-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 27-Nov-2025 17:32:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-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 27-Nov-2025 17:32:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-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 27-Nov-2025 17:32:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-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 27-Nov-2025 17:32:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-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 27-Nov-2025 17:32:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-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 27-Nov-2025 17:32:59 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-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 27-Nov-2025 17:32:59 build 27-Nov-2025 17:32:59 > Task :classes build 27-Nov-2025 17:33:01 build 27-Nov-2025 17:33:01 > Task :compileLinkCheck build 27-Nov-2025 17:33:01 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 27-Nov-2025 17:33:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-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 27-Nov-2025 17:33:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-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 27-Nov-2025 17:33:01 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-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 27-Nov-2025 17:33:05 build 27-Nov-2025 17:33:05 > Task :linkCheck build 27-Nov-2025 17:33:05 Checking help file links build 27-Nov-2025 17:35:11 build 27-Nov-2025 17:35:11 Results: build 27-Nov-2025 17:35:11 161 distinct help targets build 27-Nov-2025 17:35:11 161 help mappings build 27-Nov-2025 17:35:11 0 invalid targets build 27-Nov-2025 17:35:11 31 unused targets build 27-Nov-2025 17:35:11 uniprotfetcher: html/features/uniprotsequencefetcher.html build 27-Nov-2025 17:35:11 overviewprefs: html/features/preferences.html#overview build 27-Nov-2025 17:35:11 cdnafeatures: html/features/codingfeatures.html build 27-Nov-2025 17:35:11 startupprefs: html/features/preferences.html#startup build 27-Nov-2025 17:35:11 ensemblfetch: html/features/ensemblsequencefetcher.html build 27-Nov-2025 17:35:11 io.modellerpir: html/io/modellerpir.html build 27-Nov-2025 17:35:11 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 27-Nov-2025 17:35:11 pdbmcviewer: html/features/pdbviewer.html build 27-Nov-2025 17:35:11 groovy.colours: html/features/groovy.html#groovyColours build 27-Nov-2025 17:35:11 seqmappings: html/features/seqmappings.html build 27-Nov-2025 17:35:11 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 27-Nov-2025 17:35:11 splitframe.mirrorfonts: html/features/splitView.html#mirror build 27-Nov-2025 17:35:11 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 27-Nov-2025 17:35:11 search: html/features/search.html build 27-Nov-2025 17:35:11 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 27-Nov-2025 17:35:11 alformats: html/io/fileformats.html build 27-Nov-2025 17:35:11 strucprefs: html/features/preferences.html#structure build 27-Nov-2025 17:35:11 siftsmapping: html/features/siftsmapping.html build 27-Nov-2025 17:35:11 chimera.annotxfer: html/features/chimera.html#annotxfer build 27-Nov-2025 17:35:11 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 27-Nov-2025 17:35:11 newkeys: html/features/newkeystrokes.html build 27-Nov-2025 17:35:11 importvcf.attribs: html/features/importvcf.html#attribs build 27-Nov-2025 17:35:11 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 27-Nov-2025 17:35:11 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 27-Nov-2025 17:35:11 jalarchive: html/features/jalarchive.html build 27-Nov-2025 17:35:11 newsreader: html/webServices/newsreader.html build 27-Nov-2025 17:35:11 jalviewcltool: html/features/commandline.html#script build 27-Nov-2025 17:35:11 popMenuAddref: html/menus/popupMenu.html#addrefannot build 27-Nov-2025 17:35:11 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 27-Nov-2025 17:35:11 paematrixformat: html/io/paematrixformat.html build 27-Nov-2025 17:35:11 overview: html/features/overview.html build 27-Nov-2025 17:35:11 0 invalid map urls build 27-Nov-2025 17:35:11 0 invalid image attributes build 27-Nov-2025 17:35:11 520 internal href links (120 with anchors) build 27-Nov-2025 17:35:11 0 invalid internal href links build 27-Nov-2025 17:35:11 0 invalid internal anchor links build 27-Nov-2025 17:35:11 112 external href links build 27-Nov-2025 17:35:11 External links not verified as internet not available build 27-Nov-2025 17:35:11 *** Success *** build 27-Nov-2025 17:35:12 build 27-Nov-2025 17:35:12 > Task :jar build 27-Nov-2025 17:35:12 > Task :syncJars build 27-Nov-2025 17:35:12 > Task :makeDist build 27-Nov-2025 17:35:12 > Task :getdownWebsiteBuild build 27-Nov-2025 17:35:14 build 27-Nov-2025 17:35:14 > Task :getdownDigest build 27-Nov-2025 17:35:14 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 27-Nov-2025 17:35:14 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... error 27-Nov-2025 17:35:14 2025/11/27 17:35:13:130 WARNING Starting without install4j classes error 27-Nov-2025 17:35:14 2025/11/27 17:35:14:196 WARNING Starting without install4j classes build 27-Nov-2025 17:35:14 build 27-Nov-2025 17:35:14 > Task :getdown build 27-Nov-2025 17:35:14 build 27-Nov-2025 17:35:14 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 27-Nov-2025 17:35:14 build 27-Nov-2025 17:35:14 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 27-Nov-2025 17:35:14 build 27-Nov-2025 17:35:14 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 27-Nov-2025 17:35:14 build 27-Nov-2025 17:35:14 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 27-Nov-2025 17:35:14 Please consult deprecation warnings for more details. build 27-Nov-2025 17:35:14 build 27-Nov-2025 17:35:14 BUILD SUCCESSFUL in 2m 32s build 27-Nov-2025 17:35:14 21 actionable tasks: 20 executed, 1 up-to-date simple 27-Nov-2025 17:35:15 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 27-Nov-2025 17:35:15 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 27-Nov-2025 17:35:15 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job #1 (JB-GDL111-JOB1-1)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL111-JOB1-1-ScriptBuildTask-5938749325126168829.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_dependency_parent_0=JB-GDB729-5\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_repository_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL111-JOB1-1\nbamboo_repository_46498603_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL111-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL111-JOB1\nbamboo_shortPlanName=bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_repository_46498603_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_buildNumber=1\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-GDL111-JOB1-1\nbamboo_repository_46498603_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_shortPlanKey=GDL111\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588\nbamboo_repository_46498603_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_buildTimeStamp=2025-11-27T17:19:11.296Z\nbamboo_repository_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_buildResultKey=JB-GDL111-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588\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-GDL111 -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-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46498603_name=Jalview Gitlab\nbamboo_planRepository_branchDisplayName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\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-46302777\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-GDL111-JOB1\nbamboo_repository_46498603_git_username=\nbamboo_planKey=JB-GDL111\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus\n simple 27-Nov-2025 17:35:15 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 27-Nov-2025 17:35:15 Running post build plugin 'NCover Results Collector' simple 27-Nov-2025 17:35:15 Running post build plugin 'Artifact Copier' simple 27-Nov-2025 17:35:15 Publishing an artifact: getdown simple 27-Nov-2025 17:35:15 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 122.0 ms simple 27-Nov-2025 17:35:15 Running post build plugin 'Artifactory Release Management Staging' simple 27-Nov-2025 17:35:15 Running post build plugin 'Artifactory Build Info Copier' simple 27-Nov-2025 17:35:15 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 27-Nov-2025 17:35:15 Running post build plugin 'npm Cache Cleanup' simple 27-Nov-2025 17:35:15 Running post build plugin 'Clover Results Collector' simple 27-Nov-2025 17:35:15 Running post build plugin 'Docker Container Cleanup' simple 27-Nov-2025 17:35:15 Finalising the build... simple 27-Nov-2025 17:35:15 Stopping timer. simple 27-Nov-2025 17:35:15 Build JB-GDL111-JOB1-1 completed. simple 27-Nov-2025 17:35:15 Running on server: post build plugin 'NCover Results Collector' simple 27-Nov-2025 17:35:15 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 27-Nov-2025 17:35:15 Running on server: post build plugin 'Clover Delta Calculator' simple 27-Nov-2025 17:35:15 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 27-Nov-2025 17:35:15 All post build plugins have finished simple 27-Nov-2025 17:35:15 Generating build results summary... simple 27-Nov-2025 17:35:15 Saving build results to disk... simple 27-Nov-2025 17:35:15 Logging substituted variables... simple 27-Nov-2025 17:35:15 Indexing build results... simple 27-Nov-2025 17:35:15 Finished building JB-GDL111-JOB1-1.