simple 10-Dec-2025 18:21:16 Build Jalview Builds - Getdown Plan Channel - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job #2 (JB-GPC656-JOB1-2) started building on agent Default Agent simple 10-Dec-2025 18:21:16 simple 10-Dec-2025 18:21:16 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1 simple 10-Dec-2025 18:21:16 Executing build Jalview Builds - Getdown Plan Channel - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job #2 (JB-GPC656-JOB1-2) simple 10-Dec-2025 18:21:16 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 10-Dec-2025 18:21:16 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1 simple 10-Dec-2025 18:21:16 Updating source code to revision: b80719bcafaf18f88875dd6956bb3bd47ff21bed simple 10-Dec-2025 18:21:16 Fetching 'refs/heads/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 10-Dec-2025 18:21:17 Checking out revision b80719bcafaf18f88875dd6956bb3bd47ff21bed. simple 10-Dec-2025 18:21:17 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 10-Dec-2025 18:21:17 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 18:21:17 * [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 18:21:17 4d0c90d..5a35253 development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch simple 10-Dec-2025 18:21:17 * [new branch] patch/JAL-4606_again_and_again -> origin/patch/JAL-4606_again_and_again simple 10-Dec-2025 18:21:17 c586364..9e8107e releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch simple 10-Dec-2025 18:21:19 Already on 'bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' simple 10-Dec-2025 18:21:19 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 18:21:19 (use "git pull" to update your local branch) simple 10-Dec-2025 18:21:19 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 18:21:19 Updated source code to revision: b80719bcafaf18f88875dd6956bb3bd47ff21bed simple 10-Dec-2025 18:21:19 Finished task 'Checkout Default Repository' with result: Success simple 10-Dec-2025 18:21:19 Running pre-build action: VCS Version Collector simple 10-Dec-2025 18:21:19 Running pre-build action: Artifactory Release Staging command 10-Dec-2025 18:21:19 Substituting variable: ${bamboo.planKey} with JB-GPC656 simple 10-Dec-2025 18:21:19 Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 10-Dec-2025 18:21:19 Bamboo Artifactory Plugin version: 2.6.2 command 10-Dec-2025 18:21:19 Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job #2 (JB-GPC656-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC656 clean shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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\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-GPC656-JOB1-2\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_46498619_revision_number=b80719bcafaf18f88875dd6956bb3bd47ff21bed\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GPC656-JOB1\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_46498619_previous_revision_number=e0875267ed4b699db969bf10b30bafe83a1cbd7d\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-GPC656-JOB1-2\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_shortPlanKey=GPC656\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=b80719bcafaf18f88875dd6956bb3bd47ff21bed\nbamboo_buildTimeStamp=2025-12-10T18:18:49.873Z\nbamboo_repository_previous_revision_number=e0875267ed4b699db969bf10b30bafe83a1cbd7d\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GPC656-JOB1-2\nbamboo_repository_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - 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_repository_46498619_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_46498619_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_repository_46498619_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\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-46302807\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-GPC656-JOB1\nbamboo_repository_46498619_name=Jalview Gitlab\nbamboo_planKey=JB-GPC656\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498619_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 18:21:20 build 10-Dec-2025 18:21:20 > Configure project : build 10-Dec-2025 18:21:20 Using properties from file './utils/channels/default/channel_gradle.properties' build 10-Dec-2025 18:21:20 JALVIEW_VERSION is set to '2.12.0' build 10-Dec-2025 18:21:20 HEADLESS BUILD build 10-Dec-2025 18:21:20 J2S ENABLED build 10-Dec-2025 18:21:20 Using a BUILD profile. build 10-Dec-2025 18:21:20 eclipseDir exists build 10-Dec-2025 18:21:21 build 10-Dec-2025 18:21:21 > Task :clean build 10-Dec-2025 18:21:21 > Task :cleanPackageDir build 10-Dec-2025 18:21:21 > Task :copyHelp build 10-Dec-2025 18:21:22 > Task :buildIndices build 10-Dec-2025 18:21:22 > Task :copyResources build 10-Dec-2025 18:21:22 > Task :copyChannelResources build 10-Dec-2025 18:21:22 build 10-Dec-2025 18:21:22 > Task :createBuildProperties build 10-Dec-2025 18:21:22 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 10-Dec-2025 18:21:22 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:21:22 build 10-Dec-2025 18:21:22 > Task :buildResources build 10-Dec-2025 18:21:22 > Task :copyDocs build 10-Dec-2025 18:21:22 build 10-Dec-2025 18:21:22 > Task :convertMdFiles build 10-Dec-2025 18:21:22 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 10-Dec-2025 18:21:22 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/releaseprocess.html build 10-Dec-2025 18:21:22 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 10-Dec-2025 18:21:22 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/JalviewJS-API.html build 10-Dec-2025 18:21:22 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/building.html build 10-Dec-2025 18:21:22 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/addingWebClient.html build 10-Dec-2025 18:21:22 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/jalview-projects.html build 10-Dec-2025 18:21:22 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html build 10-Dec-2025 18:21:22 build 10-Dec-2025 18:21:22 > Task :releasesTemplates build 10-Dec-2025 18:21:22 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 10-Dec-2025 18:21:22 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:21:22 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:21:22 Stripping rc/test/etc for 2_12_0 build 10-Dec-2025 18:21:22 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/help/markdown/whatsnew/whatsnew-2_12_0.md build 10-Dec-2025 18:21:22 build 10-Dec-2025 18:21:22 > Task :prepare build 10-Dec-2025 18:21:24 build 10-Dec-2025 18:21:24 > Task :compileJava build 10-Dec-2025 18:21:24 Setting target compatibility to 11 error 10-Dec-2025 18:21:30 Note: Some input files use or override a deprecated API. error 10-Dec-2025 18:21:30 Note: Recompile with -Xlint:deprecation for details. error 10-Dec-2025 18:21:30 Note: Some input files use unchecked or unsafe operations. error 10-Dec-2025 18:21:30 Note: Recompile with -Xlint:unchecked for details. build 10-Dec-2025 18:21:30 build 10-Dec-2025 18:21:30 > Task :processResources build 10-Dec-2025 18:21:30 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 10-Dec-2025 18:21:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:21:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:21:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:21:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:21:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:21:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:21:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:21:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:21:30 build 10-Dec-2025 18:21:30 > Task :classes build 10-Dec-2025 18:21:31 build 10-Dec-2025 18:21:31 > Task :compileLinkCheck build 10-Dec-2025 18:21:31 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 10-Dec-2025 18:21:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:21:31 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:21:33 build 10-Dec-2025 18:21:33 > Task :linkCheck build 10-Dec-2025 18:21:33 Checking help file links build 10-Dec-2025 18:23:39 build 10-Dec-2025 18:23:39 Results: build 10-Dec-2025 18:23:39 162 distinct help targets build 10-Dec-2025 18:23:39 162 help mappings build 10-Dec-2025 18:23:39 0 invalid targets build 10-Dec-2025 18:23:39 31 unused targets build 10-Dec-2025 18:23:39 uniprotfetcher: html/features/uniprotsequencefetcher.html build 10-Dec-2025 18:23:39 overviewprefs: html/features/preferences.html#overview build 10-Dec-2025 18:23:39 cdnafeatures: html/features/codingfeatures.html build 10-Dec-2025 18:23:39 startupprefs: html/features/preferences.html#startup build 10-Dec-2025 18:23:39 ensemblfetch: html/features/ensemblsequencefetcher.html build 10-Dec-2025 18:23:39 io.modellerpir: html/io/modellerpir.html build 10-Dec-2025 18:23:39 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 10-Dec-2025 18:23:39 pdbmcviewer: html/features/pdbviewer.html build 10-Dec-2025 18:23:39 groovy.colours: html/features/groovy.html#groovyColours build 10-Dec-2025 18:23:39 seqmappings: html/features/seqmappings.html build 10-Dec-2025 18:23:39 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 10-Dec-2025 18:23:39 splitframe.mirrorfonts: html/features/splitView.html#mirror build 10-Dec-2025 18:23:39 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 10-Dec-2025 18:23:39 search: html/features/search.html build 10-Dec-2025 18:23:39 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 10-Dec-2025 18:23:39 alformats: html/io/fileformats.html build 10-Dec-2025 18:23:39 strucprefs: html/features/preferences.html#structure build 10-Dec-2025 18:23:39 siftsmapping: html/features/siftsmapping.html build 10-Dec-2025 18:23:39 chimera.annotxfer: html/features/chimera.html#annotxfer build 10-Dec-2025 18:23:39 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 10-Dec-2025 18:23:39 newkeys: html/features/newkeystrokes.html build 10-Dec-2025 18:23:39 importvcf.attribs: html/features/importvcf.html#attribs build 10-Dec-2025 18:23:39 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 10-Dec-2025 18:23:39 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 10-Dec-2025 18:23:39 jalarchive: html/features/jalarchive.html build 10-Dec-2025 18:23:39 newsreader: html/webServices/newsreader.html build 10-Dec-2025 18:23:39 jalviewcltool: html/features/commandline.html#script build 10-Dec-2025 18:23:39 popMenuAddref: html/menus/popupMenu.html#addrefannot build 10-Dec-2025 18:23:39 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 10-Dec-2025 18:23:39 paematrixformat: html/io/paematrixformat.html build 10-Dec-2025 18:23:39 overview: html/features/overview.html build 10-Dec-2025 18:23:39 0 invalid map urls build 10-Dec-2025 18:23:39 0 invalid image attributes build 10-Dec-2025 18:23:39 520 internal href links (119 with anchors) build 10-Dec-2025 18:23:39 0 invalid internal href links build 10-Dec-2025 18:23:39 0 invalid internal anchor links build 10-Dec-2025 18:23:39 113 external href links build 10-Dec-2025 18:23:39 External links not verified as internet not available build 10-Dec-2025 18:23:39 *** Success *** build 10-Dec-2025 18:23:40 build 10-Dec-2025 18:23:40 > Task :jar build 10-Dec-2025 18:23:40 > Task :syncJars build 10-Dec-2025 18:23:40 > Task :makeDist build 10-Dec-2025 18:23:47 > Task :shadowJar build 10-Dec-2025 18:23:47 build 10-Dec-2025 18:23:47 > Task :getdownImagesCopy build 10-Dec-2025 18:23:47 Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons: build 10-Dec-2025 18:23:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/utils/channels/default/images'. 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 18:23:48 build 10-Dec-2025 18:23:48 > Task :getdownImagesProcess build 10-Dec-2025 18:23:48 > Task :getdownImages build 10-Dec-2025 18:23:48 > Task :getdownWebsiteBuild build 10-Dec-2025 18:23:49 build 10-Dec-2025 18:23:49 > Task :getdownDigest build 10-Dec-2025 18:23:49 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... error 10-Dec-2025 18:23:49 2025/12/10 18:23:48:479 WARNING Starting without install4j classes error 10-Dec-2025 18:23:49 2025/12/10 18:23:48:993 WARNING Starting without install4j classes build 10-Dec-2025 18:23:49 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 10-Dec-2025 18:23:49 build 10-Dec-2025 18:23:49 > Task :getdown build 10-Dec-2025 18:23:49 build 10-Dec-2025 18:23:49 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 10-Dec-2025 18:23:49 build 10-Dec-2025 18:23:49 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 18:23:49 build 10-Dec-2025 18:23:49 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 10-Dec-2025 18:23:49 build 10-Dec-2025 18:23:49 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 10-Dec-2025 18:23:49 Please consult deprecation warnings for more details. build 10-Dec-2025 18:23:49 build 10-Dec-2025 18:23:49 BUILD SUCCESSFUL in 2m 29s build 10-Dec-2025 18:23:49 22 actionable tasks: 22 executed simple 10-Dec-2025 18:23:49 Finished task 'Jalview distribution for Java 11' with result: Success command 10-Dec-2025 18:23:49 Substituting variable: ${bamboo.planKey} with JB-GPC656 simple 10-Dec-2025 18:23:49 Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 10-Dec-2025 18:23:49 Bamboo Artifactory Plugin version: 2.6.2 command 10-Dec-2025 18:23:49 Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Default Job #2 (JB-GPC656-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -x clean -PCHANNEL=BUILD -PJAVA_VERSION=1.8 -Pbamboo_planKey=JB-GPC656 shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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\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-GPC656-JOB1-2\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_46498619_revision_number=b80719bcafaf18f88875dd6956bb3bd47ff21bed\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GPC656-JOB1\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_46498619_previous_revision_number=e0875267ed4b699db969bf10b30bafe83a1cbd7d\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-GPC656-JOB1-2\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_shortPlanKey=GPC656\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=b80719bcafaf18f88875dd6956bb3bd47ff21bed\nbamboo_buildTimeStamp=2025-12-10T18:18:49.873Z\nbamboo_repository_previous_revision_number=e0875267ed4b699db969bf10b30bafe83a1cbd7d\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GPC656-JOB1-2\nbamboo_repository_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - 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_repository_46498619_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\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-GPC656 clean shadowJar getdown\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_46498619_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_repository_46498619_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\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-46302807\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-GPC656-JOB1\nbamboo_repository_46498619_name=Jalview Gitlab\nbamboo_planKey=JB-GPC656\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498619_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 18:23:50 build 10-Dec-2025 18:23:50 > Configure project : build 10-Dec-2025 18:23:50 Using properties from file './utils/channels/default/channel_gradle.properties' build 10-Dec-2025 18:23:50 JALVIEW_VERSION is set to '2.12.0' build 10-Dec-2025 18:23:50 HEADLESS BUILD build 10-Dec-2025 18:23:50 J2S ENABLED build 10-Dec-2025 18:23:50 Using a BUILD profile. build 10-Dec-2025 18:23:50 eclipseDir exists build 10-Dec-2025 18:23:50 build 10-Dec-2025 18:23:50 > Task :copyHelp UP-TO-DATE build 10-Dec-2025 18:23:51 > Task :buildIndices build 10-Dec-2025 18:23:52 > Task :copyResources UP-TO-DATE build 10-Dec-2025 18:23:52 > Task :copyChannelResources UP-TO-DATE build 10-Dec-2025 18:23:52 build 10-Dec-2025 18:23:52 > Task :createBuildProperties build 10-Dec-2025 18:23:52 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 10-Dec-2025 18:23:52 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:23:52 build 10-Dec-2025 18:23:52 > Task :buildResources build 10-Dec-2025 18:23:52 > Task :copyDocs build 10-Dec-2025 18:23:52 build 10-Dec-2025 18:23:52 > Task :convertMdFiles build 10-Dec-2025 18:23:52 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 10-Dec-2025 18:23:52 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/releaseprocess.html build 10-Dec-2025 18:23:52 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 10-Dec-2025 18:23:52 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/JalviewJS-API.html build 10-Dec-2025 18:23:52 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/building.html build 10-Dec-2025 18:23:52 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/addingWebClient.html build 10-Dec-2025 18:23:52 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/jalview-projects.html build 10-Dec-2025 18:23:52 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html build 10-Dec-2025 18:23:52 build 10-Dec-2025 18:23:52 > Task :releasesTemplates build 10-Dec-2025 18:23:52 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 10-Dec-2025 18:23:52 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:23:52 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-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 18:23:52 Stripping rc/test/etc for 2_12_0 build 10-Dec-2025 18:23:52 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/help/markdown/whatsnew/whatsnew-2_12_0.md build 10-Dec-2025 18:23:52 build 10-Dec-2025 18:23:52 > Task :prepare build 10-Dec-2025 18:23:54 build 10-Dec-2025 18:23:54 > Task :compileJava build 10-Dec-2025 18:23:54 Setting target compatibility to 1.8 error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/WSClient.java:180: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var stage = jobParams.showRunDialog(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/params/ParamDatastoreI.java:39: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var presets = getPresets(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/params/ParamDatastoreI.java:51: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var parameters = getServiceParameters(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java:67: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var listener : serviceListeners) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/slivkaws/SlivkaWSInstance.java:77: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var parameters = service.getParameters(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/slivkaws/SlivkaWSInstance.java:78: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var request = new RequestValues(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/slivkaws/SlivkaWSInstance.java:129: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var jobId = client.submitJob(service, request); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/slivkaws/SlivkaWSInstance.java:254: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 final var mimetype = f.getMediaType(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/Jws2Discoverer.java:142: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var listener : serviceListeners) { error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/Jws2Discoverer.java:360: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var discoverer = getInstance(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/PreferredServiceRegistry.java:63: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var service : services) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/PreferredServiceRegistry.java:70: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var service : interactiveServices) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/PreferredServiceRegistry.java:74: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var preferred = getPreferredServiceFor(alignFrame, service.getName()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/PreferredServiceRegistry.java:77: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var ph = alternates.getOrDefault(service.getName(), new ArrayList<>()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/SequenceAnnotationWSClient.java:104: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 final var worker = tmpworker; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/Desktop.java:3260: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var tasks = new ArrayList>(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/Desktop.java:3276: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var f = new FutureTask(discoverer, null); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:927: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var menu = AlignFrame.this.slivkaMenu; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:936: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var menu = AlignFrame.this.ebiMenu; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:945: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var menu = AlignFrame.this.jpred4Menu; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:1235: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var args2 = params.getJobParams(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:1268: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var args2 = params.getJobParams(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:1301: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var args2 = params.getJobParams(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:1333: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var args2 = params.getJobParams(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:5154: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var secstrpred = Discoverer.getServices().get("SecStrPred"); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:5159: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var menuProvider = Discoverer.getServiceClient(sh); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/datamodel/ContiguousI.java:35: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var range : ranges) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/datamodel/SequenceI.java:415: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var sequence = getDatasetSequence(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/datamodel/AnnotatedCollectionI.java:79: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var annots = getAlignmentAnnotation(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTask.java:63: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var seqInfo = SeqsetUtils.SeqCharacterHash(seq); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTask.java:69: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var job = new SecStructPredJob(seq, delMap, seqInfo); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTask.java:80: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var job = jobs.get(0); // There should be exactly one job error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTask.java:81: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var status = job.getStatus(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/secstructpred/SecStructPredMsaTask.java:67: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var sequenceInfo = SeqsetUtils.uniquify(sequences, true); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/secstructpred/SecStructPredMsaTask.java:71: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var nonEmptySeqs = SeqsetUtils.getNonEmptySequenceSet(sequences); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/secstructpred/SecStructPredMsaTask.java:72: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var job = new SecStructPredJob(Arrays.asList(nonEmptySeqs), error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/secstructpred/SecStructPredMsaTask.java:82: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var job = jobs.get(0); // There shouldn't be more than one job error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/secstructpred/SecStructPredMsaTask.java:83: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var status = job.getStatus(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/hmmer/PhmmerTask.java:42: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var sequence = view.getVisibleAlignment('-').getSequenceAt(0); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/hmmer/PhmmerTask.java:43: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var seq = new Sequence(sequence.getName(), error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/hmmer/PhmmerTask.java:45: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var job = new BaseJob(List.of(seq)) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/hmmer/PhmmerTask.java:60: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var job = jobs.get(0); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/hmmer/PhmmerTask.java:61: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var status = job.getStatus(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/hmmer/PhmmerTask.java:66: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var outputAlignment = client.getAlignment(job.getServerJob()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/hmmer/PhmmerTask.java:67: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var querySeq = job.getInputSequences().get(0).deriveSequence(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/hmmer/PhmmerTask.java:70: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var annot : outputAlignment.getAlignmentAnnotation()) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/hmmer/PhmmerTask.java:89: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var sequenceBuilder = new StringBuilder(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/hmmer/PhmmerTask.java:90: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var index = 0; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/hmmer/PhmmerAction.java:63: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var task = createTask(viewport, args, credentials); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/hmmer/PhmmerAction.java:65: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var executor = PollingTaskExecutor.fromPool(viewport.getServiceExecutor()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/hmmer/PhmmerAction.java:66: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var future = executor.submit(task); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/annotation/AnnotationJob.java:134: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var gaps = seq.gapBitset(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/annotation/AlignCalcWorkerAdapter.java:44: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var newAnnot = alignViewport.getAlignment() error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/annotation/AnnotationTask.java:100: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var job = jobs.get(0); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/annotation/AnnotationTask.java:153: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var annotation : annotations) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/annotation/AnnotationTask.java:170: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var size = Math.max(annotations.length, gapMap.length); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/api/ActionI.java:56: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var name = getName(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/alignment/AlignmentTask.java:148: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var seq: alnSeqs) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/alignment/AlignmentTask.java:157: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var seq: alnSeqs) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:103: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var jobListener = new DelegateJobEventListener<>(eventHandler); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:104: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var job : jobs) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:113: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var retryCounter = 0; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:143: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var jobRef = webClient.submit(job.getInputSequences(), args, credentials); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:171: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var serverJob = job.getServerJob(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:193: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var job : jobs) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:309: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var statusName = status != null ? status.name() : "UNSET"; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:97: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var map = service.isInteractive() ? interactiveServices : oneshotServices; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:101: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var allKeysSet = new HashSet<>(oneshotServices.keySet()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:103: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var allKeys = new ArrayList<>(allKeysSet); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:107: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var categoryMenu = new JMenu(category); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:108: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var oneshot = oneshotServices.get(category); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:111: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var interactive = interactiveServices.get(category); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:128: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var res = ws1.getUrl().toString().compareTo(ws2.getUrl().toString()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:142: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var item = new JMenuItem(host.toString()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:150: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var actionsByCategory = new TreeMap>>(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:159: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var entry : actionsByCategory.entrySet()) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:161: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var category = entry.getKey(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:162: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var actions = entry.getValue(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:164: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var atMenu = category.isEmpty() ? menu : new JMenu(String.format("%s with %s", category, service.getName())); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:180: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var enabled = isActionEnabled(action); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:181: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var service = action.getWebService(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:196: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var datastore = service.getParamDatastore(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:221: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var presets = datastore.getPresets(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:224: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 final var presetsMenu = new JMenu(MessageManager.formatMessage( error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:230: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var preset : presets) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:232: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var item = new JMenuItem(preset.getName()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:266: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var service : services) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:271: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var entry : byServiceName.entrySet()) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:273: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var group = new InteractiveServiceEntryGroup(entry.getKey(), entry.getValue()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:308: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var menu = alternativesMenu; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:310: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var res = ws1.getUrl().toString().compareTo(ws2.getUrl().toString()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:316: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var service : services) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:324: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var item = new JMenuItem(host.toString()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:331: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var actionsByCategory = new TreeMap>>(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:341: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var atMenu = key.isEmpty() ? menu : new JMenu(key + " with " + service.getName()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:350: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var item = new JMenuItem(action.getFullName()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:361: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 final var arguments = new ArrayList(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:368: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var l : urlItem.getActionListeners()) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:375: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 for (var l : serviceItem.getActionListeners()) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:385: warning: as of release 10, 'var' is a restricted local variable type and cannot be used for type declarations or as the element type of an array error 10-Dec-2025 18:23:54 var datastore = service.getParamDatastore(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/datamodel/SequenceI.java:415: error: cannot find symbol error 10-Dec-2025 18:23:54 var sequence = getDatasetSequence(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: interface SequenceI error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/datamodel/AnnotatedCollectionI.java:79: error: cannot find symbol error 10-Dec-2025 18:23:54 var annots = getAlignmentAnnotation(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: interface AnnotatedCollectionI error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/Desktop.java:3260: error: cannot find symbol error 10-Dec-2025 18:23:54 var tasks = new ArrayList>(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class Desktop error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/Desktop.java:3276: error: cannot find symbol error 10-Dec-2025 18:23:54 var f = new FutureTask(discoverer, null); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class Desktop error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:927: error: cannot find symbol error 10-Dec-2025 18:23:54 var menu = AlignFrame.this.slivkaMenu; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class AlignFrame error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:936: error: cannot find symbol error 10-Dec-2025 18:23:54 var menu = AlignFrame.this.ebiMenu; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class AlignFrame error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:945: error: cannot find symbol error 10-Dec-2025 18:23:54 var menu = AlignFrame.this.jpred4Menu; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class AlignFrame error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:1235: error: cannot find symbol error 10-Dec-2025 18:23:54 var args2 = params.getJobParams(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class AlignFrame error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:1268: error: cannot find symbol error 10-Dec-2025 18:23:54 var args2 = params.getJobParams(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class AlignFrame error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:1301: error: cannot find symbol error 10-Dec-2025 18:23:54 var args2 = params.getJobParams(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class AlignFrame error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:1333: error: cannot find symbol error 10-Dec-2025 18:23:54 var args2 = params.getJobParams(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class AlignFrame error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:5154: error: cannot find symbol error 10-Dec-2025 18:23:54 var secstrpred = Discoverer.getServices().get("SecStrPred"); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class AlignFrame error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/gui/AlignFrame.java:5159: error: cannot find symbol error 10-Dec-2025 18:23:54 var menuProvider = Discoverer.getServiceClient(sh); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class AlignFrame error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:97: error: cannot find symbol error 10-Dec-2025 18:23:54 var map = service.isInteractive() ? interactiveServices : oneshotServices; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:101: error: cannot find symbol error 10-Dec-2025 18:23:54 var allKeysSet = new HashSet<>(oneshotServices.keySet()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:103: error: cannot find symbol error 10-Dec-2025 18:23:54 var allKeys = new ArrayList<>(allKeysSet); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:107: error: cannot find symbol error 10-Dec-2025 18:23:54 var categoryMenu = new JMenu(category); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:108: error: cannot find symbol error 10-Dec-2025 18:23:54 var oneshot = oneshotServices.get(category); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:111: error: cannot find symbol error 10-Dec-2025 18:23:54 var interactive = interactiveServices.get(category); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:128: error: cannot find symbol error 10-Dec-2025 18:23:54 var res = ws1.getUrl().toString().compareTo(ws2.getUrl().toString()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:142: error: cannot find symbol error 10-Dec-2025 18:23:54 var item = new JMenuItem(host.toString()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:150: error: cannot find symbol error 10-Dec-2025 18:23:54 var actionsByCategory = new TreeMap>>(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:159: error: cannot find symbol error 10-Dec-2025 18:23:54 for (var entry : actionsByCategory.entrySet()) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:161: error: cannot find symbol error 10-Dec-2025 18:23:54 var category = entry.getKey(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:162: error: cannot find symbol error 10-Dec-2025 18:23:54 var actions = entry.getValue(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:164: error: cannot find symbol error 10-Dec-2025 18:23:54 var atMenu = category.isEmpty() ? menu : new JMenu(String.format("%s with %s", category, service.getName())); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:168: error: incompatible types: cannot infer type-variable(s) T#1,U,T#2,T#3 error 10-Dec-2025 18:23:54 actions.sort(Comparator.comparing( error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 (argument mismatch; invalid method reference error 10-Dec-2025 18:23:54 method getName in interface ActionI cannot be applied to given types error 10-Dec-2025 18:23:54 required: no arguments error 10-Dec-2025 18:23:54 found: Object error 10-Dec-2025 18:23:54 reason: actual and formal argument lists differ in length) error 10-Dec-2025 18:23:54 where T#1,U,T#2,T#3,R are type-variables: error 10-Dec-2025 18:23:54 T#1 extends Object declared in method comparing(Function,Comparator) error 10-Dec-2025 18:23:54 U extends Object declared in method comparing(Function,Comparator) error 10-Dec-2025 18:23:54 T#2 extends Object declared in method nullsFirst(Comparator) error 10-Dec-2025 18:23:54 T#3 extends Comparable declared in method naturalOrder() error 10-Dec-2025 18:23:54 R extends Object declared in interface ActionI error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:180: error: cannot find symbol error 10-Dec-2025 18:23:54 var enabled = isActionEnabled(action); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:181: error: cannot find symbol error 10-Dec-2025 18:23:54 var service = action.getWebService(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:196: error: cannot find symbol error 10-Dec-2025 18:23:54 var datastore = service.getParamDatastore(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:221: error: cannot find symbol error 10-Dec-2025 18:23:54 var presets = datastore.getPresets(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:224: error: cannot find symbol error 10-Dec-2025 18:23:54 final var presetsMenu = new JMenu(MessageManager.formatMessage( error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:230: error: cannot find symbol error 10-Dec-2025 18:23:54 for (var preset : presets) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:232: error: cannot find symbol error 10-Dec-2025 18:23:54 var item = new JMenuItem(preset.getName()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:266: error: cannot find symbol error 10-Dec-2025 18:23:54 for (var service : services) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:271: error: cannot find symbol error 10-Dec-2025 18:23:54 for (var entry : byServiceName.entrySet()) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:273: error: cannot find symbol error 10-Dec-2025 18:23:54 var group = new InteractiveServiceEntryGroup(entry.getKey(), entry.getValue()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:308: error: cannot find symbol error 10-Dec-2025 18:23:54 var menu = alternativesMenu; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager.InteractiveServiceEntryGroup error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:310: error: cannot find symbol error 10-Dec-2025 18:23:54 var res = ws1.getUrl().toString().compareTo(ws2.getUrl().toString()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager.InteractiveServiceEntryGroup error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:316: error: cannot find symbol error 10-Dec-2025 18:23:54 for (var service : services) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager.InteractiveServiceEntryGroup error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:324: error: cannot find symbol error 10-Dec-2025 18:23:54 var item = new JMenuItem(host.toString()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager.InteractiveServiceEntryGroup error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:331: error: cannot find symbol error 10-Dec-2025 18:23:54 var actionsByCategory = new TreeMap>>(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager.InteractiveServiceEntryGroup error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:341: error: cannot find symbol error 10-Dec-2025 18:23:54 var atMenu = key.isEmpty() ? menu : new JMenu(key + " with " + service.getName()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager.InteractiveServiceEntryGroup error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:346: error: cannot find symbol error 10-Dec-2025 18:23:54 a -> a.getName(), error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: method getName() error 10-Dec-2025 18:23:54 location: variable a of type Object error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:350: error: cannot find symbol error 10-Dec-2025 18:23:54 var item = new JMenuItem(action.getFullName()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager.InteractiveServiceEntryGroup error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:361: error: cannot find symbol error 10-Dec-2025 18:23:54 final var arguments = new ArrayList(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager.InteractiveServiceEntryGroup error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:368: error: cannot find symbol error 10-Dec-2025 18:23:54 for (var l : urlItem.getActionListeners()) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager.InteractiveServiceEntryGroup error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:375: error: cannot find symbol error 10-Dec-2025 18:23:54 for (var l : serviceItem.getActionListeners()) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager.InteractiveServiceEntryGroup error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:385: error: cannot find symbol error 10-Dec-2025 18:23:54 var datastore = service.getParamDatastore(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager.InteractiveServiceEntryGroup error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:387: error: cannot find symbol error 10-Dec-2025 18:23:54 for (var l : editParamsItem.getActionListeners()) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager.InteractiveServiceEntryGroup error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:413: error: cannot find symbol error 10-Dec-2025 18:23:54 var item = new JMenuItem(preset.getName()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager.InteractiveServiceEntryGroup error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:444: error: cannot find symbol error 10-Dec-2025 18:23:54 var isNa = frame.getViewport().getAlignment().isNucleotide(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:457: error: cannot find symbol error 10-Dec-2025 18:23:54 var _action = (AlignmentAction) action; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:458: error: cannot find symbol error 10-Dec-2025 18:23:54 var handler = new AlignmentServiceGuiHandler(_action, frame); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:460: error: cannot find symbol error 10-Dec-2025 18:23:54 var executor = PollingTaskExecutor.fromPool(viewport.getServiceExecutor()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:462: error: cannot find symbol error 10-Dec-2025 18:23:54 var future = executor.submit(task); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:468: error: cannot find symbol error 10-Dec-2025 18:23:54 var calcManager = viewport.getCalcManager(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:470: error: cannot find symbol error 10-Dec-2025 18:23:54 var _action = (AnnotationAction) action; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:471: error: cannot find symbol error 10-Dec-2025 18:23:54 var worker = new AlignCalcWorkerAdapter(viewport, frame.alignPanel, error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:473: error: cannot find symbol error 10-Dec-2025 18:23:54 var handler = new AnnotationServiceGuiHandler(_action, frame); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:475: error: cannot find symbol error 10-Dec-2025 18:23:54 for (var w : calcManager.getWorkers()) error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:491: error: cannot find symbol error 10-Dec-2025 18:23:54 var _action = (BaseAction) action; error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:492: error: cannot find symbol error 10-Dec-2025 18:23:54 var handler = new SearchServiceGuiHandler(_action, frame); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:493: error: cannot find symbol error 10-Dec-2025 18:23:54 var task = (BaseTask) _action // FIXME: unsafe cast error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:495: error: cannot find symbol error 10-Dec-2025 18:23:54 var executor = PollingTaskExecutor.fromPool(viewport.getServiceExecutor()); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:497: error: cannot find symbol error 10-Dec-2025 18:23:54 var future = executor.submit(task); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:506: error: cannot find symbol error 10-Dec-2025 18:23:54 var task = action.createTask(viewport, args, credentials); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/gui/WebServicesMenuManager.java:523: error: cannot find symbol error 10-Dec-2025 18:23:54 var stage = jobParams.showRunDialog(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: class WebServicesMenuManager error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/api/ActionI.java:56: error: cannot find symbol error 10-Dec-2025 18:23:54 var name = getName(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: interface ActionI error 10-Dec-2025 18:23:54 where R is a type-variable: error 10-Dec-2025 18:23:54 R extends Object declared in interface ActionI error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/params/ParamDatastoreI.java:39: error: cannot find symbol error 10-Dec-2025 18:23:54 var presets = getPresets(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: interface ParamDatastoreI error 10-Dec-2025 18:23:54 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/params/ParamDatastoreI.java:51: error: cannot find symbol error 10-Dec-2025 18:23:54 var parameters = getServiceParameters(); error 10-Dec-2025 18:23:54 ^ error 10-Dec-2025 18:23:54 symbol: class var error 10-Dec-2025 18:23:54 location: interface ParamDatastoreI error 10-Dec-2025 18:23:55 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/datamodel/ContiguousI.java:35: error: cannot find symbol error 10-Dec-2025 18:23:55 for (var range : ranges) error 10-Dec-2025 18:23:55 ^ error 10-Dec-2025 18:23:55 symbol: class var error 10-Dec-2025 18:23:55 location: interface ContiguousI error 10-Dec-2025 18:23:55 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/WSClient.java:180: error: cannot find symbol error 10-Dec-2025 18:23:55 var stage = jobParams.showRunDialog(); error 10-Dec-2025 18:23:55 ^ error 10-Dec-2025 18:23:55 symbol: class var error 10-Dec-2025 18:23:55 location: class WSClient error 10-Dec-2025 18:23:55 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/analysis/SeqsetUtils.java:84: error: cannot find symbol error 10-Dec-2025 18:23:55 var pdbEntries = seq.getAllPDBEntries(); error 10-Dec-2025 18:23:55 ^ error 10-Dec-2025 18:23:55 symbol: class var error 10-Dec-2025 18:23:55 location: class SeqsetUtils error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/slivkaws/SlivkaWSInstance.java:77: error: cannot find symbol error 10-Dec-2025 18:23:56 var parameters = service.getParameters(); error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class SlivkaWSInstance error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/slivkaws/SlivkaWSInstance.java:78: error: cannot find symbol error 10-Dec-2025 18:23:56 var request = new RequestValues(); error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class SlivkaWSInstance error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/slivkaws/SlivkaWSInstance.java:129: error: cannot find symbol error 10-Dec-2025 18:23:56 var jobId = client.submitJob(service, request); error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class SlivkaWSInstance error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/slivkaws/SlivkaWSInstance.java:254: error: cannot find symbol error 10-Dec-2025 18:23:56 final var mimetype = f.getMediaType(); error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class SlivkaWSInstance error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java:67: error: cannot find symbol error 10-Dec-2025 18:23:56 for (var listener : serviceListeners) error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class SlivkaWSDiscoverer error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/Jws2Discoverer.java:142: error: cannot find symbol error 10-Dec-2025 18:23:56 for (var listener : serviceListeners) { error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class Jws2Discoverer error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/Jws2Discoverer.java:360: error: cannot find symbol error 10-Dec-2025 18:23:56 var discoverer = getInstance(); error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class Jws2Discoverer error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/PreferredServiceRegistry.java:63: error: cannot find symbol error 10-Dec-2025 18:23:56 for (var service : services) error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class PreferredServiceRegistry error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/PreferredServiceRegistry.java:70: error: cannot find symbol error 10-Dec-2025 18:23:56 for (var service : interactiveServices) error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class PreferredServiceRegistry error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/PreferredServiceRegistry.java:74: error: cannot find symbol error 10-Dec-2025 18:23:56 var preferred = getPreferredServiceFor(alignFrame, service.getName()); error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class PreferredServiceRegistry error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/PreferredServiceRegistry.java:77: error: cannot find symbol error 10-Dec-2025 18:23:56 var ph = alternates.getOrDefault(service.getName(), new ArrayList<>()); error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class PreferredServiceRegistry error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws/jws2/SequenceAnnotationWSClient.java:104: error: cannot find symbol error 10-Dec-2025 18:23:56 final var worker = tmpworker; error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class SequenceAnnotationWSClient error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:103: error: cannot find symbol error 10-Dec-2025 18:23:56 var jobListener = new DelegateJobEventListener<>(eventHandler); error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class BaseTask error 10-Dec-2025 18:23:56 where T,R are type-variables: error 10-Dec-2025 18:23:56 T extends BaseJob declared in class BaseTask error 10-Dec-2025 18:23:56 R extends Object declared in class BaseTask error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:104: error: cannot find symbol error 10-Dec-2025 18:23:56 for (var job : jobs) error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class BaseTask error 10-Dec-2025 18:23:56 where T,R are type-variables: error 10-Dec-2025 18:23:56 T extends BaseJob declared in class BaseTask error 10-Dec-2025 18:23:56 R extends Object declared in class BaseTask error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:113: error: cannot find symbol error 10-Dec-2025 18:23:56 var retryCounter = 0; error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class BaseTask error 10-Dec-2025 18:23:56 where T,R are type-variables: error 10-Dec-2025 18:23:56 T extends BaseJob declared in class BaseTask error 10-Dec-2025 18:23:56 R extends Object declared in class BaseTask error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:143: error: cannot find symbol error 10-Dec-2025 18:23:56 var jobRef = webClient.submit(job.getInputSequences(), args, credentials); error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class BaseTask error 10-Dec-2025 18:23:56 where T,R are type-variables: error 10-Dec-2025 18:23:56 T extends BaseJob declared in class BaseTask error 10-Dec-2025 18:23:56 R extends Object declared in class BaseTask error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:171: error: cannot find symbol error 10-Dec-2025 18:23:56 var serverJob = job.getServerJob(); error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class BaseTask error 10-Dec-2025 18:23:56 where T,R are type-variables: error 10-Dec-2025 18:23:56 T extends BaseJob declared in class BaseTask error 10-Dec-2025 18:23:56 R extends Object declared in class BaseTask error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:193: error: cannot find symbol error 10-Dec-2025 18:23:56 for (var job : jobs) error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class BaseTask error 10-Dec-2025 18:23:56 where T,R are type-variables: error 10-Dec-2025 18:23:56 T extends BaseJob declared in class BaseTask error 10-Dec-2025 18:23:56 R extends Object declared in class BaseTask error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/BaseTask.java:309: error: cannot find symbol error 10-Dec-2025 18:23:56 var statusName = status != null ? status.name() : "UNSET"; error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class BaseTask error 10-Dec-2025 18:23:56 where T,R are type-variables: error 10-Dec-2025 18:23:56 T extends BaseJob declared in class BaseTask error 10-Dec-2025 18:23:56 R extends Object declared in class BaseTask error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTask.java:63: error: cannot find symbol error 10-Dec-2025 18:23:56 var seqInfo = SeqsetUtils.SeqCharacterHash(seq); error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class SecStructPredPDBSearchTask error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTask.java:69: error: cannot find symbol error 10-Dec-2025 18:23:56 var job = new SecStructPredJob(seq, delMap, seqInfo); error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class SecStructPredPDBSearchTask error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTask.java:80: error: cannot find symbol error 10-Dec-2025 18:23:56 var job = jobs.get(0); // There should be exactly one job error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class SecStructPredPDBSearchTask error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTask.java:81: error: cannot find symbol error 10-Dec-2025 18:23:56 var status = job.getStatus(); error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class SecStructPredPDBSearchTask error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/helpers/TaskEventSupport.java:40: error: cannot find symbol error 10-Dec-2025 18:23:56 for (var listener : listeners) error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class TaskEventSupport error 10-Dec-2025 18:23:56 where T is a type-variable: error 10-Dec-2025 18:23:56 T extends Object declared in class TaskEventSupport error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/helpers/TaskEventSupport.java:46: error: cannot find symbol error 10-Dec-2025 18:23:56 for (var listener : listeners) error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class TaskEventSupport error 10-Dec-2025 18:23:56 where T is a type-variable: error 10-Dec-2025 18:23:56 T extends Object declared in class TaskEventSupport error 10-Dec-2025 18:23:56 /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/src/jalview/ws2/helpers/TaskEventSupport.java:52: error: cannot find symbol error 10-Dec-2025 18:23:56 for (var listener : listeners) error 10-Dec-2025 18:23:56 ^ error 10-Dec-2025 18:23:56 symbol: class var error 10-Dec-2025 18:23:56 location: class TaskEventSupport error 10-Dec-2025 18:23:56 where T is a type-variable: error 10-Dec-2025 18:23:56 T extends Object declared in class TaskEventSupport error 10-Dec-2025 18:23:57 Note: Some input files use or override a deprecated API. error 10-Dec-2025 18:23:57 Note: Recompile with -Xlint:deprecation for details. error 10-Dec-2025 18:23:57 Note: Some input files use unchecked or unsafe operations. error 10-Dec-2025 18:23:57 Note: Recompile with -Xlint:unchecked for details. error 10-Dec-2025 18:23:57 100 errors error 10-Dec-2025 18:23:57 100 warnings error 10-Dec-2025 18:23:57 error 10-Dec-2025 18:23:57 FAILURE: Build failed with an exception. error 10-Dec-2025 18:23:57 error 10-Dec-2025 18:23:57 * What went wrong: error 10-Dec-2025 18:23:57 Execution failed for task ':compileJava'. error 10-Dec-2025 18:23:57 > Compilation failed; see the compiler error output for details. error 10-Dec-2025 18:23:57 error 10-Dec-2025 18:23:57 * Try: error 10-Dec-2025 18:23:57 > Run with --stacktrace option to get the stack trace. error 10-Dec-2025 18:23:57 > Run with --info or --debug option to get more log output. error 10-Dec-2025 18:23:57 > Run with --scan to get full insights. error 10-Dec-2025 18:23:57 error 10-Dec-2025 18:23:57 * Get more help at https://help.gradle.org error 10-Dec-2025 18:23:57 error 10-Dec-2025 18:23:57 BUILD FAILED in 7s build 10-Dec-2025 18:23:57 build 10-Dec-2025 18:23:57 > Task :compileJava FAILED build 10-Dec-2025 18:23:57 build 10-Dec-2025 18:23:57 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 10-Dec-2025 18:23:57 build 10-Dec-2025 18:23:57 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 18:23:57 build 10-Dec-2025 18:23:57 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 10-Dec-2025 18:23:57 build 10-Dec-2025 18:23:57 Execution optimizations have been disabled for 2 invalid unit(s) of work during this build to ensure correctness. build 10-Dec-2025 18:23:57 Please consult deprecation warnings for more details. build 10-Dec-2025 18:23:57 9 actionable tasks: 6 executed, 3 up-to-date simple 10-Dec-2025 18:23:58 simple 10-Dec-2025 18:23:58 Failing task since return code of [/home/bamboo/buildtools/gradle/bin/gradle -x test -x clean -PCHANNEL=BUILD -PJAVA_VERSION=1.8 -Pbamboo_planKey=JB-GPC656 shadowJar getdown] was 1 while expected 0 simple 10-Dec-2025 18:23:58 Finished task 'Jalview distribution for Java 8' with result: Failed simple 10-Dec-2025 18:23:58 Running post build plugin 'NCover Results Collector' simple 10-Dec-2025 18:23:58 Running post build plugin 'Artifact Copier' simple 10-Dec-2025 18:23:58 Publishing an artifact: Jalview executables simple 10-Dec-2025 18:23:58 Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 96.52 ms simple 10-Dec-2025 18:23:58 Publishing an artifact: install4j installers error 10-Dec-2025 18:23:58 Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/install4j does not exist. simple 10-Dec-2025 18:23:58 The artifact hasn't been successfully published after 1.361 ms simple 10-Dec-2025 18:23:58 Publishing an artifact: getdown-channel error 10-Dec-2025 18:23:58 Unable to publish artifact [getdown-channel]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/getdown/website does not exist. simple 10-Dec-2025 18:23:58 The artifact hasn't been successfully published after 88.56 μs simple 10-Dec-2025 18:23:58 Publishing an artifact: Jalview getdown launcher error 10-Dec-2025 18:23:58 Unable to publish artifact [Jalview getdown launcher]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/getdown/files does not exist. simple 10-Dec-2025 18:23:58 The artifact hasn't been successfully published after 34.80 μs simple 10-Dec-2025 18:23:58 Publishing an artifact: getdown build for website simple 10-Dec-2025 18:23:58 Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 108.6 ms simple 10-Dec-2025 18:23:58 Publishing an artifact: getdown build for archive error 10-Dec-2025 18:23:58 Unable to publish artifact [getdown build for archive]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC656-JOB1/build/website/docroot/old does not exist. simple 10-Dec-2025 18:23:58 The artifact hasn't been successfully published after 118.6 μs simple 10-Dec-2025 18:23:58 Running post build plugin 'Artifactory Release Management Staging' simple 10-Dec-2025 18:23:58 Running post build plugin 'Artifactory Build Info Copier' simple 10-Dec-2025 18:23:58 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 10-Dec-2025 18:23:58 Running post build plugin 'npm Cache Cleanup' simple 10-Dec-2025 18:23:58 Running post build plugin 'Clover Results Collector' simple 10-Dec-2025 18:23:58 Running post build plugin 'Docker Container Cleanup' simple 10-Dec-2025 18:23:58 Finalising the build... simple 10-Dec-2025 18:23:58 Stopping timer. simple 10-Dec-2025 18:23:58 Build JB-GPC656-JOB1-2 completed. simple 10-Dec-2025 18:23:58 Running on server: post build plugin 'NCover Results Collector' simple 10-Dec-2025 18:23:58 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 10-Dec-2025 18:23:58 Running on server: post build plugin 'Clover Delta Calculator' simple 10-Dec-2025 18:23:58 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 10-Dec-2025 18:23:58 All post build plugins have finished simple 10-Dec-2025 18:23:58 Generating build results summary... simple 10-Dec-2025 18:23:58 Saving build results to disk... simple 10-Dec-2025 18:23:58 Logging substituted variables... simple 10-Dec-2025 18:23:58 Indexing build results... simple 10-Dec-2025 18:23:58 Finished building JB-GPC656-JOB1-2.