simple 04-Dec-2025 14:54:49 Build Jalview Builds - Getdown DEVELOP Channel - development-Release_2_12_Branch - Default Job #7 (JB-GDC330-JOB1-7) started building on agent Default Agent simple 04-Dec-2025 14:54:49 simple 04-Dec-2025 14:54:49 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 simple 04-Dec-2025 14:54:49 Executing build Jalview Builds - Getdown DEVELOP Channel - development-Release_2_12_Branch - Default Job #7 (JB-GDC330-JOB1-7) simple 04-Dec-2025 14:54:49 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 04-Dec-2025 14:54:49 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 simple 04-Dec-2025 14:54:49 Updating source code to revision: ef35c026c41b6d9fc6d3a1b11d89676881680686 simple 04-Dec-2025 14:54:49 Fetching 'refs/heads/development/Release_2_12_Branch' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 04-Dec-2025 14:54:49 Checking out revision ef35c026c41b6d9fc6d3a1b11d89676881680686. simple 04-Dec-2025 14:54:50 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 04-Dec-2025 14:54:50 7d35e28..ef35c02 development/Release_2_12_Branch -> origin/development/Release_2_12_Branch simple 04-Dec-2025 14:54:50 Already on 'development/Release_2_12_Branch' simple 04-Dec-2025 14:54:50 Your branch is behind 'origin/development/Release_2_12_Branch' by 1 commit, and can be fast-forwarded. simple 04-Dec-2025 14:54:50 (use "git pull" to update your local branch) simple 04-Dec-2025 14:54:50 HEAD is now at ef35c02 JAL-4107 fixing some broken @j2s code simple 04-Dec-2025 14:54:50 Updated source code to revision: ef35c026c41b6d9fc6d3a1b11d89676881680686 simple 04-Dec-2025 14:54:50 Finished task 'Checkout Default Repository' with result: Success simple 04-Dec-2025 14:54:50 Running pre-build action: VCS Version Collector simple 04-Dec-2025 14:54:50 Running pre-build action: Artifactory Release Staging command 04-Dec-2025 14:54:50 Substituting variable: ${bamboo.CHANNEL} with DEVELOP-2-12 command 04-Dec-2025 14:54:50 Substituting variable: ${bamboo.planKey} with JB-GDC330 simple 04-Dec-2025 14:54:50 Starting task 'Jalview ${bamboo.CHANNEL} distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 04-Dec-2025 14:54:50 Bamboo Artifactory Plugin version: 2.6.2 command 04-Dec-2025 14:54:50 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Channel - development-Release_2_12_Branch - Default Job #7 (JB-GDC330-JOB1-7)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=DEVELOP-2-12 -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDC330 clean getdown shadowJar\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_12_Branch\nbamboo_repository_46498612_git_branch=development/Release_2_12_Branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=development/Release_2_12_Branch\nbamboo_repository_revision_number=ef35c026c41b6d9fc6d3a1b11d89676881680686\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDC330-JOB1-7\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDC330-JOB1\nbamboo_repository_46498612_git_username=\nbamboo_shortPlanName=development-Release_2_12_Branch\nbamboo_repository_46498612_previous_revision_number=7d35e28797636155c3de86cbdb1030eaf9110ecc\nbamboo_repository_46498612_revision_number=ef35c026c41b6d9fc6d3a1b11d89676881680686\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=7\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-GDC330-JOB1-7\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Channel - development-Release_2_12_Branch\nbamboo_shortPlanKey=GDC330\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=ef35c026c41b6d9fc6d3a1b11d89676881680686\nbamboo_buildTimeStamp=2025-12-04T14:43:34.657Z\nbamboo_repository_previous_revision_number=7d35e28797636155c3de86cbdb1030eaf9110ecc\nbamboo_planRepository_previousRevision=7d35e28797636155c3de86cbdb1030eaf9110ecc\nbamboo_repository_git_branch=development/Release_2_12_Branch\nbamboo_buildResultKey=JB-GDC330-JOB1-7\nbamboo_repository_branch_name=development/Release_2_12_Branch\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Channel - development-Release_2_12_Branch - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=ef35c026c41b6d9fc6d3a1b11d89676881680686\nSHLVL=1\nbamboo_CHANNEL=DEVELOP-2-12\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_repository_46498612_name=Jalview Gitlab\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46498612_branch_name=development/Release_2_12_Branch\nbamboo_planRepository_branch=development/Release_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_1_previousRevision=7d35e28797636155c3de86cbdb1030eaf9110ecc\nbamboo_planRepository_branchDisplayName=development/Release_2_12_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=development/Release_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-46301203\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-GDC330-JOB1\nbamboo_planKey=JB-GDC330\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_repository_46498612_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_1_branchName=development/Release_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 04-Dec-2025 14:54:52 build 04-Dec-2025 14:54:52 > Configure project : build 04-Dec-2025 14:54:52 Using properties from file './utils/channels/develop-SUFFIX/channel_gradle.properties' build 04-Dec-2025 14:54:52 JALVIEW_VERSION is set to '2.12.0' build 04-Dec-2025 14:54:52 HEADLESS BUILD build 04-Dec-2025 14:54:52 J2S ENABLED build 04-Dec-2025 14:54:52 Using a DEVELOP-2-12 profile. build 04-Dec-2025 14:54:52 eclipseDir exists build 04-Dec-2025 14:54:53 build 04-Dec-2025 14:54:53 > Task :clean build 04-Dec-2025 14:54:53 > Task :cleanPackageDir build 04-Dec-2025 14:54:53 > Task :getdownImagesCopy build 04-Dec-2025 14:54:54 > Task :getdownImagesProcess build 04-Dec-2025 14:54:54 > Task :getdownImages build 04-Dec-2025 14:54:54 > Task :copyHelp build 04-Dec-2025 14:54:56 > Task :buildIndices build 04-Dec-2025 14:54:56 > Task :copyResources build 04-Dec-2025 14:54:56 > Task :copyChannelResources build 04-Dec-2025 14:54:56 build 04-Dec-2025 14:54:56 > Task :createBuildProperties build 04-Dec-2025 14:54:56 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 04-Dec-2025 14:54:56 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:54:56 build 04-Dec-2025 14:54:56 > Task :buildResources build 04-Dec-2025 14:54:56 > Task :copyDocs build 04-Dec-2025 14:54:56 build 04-Dec-2025 14:54:56 > Task :convertMdFiles build 04-Dec-2025 14:54:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 04-Dec-2025 14:54:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/doc_build/doc/releaseprocess.html build 04-Dec-2025 14:54:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 04-Dec-2025 14:54:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/doc_build/doc/JalviewJS-API.html build 04-Dec-2025 14:54:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/doc_build/doc/building.html build 04-Dec-2025 14:54:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/doc_build/doc/addingWebClient.html build 04-Dec-2025 14:54:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/doc_build/doc/jalview-projects.html build 04-Dec-2025 14:54:56 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html build 04-Dec-2025 14:54:57 build 04-Dec-2025 14:54:57 > Task :releasesTemplates build 04-Dec-2025 14:54:57 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 04-Dec-2025 14:54:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:54:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:54:57 Stripping rc/test/etc for 2_12_0-d2-12-20251204 build 04-Dec-2025 14:54:57 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/help/markdown/whatsnew/whatsnew-2_12_0.md build 04-Dec-2025 14:54:57 build 04-Dec-2025 14:54:57 > Task :prepare build 04-Dec-2025 14:54:59 build 04-Dec-2025 14:54:59 > Task :compileJava build 04-Dec-2025 14:54:59 Setting target compatibility to 11 error 04-Dec-2025 14:55:08 Note: Some input files use or override a deprecated API. error 04-Dec-2025 14:55:08 Note: Recompile with -Xlint:deprecation for details. error 04-Dec-2025 14:55:08 Note: Some input files use unchecked or unsafe operations. error 04-Dec-2025 14:55:08 Note: Recompile with -Xlint:unchecked for details. build 04-Dec-2025 14:55:09 build 04-Dec-2025 14:55:09 > Task :processResources build 04-Dec-2025 14:55:09 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 04-Dec-2025 14:55:09 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:55:09 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:55:09 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:55:09 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:55:09 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:55:09 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:55:09 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:55:09 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:55:09 build 04-Dec-2025 14:55:09 > Task :classes build 04-Dec-2025 14:55:10 build 04-Dec-2025 14:55:10 > Task :compileLinkCheck build 04-Dec-2025 14:55:10 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 04-Dec-2025 14:55:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:55:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:55:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/utils'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:55:13 build 04-Dec-2025 14:55:13 > Task :linkCheck build 04-Dec-2025 14:55:13 Checking help file links build 04-Dec-2025 14:57:18 build 04-Dec-2025 14:57:18 Results: build 04-Dec-2025 14:57:18 162 distinct help targets build 04-Dec-2025 14:57:18 162 help mappings build 04-Dec-2025 14:57:18 0 invalid targets build 04-Dec-2025 14:57:18 31 unused targets build 04-Dec-2025 14:57:18 uniprotfetcher: html/features/uniprotsequencefetcher.html build 04-Dec-2025 14:57:18 overviewprefs: html/features/preferences.html#overview build 04-Dec-2025 14:57:18 cdnafeatures: html/features/codingfeatures.html build 04-Dec-2025 14:57:18 startupprefs: html/features/preferences.html#startup build 04-Dec-2025 14:57:18 ensemblfetch: html/features/ensemblsequencefetcher.html build 04-Dec-2025 14:57:18 io.modellerpir: html/io/modellerpir.html build 04-Dec-2025 14:57:18 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 04-Dec-2025 14:57:18 pdbmcviewer: html/features/pdbviewer.html build 04-Dec-2025 14:57:18 groovy.colours: html/features/groovy.html#groovyColours build 04-Dec-2025 14:57:18 seqmappings: html/features/seqmappings.html build 04-Dec-2025 14:57:18 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 04-Dec-2025 14:57:18 splitframe.mirrorfonts: html/features/splitView.html#mirror build 04-Dec-2025 14:57:18 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 04-Dec-2025 14:57:18 search: html/features/search.html build 04-Dec-2025 14:57:18 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 04-Dec-2025 14:57:18 alformats: html/io/fileformats.html build 04-Dec-2025 14:57:18 strucprefs: html/features/preferences.html#structure build 04-Dec-2025 14:57:18 siftsmapping: html/features/siftsmapping.html build 04-Dec-2025 14:57:18 chimera.annotxfer: html/features/chimera.html#annotxfer build 04-Dec-2025 14:57:18 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 04-Dec-2025 14:57:18 newkeys: html/features/newkeystrokes.html build 04-Dec-2025 14:57:18 importvcf.attribs: html/features/importvcf.html#attribs build 04-Dec-2025 14:57:18 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 04-Dec-2025 14:57:18 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 04-Dec-2025 14:57:18 jalarchive: html/features/jalarchive.html build 04-Dec-2025 14:57:18 newsreader: html/webServices/newsreader.html build 04-Dec-2025 14:57:18 jalviewcltool: html/features/commandline.html#script build 04-Dec-2025 14:57:18 popMenuAddref: html/menus/popupMenu.html#addrefannot build 04-Dec-2025 14:57:18 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 04-Dec-2025 14:57:18 paematrixformat: html/io/paematrixformat.html build 04-Dec-2025 14:57:18 overview: html/features/overview.html build 04-Dec-2025 14:57:18 0 invalid map urls build 04-Dec-2025 14:57:18 0 invalid image attributes build 04-Dec-2025 14:57:18 520 internal href links (119 with anchors) build 04-Dec-2025 14:57:18 0 invalid internal href links build 04-Dec-2025 14:57:18 0 invalid internal anchor links build 04-Dec-2025 14:57:18 113 external href links build 04-Dec-2025 14:57:18 External links not verified as internet not available build 04-Dec-2025 14:57:18 *** Success *** build 04-Dec-2025 14:57:19 build 04-Dec-2025 14:57:19 > Task :jar build 04-Dec-2025 14:57:19 > Task :syncJars build 04-Dec-2025 14:57:19 > Task :makeDist build 04-Dec-2025 14:57:20 > Task :getdownWebsiteBuild build 04-Dec-2025 14:57:21 build 04-Dec-2025 14:57:21 > Task :getdownDigest build 04-Dec-2025 14:57:21 Generating digest file './build/website/docroot/getdown/develop-2-12/11/digest.txt'... build 04-Dec-2025 14:57:21 Generating digest file './build/website/docroot/getdown/develop-2-12/11/digest2.txt'... build 04-Dec-2025 14:57:21 build 04-Dec-2025 14:57:21 > Task :getdown build 04-Dec-2025 14:57:21 LIKELY RSYNC COMMAND: build 04-Dec-2025 14:57:21 mkdir -p '/Volumes/jalview/docroot/getdown/develop-2-12/11/' build 04-Dec-2025 14:57:21 rsync -avh --delete './build/website/docroot/getdown/develop-2-12/11/' '/Volumes/jalview/docroot/getdown/develop-2-12/11/' error 04-Dec-2025 14:57:21 2025/12/04 14:57:20:564 WARNING Starting without install4j classes error 04-Dec-2025 14:57:21 2025/12/04 14:57:21:268 WARNING Starting without install4j classes build 04-Dec-2025 14:57:30 build 04-Dec-2025 14:57:30 > Task :shadowJar build 04-Dec-2025 14:57:30 build 04-Dec-2025 14:57:30 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 04-Dec-2025 14:57:30 build 04-Dec-2025 14:57:30 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 04-Dec-2025 14:57:30 build 04-Dec-2025 14:57:30 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 04-Dec-2025 14:57:30 build 04-Dec-2025 14:57:30 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 04-Dec-2025 14:57:30 Please consult deprecation warnings for more details. build 04-Dec-2025 14:57:30 build 04-Dec-2025 14:57:30 BUILD SUCCESSFUL in 2m 40s build 04-Dec-2025 14:57:30 22 actionable tasks: 22 executed simple 04-Dec-2025 14:57:31 Finished task 'Jalview ${bamboo.CHANNEL} distribution for Java 11' with result: Success command 04-Dec-2025 14:57:31 Substituting variable: ${bamboo.CHANNEL} with DEVELOP-2-12 command 04-Dec-2025 14:57:31 Substituting variable: ${bamboo.planKey} with JB-GDC330 simple 04-Dec-2025 14:57:31 Starting task 'JalviewJS ${bamboo.CHANNEL} release' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 04-Dec-2025 14:57:31 Bamboo Artifactory Plugin version: 2.6.2 command 04-Dec-2025 14:57:31 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Channel - development-Release_2_12_Branch - Default Job #7 (JB-GDC330-JOB1-7)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=DEVELOP-2-12 -PJAVA_VERSION=11 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/latest -Pbamboo_planKey=JB-GDC330 --info eclipse jalviewjsCreateJ2sSettings jalviewjs\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_12_Branch\nbamboo_repository_46498612_git_branch=development/Release_2_12_Branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=development/Release_2_12_Branch\nbamboo_repository_revision_number=ef35c026c41b6d9fc6d3a1b11d89676881680686\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDC330-JOB1-7\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDC330-JOB1\nbamboo_repository_46498612_git_username=\nbamboo_shortPlanName=development-Release_2_12_Branch\nbamboo_repository_46498612_previous_revision_number=7d35e28797636155c3de86cbdb1030eaf9110ecc\nbamboo_repository_46498612_revision_number=ef35c026c41b6d9fc6d3a1b11d89676881680686\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=7\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-GDC330-JOB1-7\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Channel - development-Release_2_12_Branch\nbamboo_shortPlanKey=GDC330\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=ef35c026c41b6d9fc6d3a1b11d89676881680686\nbamboo_buildTimeStamp=2025-12-04T14:43:34.657Z\nbamboo_repository_previous_revision_number=7d35e28797636155c3de86cbdb1030eaf9110ecc\nbamboo_planRepository_previousRevision=7d35e28797636155c3de86cbdb1030eaf9110ecc\nbamboo_repository_git_branch=development/Release_2_12_Branch\nbamboo_buildResultKey=JB-GDC330-JOB1-7\nbamboo_repository_branch_name=development/Release_2_12_Branch\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Channel - development-Release_2_12_Branch - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=ef35c026c41b6d9fc6d3a1b11d89676881680686\nSHLVL=1\nbamboo_CHANNEL=DEVELOP-2-12\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=DEVELOP-2-12 -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDC330 clean getdown shadowJar\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_repository_46498612_name=Jalview Gitlab\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46498612_branch_name=development/Release_2_12_Branch\nbamboo_planRepository_branch=development/Release_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_1_previousRevision=7d35e28797636155c3de86cbdb1030eaf9110ecc\nbamboo_planRepository_branchDisplayName=development/Release_2_12_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=development/Release_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-46301203\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-GDC330-JOB1\nbamboo_planKey=JB-GDC330\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_repository_46498612_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_1_branchName=development/Release_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 04-Dec-2025 14:57:32 Initialized native services in: /srv/bamboo/home/bamboo/.gradle/native build 04-Dec-2025 14:57:32 Initialized jansi services in: /srv/bamboo/home/bamboo/.gradle/native build 04-Dec-2025 14:57:32 The client will now receive all logging from the daemon (pid: 25335). The daemon log file: /srv/bamboo/home/bamboo/.gradle/daemon/7.4.2/daemon-25335.out.log build 04-Dec-2025 14:57:32 Starting 3rd build in daemon [uptime: 14 mins 30.748 secs, performance: 100%, non-heap usage: 35% of 256 MiB] build 04-Dec-2025 14:57:32 Using 4 worker leases. build 04-Dec-2025 14:57:32 Watching the file system is configured to be enabled if available build 04-Dec-2025 14:57:32 File system watching is inactive build 04-Dec-2025 14:57:32 Starting Build build 04-Dec-2025 14:57:32 Settings evaluated using settings file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/settings.gradle'. build 04-Dec-2025 14:57:32 Projects loaded. Root project using build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build.gradle'. build 04-Dec-2025 14:57:32 Included projects: [root project 'jalview'] build 04-Dec-2025 14:57:32 build 04-Dec-2025 14:57:32 > Configure project : build 04-Dec-2025 14:57:32 Evaluating root project 'jalview' using build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build.gradle'. build 04-Dec-2025 14:57:32 Using properties from file './utils/channels/develop-SUFFIX/channel_gradle.properties' build 04-Dec-2025 14:57:32 JALVIEW_VERSION is set to '2.12.0' build 04-Dec-2025 14:57:32 HEADLESS BUILD build 04-Dec-2025 14:57:32 J2S ENABLED build 04-Dec-2025 14:57:32 Using a DEVELOP-2-12 profile. build 04-Dec-2025 14:57:32 file or directory '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/main/java', not found build 04-Dec-2025 14:57:32 eclipseDir exists build 04-Dec-2025 14:57:32 All projects evaluated. build 04-Dec-2025 14:57:32 Selected primary task 'eclipse' from project : build 04-Dec-2025 14:57:32 Selected primary task 'jalviewjsCreateJ2sSettings' from project : build 04-Dec-2025 14:57:32 Selected primary task 'jalviewjs' from project : build 04-Dec-2025 14:57:32 Tasks to be executed: [task ':eclipseClasspath', task ':eclipseJdt', task ':eclipseProject', task ':eclipse', task ':jalviewjsCreateJ2sSettings', task ':jalviewjsEclipsePaths', task ':jalviewjsEclipseCopyDropins', task ':jalviewjsSetEclipseWorkspace', task ':jalviewjsEclipseSetup', task ':jalviewjsEnableAltFileProperty', task ':eclipseSetup', task ':jalviewjsProjectImport', task ':jalviewjsTranspile', task ':jalviewjsCopyTransferSiteJs', task ':jalviewjsTransferUnzipLib', task ':jalviewjsTransferUnzipSwingJs', task ':jalviewjsTransferUnzipAllLibs', task ':jalviewjsSyncAllLibs', task ':copyResources', task ':createBuildProperties', task ':jalviewjsSyncBuildProperties', task ':jalviewjsBuildAllCores', task ':jalviewjsPublishCoreTemplates', task ':jalviewjsSyncCore', task ':copyChannelResources', task ':buildResources', task ':jalviewjsSyncResources', task ':jalviewjsSyncSiteResources', task ':jalviewjsPrepareSite', task ':jalviewjsBuildSite', task ':cleanJalviewjsChromiumUserDir', task ':jalviewjsChromiumProfile', task ':jalviewjsCopyStderrLaunchFile', task ':jalviewjsLaunchTest', task ':jalviewjs'] build 04-Dec-2025 14:57:32 Tasks that were excluded: [] build 04-Dec-2025 14:57:32 :eclipseClasspath (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:57:32 build 04-Dec-2025 14:57:32 > Task :eclipseClasspath build 04-Dec-2025 14:57:32 Caching disabled for task ':eclipseClasspath' because: build 04-Dec-2025 14:57:32 Build cache is disabled build 04-Dec-2025 14:57:32 Task ':eclipseClasspath' is not up-to-date because: build 04-Dec-2025 14:57:32 Task.upToDateWhen is false. build 04-Dec-2025 14:57:32 :eclipseClasspath (Thread[Execution worker for ':',5,main]) completed. Took 0.2 secs. build 04-Dec-2025 14:57:32 :eclipseJdt (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:57:32 build 04-Dec-2025 14:57:32 > Task :eclipseJdt build 04-Dec-2025 14:57:32 Caching disabled for task ':eclipseJdt' because: build 04-Dec-2025 14:57:32 Build cache is disabled build 04-Dec-2025 14:57:32 Task ':eclipseJdt' is not up-to-date because: build 04-Dec-2025 14:57:32 Task.upToDateWhen is false. build 04-Dec-2025 14:57:32 :eclipseJdt (Thread[Execution worker for ':',5,main]) completed. Took 0.035 secs. build 04-Dec-2025 14:57:32 :eclipseProject (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:57:32 build 04-Dec-2025 14:57:32 > Task :eclipseProject build 04-Dec-2025 14:57:32 Caching disabled for task ':eclipseProject' because: build 04-Dec-2025 14:57:32 Build cache is disabled build 04-Dec-2025 14:57:32 Task ':eclipseProject' is not up-to-date because: build 04-Dec-2025 14:57:32 Task.upToDateWhen is false. build 04-Dec-2025 14:57:32 :eclipseProject (Thread[Execution worker for ':',5,main]) completed. Took 0.008 secs. build 04-Dec-2025 14:57:32 :eclipse (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:57:32 build 04-Dec-2025 14:57:32 > Task :eclipse build 04-Dec-2025 14:57:32 Skipping task ':eclipse' as it has no actions. build 04-Dec-2025 14:57:32 :eclipse (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 04-Dec-2025 14:57:32 :jalviewjsCreateJ2sSettings (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:57:32 build 04-Dec-2025 14:57:32 > Task :jalviewjsCreateJ2sSettings build 04-Dec-2025 14:57:32 Caching disabled for task ':jalviewjsCreateJ2sSettings' because: build 04-Dec-2025 14:57:32 Build cache is disabled build 04-Dec-2025 14:57:32 Task ':jalviewjsCreateJ2sSettings' is not up-to-date because: build 04-Dec-2025 14:57:32 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/config/j2s has been removed. build 04-Dec-2025 14:57:32 Output property 'outputFile' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/config/j2s has been removed. build 04-Dec-2025 14:57:32 :jalviewjsCreateJ2sSettings (Thread[Execution worker for ':',5,main]) completed. Took 0.002 secs. build 04-Dec-2025 14:57:32 :jalviewjsEclipsePaths (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:57:32 build 04-Dec-2025 14:57:32 > Task :jalviewjsEclipsePaths build 04-Dec-2025 14:57:32 Caching disabled for task ':jalviewjsEclipsePaths' because: build 04-Dec-2025 14:57:32 Build cache is disabled build 04-Dec-2025 14:57:32 Task ':jalviewjsEclipsePaths' is not up-to-date because: build 04-Dec-2025 14:57:32 Task has not declared any outputs despite executing actions. build 04-Dec-2025 14:57:32 Running task jalviewjsEclipsePaths as IN_ECLIPSE=false build 04-Dec-2025 14:57:32 ECLIPSE VERSION=4.28.0 build 04-Dec-2025 14:57:32 :jalviewjsEclipsePaths (Thread[Execution worker for ':',5,main]) completed. Took 0.001 secs. build 04-Dec-2025 14:57:32 :jalviewjsEclipseCopyDropins (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:57:32 build 04-Dec-2025 14:57:32 > Task :jalviewjsEclipseCopyDropins build 04-Dec-2025 14:57:32 Caching disabled for task ':jalviewjsEclipseCopyDropins' because: build 04-Dec-2025 14:57:32 Build cache is disabled build 04-Dec-2025 14:57:32 Task ':jalviewjsEclipseCopyDropins' is not up-to-date because: build 04-Dec-2025 14:57:32 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/eclipse_dropins has been removed. build 04-Dec-2025 14:57:32 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/eclipse_dropins/com.seeq.eclipse.importprojects.jar has been removed. build 04-Dec-2025 14:57:32 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/eclipse_dropins/net.sf.j2s.core-j11.jar has been removed. build 04-Dec-2025 14:57:32 :jalviewjsEclipseCopyDropins (Thread[Execution worker for ':',5,main]) completed. Took 0.006 secs. build 04-Dec-2025 14:57:32 :jalviewjsSetEclipseWorkspace (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:57:32 build 04-Dec-2025 14:57:32 > Task :jalviewjsSetEclipseWorkspace build 04-Dec-2025 14:57:32 Caching disabled for task ':jalviewjsSetEclipseWorkspace' because: build 04-Dec-2025 14:57:32 Build cache is disabled build 04-Dec-2025 14:57:32 Task ':jalviewjsSetEclipseWorkspace' is not up-to-date because: build 04-Dec-2025 14:57:32 Task.upToDateWhen is false. build 04-Dec-2025 14:57:32 Running task jalviewjsSetEclipseWorkspace as IN_ECLIPSE=false build 04-Dec-2025 14:57:32 NEW ECLIPSE WORKSPACE: /tmp/groovy-generated-tmpdir-14800183293558786939 build 04-Dec-2025 14:57:32 :jalviewjsSetEclipseWorkspace (Thread[Execution worker for ':',5,main]) completed. Took 0.005 secs. build 04-Dec-2025 14:57:32 :jalviewjsEclipseSetup (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:57:32 build 04-Dec-2025 14:57:32 > Task :jalviewjsEclipseSetup build 04-Dec-2025 14:57:32 Skipping task ':jalviewjsEclipseSetup' as it has no actions. build 04-Dec-2025 14:57:32 :jalviewjsEclipseSetup (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 04-Dec-2025 14:57:32 :jalviewjsEnableAltFileProperty (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:57:32 build 04-Dec-2025 14:57:32 > Task :jalviewjsEnableAltFileProperty UP-TO-DATE build 04-Dec-2025 14:57:32 Caching disabled for task ':jalviewjsEnableAltFileProperty' because: build 04-Dec-2025 14:57:32 Build cache is disabled build 04-Dec-2025 14:57:32 Skipping task ':jalviewjsEnableAltFileProperty' as it is up-to-date. build 04-Dec-2025 14:57:32 :jalviewjsEnableAltFileProperty (Thread[Execution worker for ':',5,main]) completed. Took 0.004 secs. build 04-Dec-2025 14:57:32 :eclipseSetup (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:57:32 build 04-Dec-2025 14:57:32 > Task :eclipseSetup build 04-Dec-2025 14:57:32 Skipping task ':eclipseSetup' as it has no actions. build 04-Dec-2025 14:57:32 :eclipseSetup (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 04-Dec-2025 14:57:32 :jalviewjsProjectImport (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:57:34 build 04-Dec-2025 14:57:34 > Task :jalviewjsProjectImport build 04-Dec-2025 14:57:34 Caching disabled for task ':jalviewjsProjectImport' because: build 04-Dec-2025 14:57:34 Build cache is disabled build 04-Dec-2025 14:57:34 Task ':jalviewjsProjectImport' is not up-to-date because: build 04-Dec-2025 14:57:34 Task.upToDateWhen is false. build 04-Dec-2025 14:57:34 Running task jalviewjsProjectImport as IN_ECLIPSE=false build 04-Dec-2025 14:57:34 Starting process 'command '/home/bamboo/buildtools/eclipse/latest/eclipse/eclipse''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 Command: /home/bamboo/buildtools/eclipse/latest/eclipse/eclipse -nosplash --launcher.suppressErrors -application com.seeq.eclipse.importprojects.headlessimport -data /tmp/groovy-generated-tmpdir-14800183293558786939 -import /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 --launcher.appendVmargs -vmargs -Dorg.eclipse.equinox.p2.reconciler.dropins.directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/eclipse_dropins -Dnet.sf.j2s.core.headlessbuild=true -Dorg.jalview.jalviewjsj2sfilename=./build/jalviewjs/config/j2s build 04-Dec-2025 14:57:34 Successfully started process 'command '/home/bamboo/buildtools/eclipse/latest/eclipse/eclipse'' error 04-Dec-2025 14:57:35 SLF4J: No SLF4J providers were found. error 04-Dec-2025 14:57:35 SLF4J: Defaulting to no-operation (NOP) logger implementation error 04-Dec-2025 14:57:35 SLF4J: See https://www.slf4j.org/codes.html#noProviders for further details. build 04-Dec-2025 14:57:47 :jalviewjsProjectImport (Thread[Execution worker for ':',5,main]) completed. Took 14.376 secs. build 04-Dec-2025 14:57:47 :jalviewjsTranspile (Thread[Execution worker for ':',5,main]) started. error 04-Dec-2025 14:57:49 SLF4J: No SLF4J providers were found. error 04-Dec-2025 14:57:49 SLF4J: Defaulting to no-operation (NOP) logger implementation error 04-Dec-2025 14:57:49 SLF4J: See https://www.slf4j.org/codes.html#noProviders for further details. build 04-Dec-2025 14:57:49 build 04-Dec-2025 14:57:49 > Task :jalviewjsTranspile build 04-Dec-2025 14:57:49 Caching disabled for task ':jalviewjsTranspile' because: build 04-Dec-2025 14:57:49 Build cache is disabled build 04-Dec-2025 14:57:49 Task ':jalviewjsTranspile' is not up-to-date because: build 04-Dec-2025 14:57:49 Task.upToDateWhen is false. build 04-Dec-2025 14:57:49 Running task jalviewjsTranspile as IN_ECLIPSE=false build 04-Dec-2025 14:57:49 Starting process 'command '/home/bamboo/buildtools/eclipse/latest/eclipse/eclipse''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 Command: /home/bamboo/buildtools/eclipse/latest/eclipse/eclipse -nosplash --launcher.suppressErrors -application org.eclipse.jdt.apt.core.aptBuild -data /tmp/groovy-generated-tmpdir-14800183293558786939 -cleanBuild jalview --launcher.appendVmargs -vmargs -Dorg.eclipse.equinox.p2.reconciler.dropins.directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/eclipse_dropins -Dnet.sf.j2s.core.headlessbuild=true -Dorg.jalview.jalviewjsj2sfilename=./build/jalviewjs/config/j2s build 04-Dec-2025 14:57:49 Successfully started process 'command '/home/bamboo/buildtools/eclipse/latest/eclipse/eclipse'' build 04-Dec-2025 14:57:50 Invoking 'Java Builder' on '/jalview'. build 04-Dec-2025 14:57:50 net.sf.j2s.core.3.3.1/3.3.1-v1 started build 04-Dec-2025 14:57:50 J2S CompilationParticipant started build 04-Dec-2025 14:57:50 J2S isActive true /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 build 04-Dec-2025 14:57:50 J2S aboutToBuild jalview /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 build 04-Dec-2025 14:58:22 J2S cleanStarting /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 build 04-Dec-2025 14:58:22 Cleaning output folder for jalview build 04-Dec-2025 14:58:22 Build done build 04-Dec-2025 14:58:22 Invoking 'Gradle Project Builder' on '/jalview'. build 04-Dec-2025 14:58:22 Invoking 'Java Builder' on '/jalview'. build 04-Dec-2025 14:58:22 J2S aboutToBuild jalview /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 build 04-Dec-2025 14:58:22 Preparing to build jalview build 04-Dec-2025 14:58:22 Cleaning output folder for jalview build 04-Dec-2025 14:58:22 J2S cleanStarting /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 build 04-Dec-2025 14:58:22 Copying resources to the output folder build 04-Dec-2025 14:58:22 Analyzing sources build 04-Dec-2025 14:58:22 J2S buildStarting 1253 files, contexts.size() = 1, isBatch=true build 04-Dec-2025 14:58:22 Compiling jalview/src/com/github/reinert/jjschema build 04-Dec-2025 14:58:25 Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 1 warning) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 2 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 3 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 4 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 5 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 9 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 12 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 13 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 14 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 15 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 37 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 38 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 46 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 47 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 48 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 49 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 50 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 51 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 52 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 59 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 63 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 67 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 69 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 89 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 90 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 91 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 98 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 108 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 113 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 114 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 115 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 119 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:25 (Found 120 warnings) Compiling jalview/src/com/stevesoft/pat build 04-Dec-2025 14:58:26 (Found 120 warnings) Compiling jalview/src/com/stevesoft/pat/wrap build 04-Dec-2025 14:58:26 (Found 124 warnings) Compiling jalview/src/darrylbu/util build 04-Dec-2025 14:58:26 (Found 124 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2 build 04-Dec-2025 14:58:26 (Found 126 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2 build 04-Dec-2025 14:58:26 (Found 135 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2 build 04-Dec-2025 14:58:26 (Found 138 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2/port build 04-Dec-2025 14:58:26 (Found 138 warnings) Compiling jalview/src/ext/vamsas build 04-Dec-2025 14:58:26 (Found 145 warnings) Compiling jalview/src/ext/vamsas build 04-Dec-2025 14:58:26 (Found 152 warnings) Compiling jalview/src/ext/vamsas build 04-Dec-2025 14:58:26 (Found 190 warnings) Compiling jalview/src/ext/vamsas build 04-Dec-2025 14:58:26 (Found 197 warnings) Compiling jalview/src/ext/vamsas build 04-Dec-2025 14:58:26 (Found 253 warnings) Compiling jalview/src/ext/vamsas build 04-Dec-2025 14:58:26 (Found 285 warnings) Compiling jalview/src/ext/vamsas build 04-Dec-2025 14:58:26 (Found 292 warnings) Compiling jalview/src/ext/vamsas build 04-Dec-2025 14:58:26 (Found 360 warnings) Compiling jalview/src/ext/vamsas build 04-Dec-2025 14:58:26 (Found 363 warnings) Compiling jalview/src/ext/vamsas build 04-Dec-2025 14:58:26 (Found 366 warnings) Compiling jalview/src/ext/vamsas build 04-Dec-2025 14:58:26 (Found 367 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:26 (Found 372 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:26 (Found 375 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:27 (Found 383 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:27 (Found 388 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:27 (Found 423 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:27 (Found 432 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:27 (Found 433 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:27 (Found 434 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:27 (Found 435 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:27 (Found 436 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:27 (Found 437 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:28 (Found 438 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:28 (Found 439 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:28 (Found 446 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:28 (Found 455 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:28 (Found 459 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:28 (Found 463 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:28 (Found 466 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:28 (Found 501 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:28 (Found 567 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:28 (Found 568 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:28 (Found 574 warnings) Compiling jalview/src/jalview/analysis build 04-Dec-2025 14:58:28 (Found 574 warnings) Compiling jalview/src/jalview/analysis/scoremodels build 04-Dec-2025 14:58:28 (Found 584 warnings) Compiling jalview/src/jalview/analytics build 04-Dec-2025 14:58:28 (Found 584 warnings) Compiling jalview/src/jalview/api build 04-Dec-2025 14:58:28 (Found 585 warnings) Compiling jalview/src/jalview/api build 04-Dec-2025 14:58:28 (Found 587 warnings) Compiling jalview/src/jalview/api build 04-Dec-2025 14:58:28 (Found 587 warnings) Compiling jalview/src/jalview/api/analysis build 04-Dec-2025 14:58:28 (Found 588 warnings) Compiling jalview/src/jalview/api/structures build 04-Dec-2025 14:58:28 (Found 591 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 651 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 660 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 661 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 666 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 667 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 679 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 690 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 692 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 697 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 698 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 699 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 700 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 703 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 705 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 706 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 708 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 709 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 715 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 716 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 717 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 719 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 723 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 725 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 733 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 743 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 746 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 747 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 748 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 751 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 752 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 756 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 759 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 762 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 800 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 802 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 803 warnings) Compiling jalview/src/jalview/appletgui build 04-Dec-2025 14:58:28 (Found 1 error + 812 warnings) Compiling jalview/src/jalview/appletgui/js build 04-Dec-2025 14:58:28 (Found 1 error + 817 warnings) Compiling jalview/src/jalview/appletgui/js build 04-Dec-2025 14:58:28 (Found 1 error + 817 warnings) Compiling jalview/src/jalview/bin build 04-Dec-2025 14:58:29 (Found 1 error + 821 warnings) Compiling jalview/src/jalview/bin build 04-Dec-2025 14:58:29 (Found 1 error + 823 warnings) Compiling jalview/src/jalview/bin build 04-Dec-2025 14:58:29 (Found 1 error + 824 warnings) Compiling jalview/src/jalview/bin build 04-Dec-2025 14:58:29 (Found 1 error + 832 warnings) Compiling jalview/src/jalview/bin build 04-Dec-2025 14:58:29 (Found 1 error + 834 warnings) Compiling jalview/src/jalview/bin build 04-Dec-2025 14:58:29 (Found 1 error + 836 warnings) Compiling jalview/src/jalview/bin build 04-Dec-2025 14:58:29 (Found 4 errors + 894 warnings) Compiling jalview/src/jalview/bin build 04-Dec-2025 14:58:29 (Found 4 errors + 899 warnings) Compiling jalview/src/jalview/bin build 04-Dec-2025 14:58:29 (Found 4 errors + 901 warnings) Compiling jalview/src/jalview/bin build 04-Dec-2025 14:58:29 (Found 4 errors + 901 warnings) Compiling jalview/src/jalview/bin/argparser build 04-Dec-2025 14:58:29 (Found 4 errors + 902 warnings) Compiling jalview/src/jalview/bin/argparser build 04-Dec-2025 14:58:29 (Found 4 errors + 904 warnings) Compiling jalview/src/jalview/bin/argparser build 04-Dec-2025 14:58:29 (Found 4 errors + 905 warnings) Compiling jalview/src/jalview/bin/argparser build 04-Dec-2025 14:58:29 (Found 4 errors + 905 warnings) Compiling jalview/src/jalview/bin/groovy build 04-Dec-2025 14:58:29 (Found 4 errors + 905 warnings) Compiling jalview/src/jalview/commands build 04-Dec-2025 14:58:29 (Found 4 errors + 905 warnings) Compiling jalview/src/jalview/controller build 04-Dec-2025 14:58:29 (Found 4 errors + 905 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:29 (Found 4 errors + 918 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:29 (Found 4 errors + 919 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:29 (Found 4 errors + 920 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:29 (Found 4 errors + 923 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:29 (Found 4 errors + 924 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:29 (Found 4 errors + 925 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:29 (Found 4 errors + 931 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:29 (Found 4 errors + 935 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:29 (Found 4 errors + 937 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:29 (Found 4 errors + 938 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:29 (Found 4 errors + 939 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:29 (Found 4 errors + 940 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:29 (Found 4 errors + 945 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:30 (Found 4 errors + 946 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:30 (Found 4 errors + 954 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:30 (Found 4 errors + 955 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:30 (Found 4 errors + 956 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:30 (Found 4 errors + 959 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:30 (Found 4 errors + 964 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:30 (Found 4 errors + 968 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:31 (Found 4 errors + 972 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:31 (Found 4 errors + 974 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:31 (Found 4 errors + 975 warnings) Compiling jalview/src/jalview/datamodel build 04-Dec-2025 14:58:31 (Found 4 errors + 976 warnings) Compiling jalview/src/jalview/datamodel/annotations build 04-Dec-2025 14:58:31 (Found 4 errors + 976 warnings) Compiling jalview/src/jalview/datamodel/features build 04-Dec-2025 14:58:31 (Found 4 errors + 976 warnings) Compiling jalview/src/jalview/exceptions build 04-Dec-2025 14:58:31 (Found 4 errors + 976 warnings) Compiling jalview/src/jalview/ext/android build 04-Dec-2025 14:58:31 (Found 4 errors + 976 warnings) Compiling jalview/src/jalview/ext/ensembl build 04-Dec-2025 14:58:31 (Found 4 errors + 978 warnings) Compiling jalview/src/jalview/ext/ensembl build 04-Dec-2025 14:58:31 (Found 4 errors + 979 warnings) Compiling jalview/src/jalview/ext/ensembl build 04-Dec-2025 14:58:31 (Found 4 errors + 982 warnings) Compiling jalview/src/jalview/ext/htsjdk build 04-Dec-2025 14:58:31 (Found 4 errors + 983 warnings) Compiling jalview/src/jalview/ext/htsjdk build 04-Dec-2025 14:58:31 (Found 4 errors + 989 warnings) Compiling jalview/src/jalview/ext/jmol build 04-Dec-2025 14:58:31 (Found 4 errors + 993 warnings) Compiling jalview/src/jalview/ext/paradise build 04-Dec-2025 14:58:31 (Found 4 errors + 993 warnings) Compiling jalview/src/jalview/ext/pymol build 04-Dec-2025 14:58:31 (Found 4 errors + 995 warnings) Compiling jalview/src/jalview/ext/pymol build 04-Dec-2025 14:58:31 (Found 4 errors + 995 warnings) Compiling jalview/src/jalview/ext/rbvi/chimera build 04-Dec-2025 14:58:31 (Found 4 errors + 996 warnings) Compiling jalview/src/jalview/ext/rbvi/chimera build 04-Dec-2025 14:58:31 (Found 4 errors + 997 warnings) Compiling jalview/src/jalview/ext/rbvi/chimera build 04-Dec-2025 14:58:31 (Found 4 errors + 997 warnings) Compiling jalview/src/jalview/ext/so build 04-Dec-2025 14:58:31 (Found 4 errors + 997 warnings) Compiling jalview/src/jalview/ext/varna build 04-Dec-2025 14:58:31 (Found 4 errors + 997 warnings) Compiling jalview/src/jalview/fts/api build 04-Dec-2025 14:58:31 (Found 4 errors + 998 warnings) Compiling jalview/src/jalview/fts/api build 04-Dec-2025 14:58:31 (Found 4 errors + 999 warnings) Compiling jalview/src/jalview/fts/core build 04-Dec-2025 14:58:31 (Found 4 errors + 1002 warnings) Compiling jalview/src/jalview/fts/core build 04-Dec-2025 14:58:31 (Found 4 errors + 1003 warnings) Compiling jalview/src/jalview/fts/core build 04-Dec-2025 14:58:31 (Found 4 errors + 1004 warnings) Compiling jalview/src/jalview/fts/core build 04-Dec-2025 14:58:31 (Found 4 errors + 1004 warnings) Compiling jalview/src/jalview/fts/service/alphafold build 04-Dec-2025 14:58:31 (Found 4 errors + 1004 warnings) Compiling jalview/src/jalview/fts/service/pdb build 04-Dec-2025 14:58:31 (Found 4 errors + 1012 warnings) Compiling jalview/src/jalview/fts/service/pdb build 04-Dec-2025 14:58:31 (Found 4 errors + 1012 warnings) Compiling jalview/src/jalview/fts/service/threedbeacons build 04-Dec-2025 14:58:31 (Found 4 errors + 1014 warnings) Compiling jalview/src/jalview/fts/service/threedbeacons build 04-Dec-2025 14:58:31 (Found 4 errors + 1018 warnings) Compiling jalview/src/jalview/fts/service/threedbeacons build 04-Dec-2025 14:58:31 (Found 4 errors + 1023 warnings) Compiling jalview/src/jalview/fts/service/uniprot build 04-Dec-2025 14:58:31 (Found 4 errors + 1023 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1024 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1031 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1047 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1049 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1050 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1051 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1052 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1072 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1079 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1082 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1083 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1084 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1093 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1123 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1125 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1126 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1127 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1132 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1135 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:31 (Found 4 errors + 1136 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1143 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1144 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1148 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1153 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1154 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1156 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1157 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1158 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1160 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1161 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1167 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1168 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1169 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1170 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1171 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1173 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1174 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1176 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1178 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1183 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1186 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1194 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1197 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1199 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1200 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1201 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1204 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1208 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1216 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1225 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1229 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1230 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1232 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1234 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1235 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1238 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1239 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1247 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1251 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1253 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1254 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1314 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1324 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1325 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1354 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1357 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1364 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1370 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1384 warnings) Compiling jalview/src/jalview/gui build 04-Dec-2025 14:58:32 (Found 4 errors + 1386 warnings) Compiling jalview/src/jalview/gui/structurechooser build 04-Dec-2025 14:58:32 (Found 4 errors + 1388 warnings) Compiling jalview/src/jalview/gui/structurechooser build 04-Dec-2025 14:58:33 (Found 4 errors + 1393 warnings) Compiling jalview/src/jalview/gui/structurechooser build 04-Dec-2025 14:58:33 (Found 4 errors + 1395 warnings) Compiling jalview/src/jalview/hmmer build 04-Dec-2025 14:58:33 (Found 4 errors + 1398 warnings) Compiling jalview/src/jalview/hmmer build 04-Dec-2025 14:58:33 (Found 4 errors + 1405 warnings) Compiling jalview/src/jalview/hmmer build 04-Dec-2025 14:58:33 (Found 4 errors + 1406 warnings) Compiling jalview/src/jalview/hmmer build 04-Dec-2025 14:58:33 (Found 4 errors + 1408 warnings) Compiling jalview/src/jalview/hmmer build 04-Dec-2025 14:58:33 (Found 4 errors + 1410 warnings) Compiling jalview/src/jalview/hmmer build 04-Dec-2025 14:58:33 (Found 4 errors + 1414 warnings) Compiling jalview/src/jalview/hmmer build 04-Dec-2025 14:58:33 (Found 4 errors + 1414 warnings) Compiling jalview/src/jalview/httpserver build 04-Dec-2025 14:58:33 (Found 4 errors + 1414 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:33 (Found 4 errors + 1419 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1421 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1442 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1444 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1446 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1447 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1451 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1454 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1455 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1456 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1459 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1460 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1461 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1499 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1502 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1504 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1524 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1555 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1557 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1559 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1560 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1561 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1574 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1634 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1635 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1636 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1729 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1734 warnings) Compiling jalview/src/jalview/io build 04-Dec-2025 14:58:34 (Found 4 errors + 1734 warnings) Compiling jalview/src/jalview/io/cache build 04-Dec-2025 14:58:34 (Found 4 errors + 1735 warnings) Compiling jalview/src/jalview/io/exceptions build 04-Dec-2025 14:58:34 (Found 4 errors + 1735 warnings) Compiling jalview/src/jalview/io/gff build 04-Dec-2025 14:58:34 (Found 4 errors + 1736 warnings) Compiling jalview/src/jalview/io/gff build 04-Dec-2025 14:58:34 (Found 4 errors + 1736 warnings) Compiling jalview/src/jalview/io/packed build 04-Dec-2025 14:58:34 (Found 4 errors + 1740 warnings) Compiling jalview/src/jalview/io/packed build 04-Dec-2025 14:58:34 (Found 4 errors + 1741 warnings) Compiling jalview/src/jalview/io/packed build 04-Dec-2025 14:58:34 (Found 4 errors + 1741 warnings) Compiling jalview/src/jalview/io/vamsas build 04-Dec-2025 14:58:34 (Found 4 errors + 1759 warnings) Compiling jalview/src/jalview/io/vamsas build 04-Dec-2025 14:58:34 (Found 4 errors + 1770 warnings) Compiling jalview/src/jalview/io/vamsas build 04-Dec-2025 14:58:34 (Found 4 errors + 1771 warnings) Compiling jalview/src/jalview/io/vamsas build 04-Dec-2025 14:58:34 (Found 4 errors + 1784 warnings) Compiling jalview/src/jalview/io/vamsas build 04-Dec-2025 14:58:34 (Found 4 errors + 1788 warnings) Compiling jalview/src/jalview/io/vamsas build 04-Dec-2025 14:58:34 (Found 4 errors + 1792 warnings) Compiling jalview/src/jalview/io/vamsas build 04-Dec-2025 14:58:34 (Found 4 errors + 1817 warnings) Compiling jalview/src/jalview/io/vamsas build 04-Dec-2025 14:58:34 (Found 4 errors + 1820 warnings) Compiling jalview/src/jalview/io/vcf build 04-Dec-2025 14:58:34 (Found 4 errors + 1821 warnings) Compiling jalview/src/jalview/javascript/json build 04-Dec-2025 14:58:34 (Found 4 errors + 1821 warnings) Compiling jalview/src/jalview/javascript/web build 04-Dec-2025 14:58:34 (Found 4 errors + 1822 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1823 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1824 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1825 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1826 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1829 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1830 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1831 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1832 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1833 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1836 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1838 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1846 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1847 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1848 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1853 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1855 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1856 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1857 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1860 warnings) Compiling jalview/src/jalview/jbgui build 04-Dec-2025 14:58:34 (Found 4 errors + 1860 warnings) Compiling jalview/src/jalview/json/binding/biojs build 04-Dec-2025 14:58:34 (Found 4 errors + 1860 warnings) Compiling jalview/src/jalview/json/binding/biojson/v1 build 04-Dec-2025 14:58:34 (Found 4 errors + 1863 warnings) Compiling jalview/src/jalview/log build 04-Dec-2025 14:58:34 (Found 4 errors + 1865 warnings) Compiling jalview/src/jalview/log build 04-Dec-2025 14:58:34 (Found 4 errors + 1866 warnings) Compiling jalview/src/jalview/log build 04-Dec-2025 14:58:34 (Found 4 errors + 1866 warnings) Compiling jalview/src/jalview/math build 04-Dec-2025 14:58:34 (Found 4 errors + 1867 warnings) Compiling jalview/src/jalview/math build 04-Dec-2025 14:58:34 (Found 4 errors + 1868 warnings) Compiling jalview/src/jalview/math build 04-Dec-2025 14:58:34 (Found 4 errors + 1901 warnings) Compiling jalview/src/jalview/project build 04-Dec-2025 14:58:34 (Found 4 errors + 1903 warnings) Compiling jalview/src/jalview/renderer build 04-Dec-2025 14:58:34 (Found 4 errors + 1904 warnings) Compiling jalview/src/jalview/renderer build 04-Dec-2025 14:58:34 (Found 4 errors + 1904 warnings) Compiling jalview/src/jalview/renderer/api build 04-Dec-2025 14:58:34 (Found 4 errors + 1904 warnings) Compiling jalview/src/jalview/renderer/seqfeatures build 04-Dec-2025 14:58:34 (Found 4 errors + 1904 warnings) Compiling jalview/src/jalview/rest build 04-Dec-2025 14:58:34 (Found 4 errors + 1904 warnings) Compiling jalview/src/jalview/schemes build 04-Dec-2025 14:58:34 (Found 4 errors + 1907 warnings) Compiling jalview/src/jalview/schemes build 04-Dec-2025 14:58:34 (Found 4 errors + 1909 warnings) Compiling jalview/src/jalview/schemes build 04-Dec-2025 14:58:34 (Found 4 errors + 1909 warnings) Compiling jalview/src/jalview/structure build 04-Dec-2025 14:58:34 (Found 4 errors + 1910 warnings) Compiling jalview/src/jalview/structure build 04-Dec-2025 14:58:34 (Found 4 errors + 1911 warnings) Compiling jalview/src/jalview/structure build 04-Dec-2025 14:58:34 (Found 4 errors + 1917 warnings) Compiling jalview/src/jalview/structure build 04-Dec-2025 14:58:34 (Found 4 errors + 1919 warnings) Compiling jalview/src/jalview/structure build 04-Dec-2025 14:58:34 (Found 4 errors + 1920 warnings) Compiling jalview/src/jalview/structures/models build 04-Dec-2025 14:58:34 (Found 4 errors + 1920 warnings) Compiling jalview/src/jalview/urls build 04-Dec-2025 14:58:34 (Found 4 errors + 1921 warnings) Compiling jalview/src/jalview/urls build 04-Dec-2025 14:58:34 (Found 4 errors + 1921 warnings) Compiling jalview/src/jalview/urls/api build 04-Dec-2025 14:58:34 (Found 4 errors + 1921 warnings) Compiling jalview/src/jalview/urls/applet build 04-Dec-2025 14:58:34 (Found 4 errors + 1921 warnings) Compiling jalview/src/jalview/urls/desktop build 04-Dec-2025 14:58:34 (Found 4 errors + 1921 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1922 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1923 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1928 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1934 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1935 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1947 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1952 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1954 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1957 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1962 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1965 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1966 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1968 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1970 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1974 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 1978 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 2002 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 2003 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 2003 warnings) Compiling jalview/src/jalview/util/dialogrunner build 04-Dec-2025 14:58:34 (Found 4 errors + 2003 warnings) Compiling jalview/src/jalview/util/imagemaker build 04-Dec-2025 14:58:34 (Found 4 errors + 2003 warnings) Compiling jalview/src/jalview/util build 04-Dec-2025 14:58:34 (Found 4 errors + 2003 warnings) Compiling jalview/src/jalview/util/matcher build 04-Dec-2025 14:58:34 (Found 4 errors + 2015 warnings) Compiling jalview/src/jalview/viewmodel build 04-Dec-2025 14:58:35 (Found 4 errors + 2022 warnings) Compiling jalview/src/jalview/viewmodel build 04-Dec-2025 14:58:35 (Found 4 errors + 2022 warnings) Compiling jalview/src/jalview/viewmodel/annotationfilter build 04-Dec-2025 14:58:35 (Found 4 errors + 2023 warnings) Compiling jalview/src/jalview/viewmodel/seqfeatures build 04-Dec-2025 14:58:35 (Found 4 errors + 2023 warnings) Compiling jalview/src/jalview/viewmodel/styles build 04-Dec-2025 14:58:35 (Found 4 errors + 2029 warnings) Compiling jalview/src/jalview/workers build 04-Dec-2025 14:58:35 (Found 4 errors + 2031 warnings) Compiling jalview/src/jalview/workers build 04-Dec-2025 14:58:35 (Found 4 errors + 2035 warnings) Compiling jalview/src/jalview/workers build 04-Dec-2025 14:58:35 (Found 4 errors + 2035 warnings) Compiling jalview/src/jalview/ws build 04-Dec-2025 14:58:35 (Found 4 errors + 2038 warnings) Compiling jalview/src/jalview/ws build 04-Dec-2025 14:58:35 (Found 4 errors + 2090 warnings) Compiling jalview/src/jalview/ws build 04-Dec-2025 14:58:35 (Found 4 errors + 2092 warnings) Compiling jalview/src/jalview/ws build 04-Dec-2025 14:58:35 (Found 4 errors + 2097 warnings) Compiling jalview/src/jalview/ws build 04-Dec-2025 14:58:35 (Found 4 errors + 2097 warnings) Compiling jalview/src/jalview/ws/api build 04-Dec-2025 14:58:35 (Found 4 errors + 2098 warnings) Compiling jalview/src/jalview/ws/api build 04-Dec-2025 14:58:35 (Found 4 errors + 2098 warnings) Compiling jalview/src/jalview/ws/datamodel build 04-Dec-2025 14:58:35 (Found 4 errors + 2101 warnings) Compiling jalview/src/jalview/ws/datamodel/alphafold build 04-Dec-2025 14:58:35 (Found 4 errors + 2106 warnings) Compiling jalview/src/jalview/ws/datamodel/alphafold build 04-Dec-2025 14:58:35 (Found 4 errors + 2109 warnings) Compiling jalview/src/jalview/ws/dbsources build 04-Dec-2025 14:58:35 (Found 4 errors + 2110 warnings) Compiling jalview/src/jalview/ws/dbsources build 04-Dec-2025 14:58:35 (Found 4 errors + 2113 warnings) Compiling jalview/src/jalview/ws/dbsources build 04-Dec-2025 14:58:35 (Found 4 errors + 2114 warnings) Compiling jalview/src/jalview/ws/dbsources build 04-Dec-2025 14:58:35 (Found 4 errors + 2114 warnings) Compiling jalview/src/jalview/ws/ebi build 04-Dec-2025 14:58:35 (Found 4 errors + 2127 warnings) Compiling jalview/src/jalview/ws/ebi build 04-Dec-2025 14:58:35 (Found 4 errors + 2137 warnings) Compiling jalview/src/jalview/ws/ebi build 04-Dec-2025 14:58:35 (Found 4 errors + 2137 warnings) Compiling jalview/src/jalview/ws/gui build 04-Dec-2025 14:58:35 (Found 4 errors + 2141 warnings) Compiling jalview/src/jalview/ws/gui build 04-Dec-2025 14:58:35 (Found 4 errors + 2144 warnings) Compiling jalview/src/jalview/ws/gui build 04-Dec-2025 14:58:35 (Found 4 errors + 2144 warnings) Compiling jalview/src/jalview/ws/io/mime build 04-Dec-2025 14:58:35 (Found 4 errors + 2144 warnings) Compiling jalview/src/jalview/ws/jws1 build 04-Dec-2025 14:58:35 (Found 4 errors + 2145 warnings) Compiling jalview/src/jalview/ws/jws1 build 04-Dec-2025 14:58:35 (Found 4 errors + 2146 warnings) Compiling jalview/src/jalview/ws/jws1 build 04-Dec-2025 14:58:35 (Found 4 errors + 2153 warnings) Compiling jalview/src/jalview/ws/jws1 build 04-Dec-2025 14:58:35 (Found 4 errors + 2163 warnings) Compiling jalview/src/jalview/ws/jws1 build 04-Dec-2025 14:58:35 (Found 4 errors + 2177 warnings) Compiling jalview/src/jalview/ws/jws1 build 04-Dec-2025 14:58:35 (Found 4 errors + 2180 warnings) Compiling jalview/src/jalview/ws/jws1 build 04-Dec-2025 14:58:35 (Found 4 errors + 2180 warnings) Compiling jalview/src/jalview/ws/jws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2187 warnings) Compiling jalview/src/jalview/ws/jws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2201 warnings) Compiling jalview/src/jalview/ws/jws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2205 warnings) Compiling jalview/src/jalview/ws/jws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2227 warnings) Compiling jalview/src/jalview/ws/jws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2231 warnings) Compiling jalview/src/jalview/ws/jws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2235 warnings) Compiling jalview/src/jalview/ws/jws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2251 warnings) Compiling jalview/src/jalview/ws/jws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2252 warnings) Compiling jalview/src/jalview/ws/jws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2274 warnings) Compiling jalview/src/jalview/ws/jws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2280 warnings) Compiling jalview/src/jalview/ws/jws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2283 warnings) Compiling jalview/src/jalview/ws/jws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2286 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 04-Dec-2025 14:58:35 (Found 4 errors + 2290 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 04-Dec-2025 14:58:35 (Found 4 errors + 2293 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 04-Dec-2025 14:58:35 (Found 4 errors + 2304 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 04-Dec-2025 14:58:35 (Found 4 errors + 2304 warnings) Compiling jalview/src/jalview/ws/jws2/jabaws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2307 warnings) Compiling jalview/src/jalview/ws/jws2/jabaws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2314 warnings) Compiling jalview/src/jalview/ws/jws2/jabaws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2319 warnings) Compiling jalview/src/jalview/ws/jws2/jabaws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2325 warnings) Compiling jalview/src/jalview/ws/jws2/jabaws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2333 warnings) Compiling jalview/src/jalview/ws/jws2/jabaws2 build 04-Dec-2025 14:58:35 (Found 4 errors + 2333 warnings) Compiling jalview/src/jalview/ws/params build 04-Dec-2025 14:58:35 (Found 4 errors + 2334 warnings) Compiling jalview/src/jalview/ws/params build 04-Dec-2025 14:58:35 (Found 4 errors + 2334 warnings) Compiling jalview/src/jalview/ws/params/simple build 04-Dec-2025 14:58:35 (Found 4 errors + 2334 warnings) Compiling jalview/src/jalview/ws/rest build 04-Dec-2025 14:58:35 (Found 4 errors + 2338 warnings) Compiling jalview/src/jalview/ws/rest build 04-Dec-2025 14:58:35 (Found 4 errors + 2344 warnings) Compiling jalview/src/jalview/ws/rest build 04-Dec-2025 14:58:35 (Found 4 errors + 2345 warnings) Compiling jalview/src/jalview/ws/rest build 04-Dec-2025 14:58:35 (Found 4 errors + 2350 warnings) Compiling jalview/src/jalview/ws/rest build 04-Dec-2025 14:58:35 (Found 4 errors + 2367 warnings) Compiling jalview/src/jalview/ws/rest build 04-Dec-2025 14:58:35 (Found 4 errors + 2373 warnings) Compiling jalview/src/jalview/ws/rest build 04-Dec-2025 14:58:35 (Found 4 errors + 2374 warnings) Compiling jalview/src/jalview/ws/rest/clientdefs build 04-Dec-2025 14:58:35 (Found 4 errors + 2376 warnings) Compiling jalview/src/jalview/ws/rest/params build 04-Dec-2025 14:58:35 (Found 4 errors + 2378 warnings) Compiling jalview/src/jalview/ws/rest/params build 04-Dec-2025 14:58:35 (Found 4 errors + 2379 warnings) Compiling jalview/src/jalview/ws/rest/params build 04-Dec-2025 14:58:35 (Found 4 errors + 2380 warnings) Compiling jalview/src/jalview/ws/rest/params build 04-Dec-2025 14:58:35 (Found 4 errors + 2381 warnings) Compiling jalview/src/jalview/ws/rest/params build 04-Dec-2025 14:58:35 (Found 4 errors + 2382 warnings) Compiling jalview/src/jalview/ws/rest/params build 04-Dec-2025 14:58:35 (Found 4 errors + 2385 warnings) Compiling jalview/src/jalview/ws/seqfetcher build 04-Dec-2025 14:58:35 (Found 4 errors + 2385 warnings) Compiling jalview/src/jalview/ws/sifts build 04-Dec-2025 14:58:35 (Found 4 errors + 2394 warnings) Compiling jalview/src/jalview/ws/sifts build 04-Dec-2025 14:58:35 (Found 4 errors + 2394 warnings) Compiling jalview/src/jalview/ws/slivkaws build 04-Dec-2025 14:58:35 (Found 4 errors + 2395 warnings) Compiling jalview/src/jalview/ws/slivkaws build 04-Dec-2025 14:58:35 (Found 4 errors + 2396 warnings) Compiling jalview/src/jalview/ws/slivkaws build 04-Dec-2025 14:58:35 (Found 4 errors + 2397 warnings) Compiling jalview/src/jalview/ws/slivkaws build 04-Dec-2025 14:58:35 (Found 4 errors + 2400 warnings) Compiling jalview/src/jalview/ws/uimodel build 04-Dec-2025 14:58:35 (Found 4 errors + 2400 warnings) Compiling jalview/src/jalview/ws/utils build 04-Dec-2025 14:58:35 (Found 4 errors + 2407 warnings) Compiling jalview/src/jalview/ws2/actions build 04-Dec-2025 14:58:35 (Found 4 errors + 2408 warnings) Compiling jalview/src/jalview/ws2/actions build 04-Dec-2025 14:58:35 (Found 4 errors + 2409 warnings) Compiling jalview/src/jalview/ws2/actions build 04-Dec-2025 14:58:35 (Found 4 errors + 2410 warnings) Compiling jalview/src/jalview/ws2/actions build 04-Dec-2025 14:58:35 (Found 4 errors + 2415 warnings) Compiling jalview/src/jalview/ws2/actions/alignment build 04-Dec-2025 14:58:35 (Found 4 errors + 2416 warnings) Compiling jalview/src/jalview/ws2/actions/alignment build 04-Dec-2025 14:58:35 (Found 4 errors + 2417 warnings) Compiling jalview/src/jalview/ws2/actions/alignment build 04-Dec-2025 14:58:35 (Found 4 errors + 2418 warnings) Compiling jalview/src/jalview/ws2/actions/annotation build 04-Dec-2025 14:58:35 (Found 4 errors + 2421 warnings) Compiling jalview/src/jalview/ws2/actions/annotation build 04-Dec-2025 14:58:35 (Found 4 errors + 2423 warnings) Compiling jalview/src/jalview/ws2/actions/api build 04-Dec-2025 14:58:35 (Found 4 errors + 2424 warnings) Compiling jalview/src/jalview/ws2/actions/api build 04-Dec-2025 14:58:35 (Found 4 errors + 2425 warnings) Compiling jalview/src/jalview/ws2/actions/api build 04-Dec-2025 14:58:35 (Found 4 errors + 2428 warnings) Compiling jalview/src/jalview/ws2/actions/hmmer build 04-Dec-2025 14:58:35 (Found 4 errors + 2430 warnings) Compiling jalview/src/jalview/ws2/actions/secstructpred build 04-Dec-2025 14:58:35 (Found 4 errors + 2433 warnings) Compiling jalview/src/jalview/ws2/actions/secstructpred build 04-Dec-2025 14:58:35 (Found 4 errors + 2433 warnings) Compiling jalview/src/jalview/ws2/api build 04-Dec-2025 14:58:35 (Found 4 errors + 2433 warnings) Compiling jalview/src/jalview/ws2/client/api build 04-Dec-2025 14:58:35 (Found 4 errors + 2435 warnings) Compiling jalview/src/jalview/ws2/client/ebi build 04-Dec-2025 14:58:35 (Found 4 errors + 2437 warnings) Compiling jalview/src/jalview/ws2/client/ebi build 04-Dec-2025 14:58:35 (Found 4 errors + 2438 warnings) Compiling jalview/src/jalview/ws2/client/jpred4 build 04-Dec-2025 14:58:35 (Found 4 errors + 2440 warnings) Compiling jalview/src/jalview/ws2/client/jpred4 build 04-Dec-2025 14:58:35 (Found 4 errors + 2443 warnings) Compiling jalview/src/jalview/ws2/client/slivka build 04-Dec-2025 14:58:35 (Found 4 errors + 2445 warnings) Compiling jalview/src/jalview/ws2/client/slivka build 04-Dec-2025 14:58:35 (Found 4 errors + 2446 warnings) Compiling jalview/src/jalview/ws2/client/slivka build 04-Dec-2025 14:58:35 (Found 4 errors + 2454 warnings) Compiling jalview/src/jalview/ws2/gui build 04-Dec-2025 14:58:35 (Found 4 errors + 2458 warnings) Compiling jalview/src/jalview/ws2/gui build 04-Dec-2025 14:58:35 (Found 4 errors + 2461 warnings) Compiling jalview/src/jalview/ws2/gui build 04-Dec-2025 14:58:35 (Found 4 errors + 2461 warnings) Compiling jalview/src/jalview/ws2/helpers build 04-Dec-2025 14:58:35 (Found 4 errors + 2462 warnings) Compiling jalview/src/jalview/ws2/helpers build 04-Dec-2025 14:58:35 (Found 4 errors + 2462 warnings) Compiling jalview/src/jalview/ws2/params build 04-Dec-2025 14:58:36 (Found 4 errors + 2463 warnings) Compiling jalview/src/jalview/ws2/params build 04-Dec-2025 14:58:36 (Found 4 errors + 2463 warnings) Compiling jalview/src/jalview/xml/binding/embl build 04-Dec-2025 14:58:36 (Found 4 errors + 2463 warnings) Compiling jalview/src/jalview/xml/binding/jalview build 04-Dec-2025 14:58:36 (Found 4 errors + 2463 warnings) Compiling jalview/src/jalview/xml/binding/sifts build 04-Dec-2025 14:58:36 (Found 4 errors + 2463 warnings) Compiling jalview/src/jalview/xml/binding/uniprot build 04-Dec-2025 14:58:36 (Found 4 errors + 2464 warnings) Compiling jalview/src/javajs/async build 04-Dec-2025 14:58:36 (Found 4 errors + 2465 warnings) Compiling jalview/src/javajs/async build 04-Dec-2025 14:58:36 (Found 4 errors + 2467 warnings) Compiling jalview/src/javajs/async build 04-Dec-2025 14:58:36 (Found 4 errors + 2474 warnings) Compiling jalview/src/mc_view build 04-Dec-2025 14:58:36 (Found 4 errors + 2475 warnings) Compiling jalview/src/mc_view build 04-Dec-2025 14:58:36 (Found 4 errors + 2480 warnings) Compiling jalview/src/mc_view build 04-Dec-2025 14:58:36 (Found 4 errors + 2487 warnings) Compiling jalview/src/mc_view build 04-Dec-2025 14:58:36 (Found 4 errors + 2490 warnings) Compiling jalview/src/mc_view build 04-Dec-2025 14:58:36 (Found 4 errors + 2491 warnings) Compiling jalview/src/mc_view build 04-Dec-2025 14:58:36 (Found 4 errors + 2491 warnings) Compiling jalview/src/net/meyfa/sha256 build 04-Dec-2025 14:58:36 (Found 4 errors + 2491 warnings) Compiling jalview/src/org/jibble/epsgraphics build 04-Dec-2025 14:58:36 (Found 4 errors + 2492 warnings) Compiling jalview/src/org/jibble/epsgraphics build 04-Dec-2025 14:58:36 (Found 4 errors + 2498 warnings) Compiling jalview/src/org/jibble/epsgraphics build 04-Dec-2025 14:58:36 (Found 4 errors + 2498 warnings) Compiling jalview/src/org/json build 04-Dec-2025 14:58:36 (Found 4 errors + 2499 warnings) Compiling jalview/src/org/json build 04-Dec-2025 14:58:36 (Found 4 errors + 2500 warnings) Compiling jalview/src/org/json build 04-Dec-2025 14:58:36 (Found 4 errors + 2511 warnings) Compiling jalview/src/org/json/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2517 warnings) Compiling jalview/src/org/json/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2526 warnings) Compiling jalview/src/org/json/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2528 warnings) Compiling jalview/src/org/json/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2530 warnings) Compiling jalview/src/org/json/simple/parser build 04-Dec-2025 14:58:36 (Found 4 errors + 2605 warnings) Compiling jalview/src/org/json/simple/parser build 04-Dec-2025 14:58:36 (Found 4 errors + 2609 warnings) Compiling jalview/src/org/json/simple/parser build 04-Dec-2025 14:58:36 (Found 4 errors + 2609 warnings) Compiling jalview/src/org/stackoverflowusers/file build 04-Dec-2025 14:58:36 (Found 4 errors + 2610 warnings) Compiling jalview/src/swingjs/api build 04-Dec-2025 14:58:36 (Found 4 errors + 2610 warnings) Compiling jalview/src/swingjs/api/js build 04-Dec-2025 14:58:36 (Found 4 errors + 2611 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 04-Dec-2025 14:58:36 (Found 4 errors + 2613 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 04-Dec-2025 14:58:36 (Found 4 errors + 2614 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 04-Dec-2025 14:58:36 (Found 4 errors + 2616 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 04-Dec-2025 14:58:36 (Found 4 errors + 2619 warnings) Compiling jalview/src/uk/ac/ebi/www build 04-Dec-2025 14:58:36 (Found 4 errors + 2622 warnings) Compiling jalview/src/uk/ac/ebi/www build 04-Dec-2025 14:58:36 (Found 4 errors + 2625 warnings) Compiling jalview/src/uk/ac/ebi/www build 04-Dec-2025 14:58:36 (Found 4 errors + 2632 warnings) Compiling jalview/src/uk/ac/ebi/www build 04-Dec-2025 14:58:36 (Found 4 errors + 2680 warnings) Compiling jalview/src/uk/ac/ebi/www build 04-Dec-2025 14:58:36 (Found 4 errors + 2722 warnings) Compiling jalview/src/uk/ac/ebi/www/picr/AccessionMappingService build 04-Dec-2025 14:58:36 (Found 4 errors + 2729 warnings) Compiling jalview/src/uk/ac/ebi/www/picr/AccessionMappingService build 04-Dec-2025 14:58:36 (Found 4 errors + 2729 warnings) Compiling jalview/src/vamsas build 04-Dec-2025 14:58:36 (Found 4 errors + 2730 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2732 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2733 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2735 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2736 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2738 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2739 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2741 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2742 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2744 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2745 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2747 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2748 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2750 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2751 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2753 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2754 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2755 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2757 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2759 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2760 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2762 warnings) Compiling jalview/src/vamsas/objects/simple build 04-Dec-2025 14:58:36 (Found 4 errors + 2762 warnings) Cleaning output folder for jalview build 04-Dec-2025 14:58:36 (Found 4 errors + 2762 warnings) Copying resources to the output folder build 04-Dec-2025 14:58:37 (Found 4 errors + 2762 warnings) Analyzing sources build 04-Dec-2025 14:58:37 J2S buildStarting 315 files, contexts.size() = 2, isBatch=true build 04-Dec-2025 14:58:37 (Found 4 errors + 2762 warnings) Compiling jalview/test/jalview/analysis build 04-Dec-2025 14:58:37 (Found 4 errors + 2772 warnings) Compiling jalview/test/jalview/analysis build 04-Dec-2025 14:58:37 (Found 4 errors + 2787 warnings) Compiling jalview/test/jalview/analysis build 04-Dec-2025 14:58:37 (Found 4 errors + 2800 warnings) Compiling jalview/test/jalview/analysis build 04-Dec-2025 14:58:37 (Found 4 errors + 2802 warnings) Compiling jalview/test/jalview/analysis build 04-Dec-2025 14:58:37 (Found 4 errors + 2804 warnings) Compiling jalview/test/jalview/analysis build 04-Dec-2025 14:58:37 (Found 4 errors + 2845 warnings) Compiling jalview/test/jalview/analysis build 04-Dec-2025 14:58:37 (Found 4 errors + 2845 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 04-Dec-2025 14:58:37 (Found 4 errors + 2850 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 04-Dec-2025 14:58:37 (Found 4 errors + 2851 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 04-Dec-2025 14:58:37 (Found 4 errors + 2857 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 04-Dec-2025 14:58:37 (Found 4 errors + 2858 warnings) Compiling jalview/test/jalview/bin build 04-Dec-2025 14:58:37 (Found 4 errors + 2859 warnings) Compiling jalview/test/jalview/bin build 04-Dec-2025 14:58:37 (Found 4 errors + 2860 warnings) Compiling jalview/test/jalview/bin build 04-Dec-2025 14:58:37 (Found 4 errors + 2863 warnings) Compiling jalview/test/jalview/bin/argparser build 04-Dec-2025 14:58:37 (Found 4 errors + 2870 warnings) Compiling jalview/test/jalview/commands build 04-Dec-2025 14:58:37 (Found 4 errors + 2871 warnings) Compiling jalview/test/jalview/controller build 04-Dec-2025 14:58:37 (Found 4 errors + 2871 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2872 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2886 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2889 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2890 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2892 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2902 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2903 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2905 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2907 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2909 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2910 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2911 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2914 warnings) Compiling jalview/test/jalview/datamodel build 04-Dec-2025 14:58:37 (Found 4 errors + 2915 warnings) Compiling jalview/test/jalview/datamodel/features build 04-Dec-2025 14:58:38 (Found 4 errors + 2916 warnings) Compiling jalview/test/jalview/datamodel/features build 04-Dec-2025 14:58:38 (Found 4 errors + 2916 warnings) Compiling jalview/test/jalview/ext/android build 04-Dec-2025 14:58:38 (Found 4 errors + 2916 warnings) Compiling jalview/test/jalview/ext/ensembl build 04-Dec-2025 14:58:38 (Found 4 errors + 2916 warnings) Compiling jalview/test/jalview/ext/htsjdk build 04-Dec-2025 14:58:38 (Found 4 errors + 2917 warnings) Compiling jalview/test/jalview/ext/jmol build 04-Dec-2025 14:58:38 (Found 4 errors + 2918 warnings) Compiling jalview/test/jalview/ext/jmol build 04-Dec-2025 14:58:38 (Found 4 errors + 2918 warnings) Compiling jalview/test/jalview/ext/paradise build 04-Dec-2025 14:58:38 (Found 4 errors + 2918 warnings) Compiling jalview/test/jalview/ext/pymol build 04-Dec-2025 14:58:38 (Found 4 errors + 2918 warnings) Compiling jalview/test/jalview/ext/rbvi/chimera build 04-Dec-2025 14:58:38 (Found 4 errors + 2918 warnings) Compiling jalview/test/jalview/ext/so build 04-Dec-2025 14:58:38 (Found 4 errors + 2918 warnings) Compiling jalview/test/jalview/fts/core build 04-Dec-2025 14:58:38 (Found 4 errors + 2918 warnings) Compiling jalview/test/jalview/fts/service/pdb build 04-Dec-2025 14:58:38 (Found 4 errors + 2919 warnings) Compiling jalview/test/jalview/fts/service/pdb build 04-Dec-2025 14:58:38 (Found 4 errors + 2926 warnings) Compiling jalview/test/jalview/fts/threedbeacons build 04-Dec-2025 14:58:38 (Found 4 errors + 2931 warnings) Compiling jalview/test/jalview/fts/threedbeacons build 04-Dec-2025 14:58:38 (Found 4 errors + 2932 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 2934 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 2935 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 2937 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 2938 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 2958 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 2983 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 2984 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 2986 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 2989 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 2990 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 2991 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 2992 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 2994 warnings) Compiling jalview/test/jalview/gui build 04-Dec-2025 14:58:38 (Found 4 errors + 3000 warnings) Compiling jalview/test/jalview/gui/structurechooser build 04-Dec-2025 14:58:38 (Found 4 errors + 3000 warnings) Compiling jalview/test/jalview/hmmer build 04-Dec-2025 14:58:38 (Found 4 errors + 3001 warnings) Compiling jalview/test/jalview/io build 04-Dec-2025 14:58:38 (Found 4 errors + 3005 warnings) Compiling jalview/test/jalview/io build 04-Dec-2025 14:58:38 (Found 4 errors + 3009 warnings) Compiling jalview/test/jalview/io build 04-Dec-2025 14:58:38 (Found 4 errors + 3013 warnings) Compiling jalview/test/jalview/io build 04-Dec-2025 14:58:38 (Found 4 errors + 3015 warnings) Compiling jalview/test/jalview/io build 04-Dec-2025 14:58:38 (Found 4 errors + 3016 warnings) Compiling jalview/test/jalview/io build 04-Dec-2025 14:58:38 (Found 4 errors + 3017 warnings) Compiling jalview/test/jalview/io build 04-Dec-2025 14:58:38 (Found 4 errors + 3024 warnings) Compiling jalview/test/jalview/io build 04-Dec-2025 14:58:38 (Found 4 errors + 3026 warnings) Compiling jalview/test/jalview/io build 04-Dec-2025 14:58:39 (Found 4 errors + 3026 warnings) Compiling jalview/test/jalview/io/cache build 04-Dec-2025 14:58:39 (Found 4 errors + 3026 warnings) Compiling jalview/test/jalview/io/gff build 04-Dec-2025 14:58:39 (Found 4 errors + 3027 warnings) Compiling jalview/test/jalview/io/gff build 04-Dec-2025 14:58:39 (Found 4 errors + 3036 warnings) Compiling jalview/test/jalview/io/vcf build 04-Dec-2025 14:58:39 (Found 4 errors + 3036 warnings) Compiling jalview/test/jalview/math build 04-Dec-2025 14:58:39 (Found 4 errors + 3048 warnings) Compiling jalview/test/jalview/project build 04-Dec-2025 14:58:39 (Found 4 errors + 3049 warnings) Compiling jalview/test/jalview/renderer build 04-Dec-2025 14:58:39 (Found 4 errors + 3051 warnings) Compiling jalview/test/jalview/renderer build 04-Dec-2025 14:58:39 (Found 4 errors + 3057 warnings) Compiling jalview/test/jalview/renderer build 04-Dec-2025 14:58:39 (Found 4 errors + 3058 warnings) Compiling jalview/test/jalview/renderer build 04-Dec-2025 14:58:39 (Found 4 errors + 3059 warnings) Compiling jalview/test/jalview/renderer/seqfeatures build 04-Dec-2025 14:58:39 (Found 4 errors + 3059 warnings) Compiling jalview/test/jalview/schemes build 04-Dec-2025 14:58:39 (Found 4 errors + 3060 warnings) Compiling jalview/test/jalview/schemes build 04-Dec-2025 14:58:39 (Found 4 errors + 3060 warnings) Compiling jalview/test/jalview/structure build 04-Dec-2025 14:58:39 (Found 4 errors + 3062 warnings) Compiling jalview/test/jalview/structure build 04-Dec-2025 14:58:39 (Found 4 errors + 3063 warnings) Compiling jalview/test/jalview/structure build 04-Dec-2025 14:58:39 (Found 4 errors + 3064 warnings) Compiling jalview/test/jalview/structure build 04-Dec-2025 14:58:39 (Found 4 errors + 3067 warnings) Compiling jalview/test/jalview/structure build 04-Dec-2025 14:58:39 (Found 4 errors + 3067 warnings) Compiling jalview/test/jalview/structures/models build 04-Dec-2025 14:58:39 (Found 4 errors + 3067 warnings) Compiling jalview/test/jalview/testutils build 04-Dec-2025 14:58:39 (Found 4 errors + 3068 warnings) Compiling jalview/test/jalview/testutils build 04-Dec-2025 14:58:39 (Found 4 errors + 3069 warnings) Compiling jalview/test/jalview/urls build 04-Dec-2025 14:58:39 (Found 4 errors + 3074 warnings) Compiling jalview/test/jalview/urls build 04-Dec-2025 14:58:39 (Found 4 errors + 3079 warnings) Compiling jalview/test/jalview/urls build 04-Dec-2025 14:58:39 (Found 4 errors + 3079 warnings) Compiling jalview/test/jalview/util build 04-Dec-2025 14:58:39 (Found 4 errors + 3086 warnings) Compiling jalview/test/jalview/util build 04-Dec-2025 14:58:39 (Found 4 errors + 3087 warnings) Compiling jalview/test/jalview/util build 04-Dec-2025 14:58:39 (Found 4 errors + 3088 warnings) Compiling jalview/test/jalview/util build 04-Dec-2025 14:58:39 (Found 4 errors + 3092 warnings) Compiling jalview/test/jalview/util build 04-Dec-2025 14:58:39 (Found 4 errors + 3093 warnings) Compiling jalview/test/jalview/util build 04-Dec-2025 14:58:39 (Found 4 errors + 3098 warnings) Compiling jalview/test/jalview/util build 04-Dec-2025 14:58:39 (Found 4 errors + 3098 warnings) Compiling jalview/test/jalview/util/dialogrunner build 04-Dec-2025 14:58:39 (Found 4 errors + 3098 warnings) Compiling jalview/test/jalview/util/imagemaker build 04-Dec-2025 14:58:39 (Found 4 errors + 3098 warnings) Compiling jalview/test/jalview/util/matcher build 04-Dec-2025 14:58:39 (Found 4 errors + 3101 warnings) Compiling jalview/test/jalview/util/matcher build 04-Dec-2025 14:58:39 (Found 4 errors + 3107 warnings) Compiling jalview/test/jalview/viewmodel build 04-Dec-2025 14:58:39 (Found 4 errors + 3113 warnings) Compiling jalview/test/jalview/viewmodel build 04-Dec-2025 14:58:39 (Found 4 errors + 3115 warnings) Compiling jalview/test/jalview/viewmodel/styles build 04-Dec-2025 14:58:39 (Found 4 errors + 3115 warnings) Compiling jalview/test/jalview/workers build 04-Dec-2025 14:58:39 (Found 4 errors + 3115 warnings) Compiling jalview/test/jalview/ws build 04-Dec-2025 14:58:39 (Found 4 errors + 3117 warnings) Compiling jalview/test/jalview/ws build 04-Dec-2025 14:58:39 (Found 4 errors + 3120 warnings) Compiling jalview/test/jalview/ws/dbsources build 04-Dec-2025 14:58:39 (Found 4 errors + 3138 warnings) Compiling jalview/test/jalview/ws/dbsources build 04-Dec-2025 14:58:39 (Found 4 errors + 3139 warnings) Compiling jalview/test/jalview/ws/dbsources build 04-Dec-2025 14:58:39 (Found 4 errors + 3139 warnings) Compiling jalview/test/jalview/ws/ebi build 04-Dec-2025 14:58:39 (Found 4 errors + 3147 warnings) Compiling jalview/test/jalview/ws/gui build 04-Dec-2025 14:58:39 (Found 4 errors + 3147 warnings) Compiling jalview/test/jalview/ws/jabaws build 04-Dec-2025 14:58:39 (Found 4 errors + 3148 warnings) Compiling jalview/test/jalview/ws/jabaws build 04-Dec-2025 14:58:39 (Found 4 errors + 3149 warnings) Compiling jalview/test/jalview/ws/jabaws build 04-Dec-2025 14:58:39 (Found 4 errors + 3150 warnings) Compiling jalview/test/jalview/ws/jabaws build 04-Dec-2025 14:58:39 (Found 4 errors + 3154 warnings) Compiling jalview/test/jalview/ws/jabaws build 04-Dec-2025 14:58:39 (Found 4 errors + 3172 warnings) Compiling jalview/test/jalview/ws/jws2 build 04-Dec-2025 14:58:39 (Found 4 errors + 3172 warnings) Compiling jalview/test/jalview/ws/rest build 04-Dec-2025 14:58:39 (Found 4 errors + 3173 warnings) Compiling jalview/test/jalview/ws/rest build 04-Dec-2025 14:58:39 (Found 4 errors + 3173 warnings) Compiling jalview/test/jalview/ws/seqfetcher build 04-Dec-2025 14:58:39 (Found 4 errors + 3173 warnings) Compiling jalview/test/jalview/ws/sifts build 04-Dec-2025 14:58:39 (Found 4 errors + 3175 warnings) Compiling jalview/test/jalview/ws/utils build 04-Dec-2025 14:58:39 (Found 4 errors + 3183 warnings) Compiling jalview/test/jalview/ws2/actions/alignment build 04-Dec-2025 14:58:39 (Found 4 errors + 3183 warnings) Compiling jalview/test/jalview/ws2/actions/annotation build 04-Dec-2025 14:58:39 (Found 4 errors + 3183 warnings) Compiling jalview/test/jalview/ws2/actions/secstructpred build 04-Dec-2025 14:58:39 (Found 4 errors + 3183 warnings) Compiling jalview/test/jalview/ws2/client/slivka build 04-Dec-2025 14:58:39 (Found 4 errors + 3199 warnings) Compiling jalview/test/junit/extensions build 04-Dec-2025 14:58:39 (Found 4 errors + 3201 warnings) Compiling jalview/test/junit/extensions build 04-Dec-2025 14:58:39 (Found 4 errors + 3201 warnings) Compiling jalview/test/mc_view build 04-Dec-2025 14:58:39 (Found 4 errors + 3202 warnings) Compiling jalview/test/mc_view build 04-Dec-2025 14:58:39 J2S using configuration file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/.j2s build 04-Dec-2025 14:58:39 j2s.config.altfileproperty = org.jalview.jalviewjsj2sfilename build 04-Dec-2025 14:58:39 J2S System.getProperty("org.jalview.jalviewjsj2sfilename") = ./build/jalviewjs/config/j2s build 04-Dec-2025 14:58:39 J2S using configuration file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/./build/jalviewjs/config/j2s build 04-Dec-2025 14:58:39 j2s.compiler.status = enable build 04-Dec-2025 14:58:39 j2s.compiler.java.version = 8 build 04-Dec-2025 14:58:39 J2S compiler version set to 8 build 04-Dec-2025 14:58:39 j2s.break.on.error = false build 04-Dec-2025 14:58:39 j2s.exact.long = true build 04-Dec-2025 14:58:39 j2s.async.thread = false build 04-Dec-2025 14:58:39 j2s.compiler.mode = nodebug build 04-Dec-2025 14:58:39 j2s.site.directory = ./build/jalviewjs/tmp/site_js build 04-Dec-2025 14:58:39 J2S writing to /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/./build/jalviewjs/tmp/site_js/swingjs/j2s build 04-Dec-2025 14:58:39 j2s.log.methods.declared = build 04-Dec-2025 14:58:39 j2s.log.methods.called = build 04-Dec-2025 14:58:39 j2s.excluded.paths = test;testng;util build 04-Dec-2025 14:58:39 j2s.compiler.read.annotations = true build 04-Dec-2025 14:58:39 j2s.compiler.ignored.annotations = CallerSensitive;ConstructorProperties;Deprecated;Override;SafeVarargs;SuppressWarnings;FunctionalInterface;Documented;Inherited;Native;Repeatable;Retention; build 04-Dec-2025 14:58:39 j2s.testing = false build 04-Dec-2025 14:58:39 j2s.compiler.nonqualified.packages = build 04-Dec-2025 14:58:39 j2s.compiler.nonqualified.classes = build 04-Dec-2025 14:58:39 j2s.class.replacements = build 04-Dec-2025 14:58:39 j2s.template.html = utils/jalviewjs/template.html build 04-Dec-2025 14:58:39 J2S using HTML template /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/utils/jalviewjs/template.html build 04-Dec-2025 14:58:39 J2S building JavaScript jalview /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 Thu Dec 04 14:58:39 GMT 2025 build 04-Dec-2025 14:58:39 J2S building JavaScript for 1253 files build 04-Dec-2025 14:58:39 J2S transpiling (1/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/github/reinert/jjschema/Attributes.java build 04-Dec-2025 14:58:39 j2s copying resources from /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com to /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/./build/jalviewjs/tmp/site_js/swingjs/j2s/com build 04-Dec-2025 14:58:39 J2S transpiling (2/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/AmpersandRule.java build 04-Dec-2025 14:58:39 J2S transpiling (3/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Any.java build 04-Dec-2025 14:58:39 J2S transpiling (4/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/BackG.java build 04-Dec-2025 14:58:40 J2S transpiling (5/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/BackMatch.java build 04-Dec-2025 14:58:40 J2S transpiling (6/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/BackRefRule.java build 04-Dec-2025 14:58:40 J2S transpiling (7/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Backup.java build 04-Dec-2025 14:58:40 J2S transpiling (8/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/BasicStringBufferLike.java build 04-Dec-2025 14:58:40 J2S transpiling (9/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Bits.java build 04-Dec-2025 14:58:40 J2S transpiling (10/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Boundary.java build 04-Dec-2025 14:58:40 J2S transpiling (11/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Bracket.java build 04-Dec-2025 14:58:40 J2S transpiling (12/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/CaseMgr.java build 04-Dec-2025 14:58:40 J2S transpiling (13/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/ChangeRule.java build 04-Dec-2025 14:58:40 J2S transpiling (14/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/CodeRule.java build 04-Dec-2025 14:58:40 J2S transpiling (15/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Ctrl.java build 04-Dec-2025 14:58:40 J2S transpiling (16/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Custom.java build 04-Dec-2025 14:58:40 J2S transpiling (17/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/CustomEndpoint.java build 04-Dec-2025 14:58:40 J2S transpiling (18/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/DirFileRegex.java build 04-Dec-2025 14:58:40 J2S transpiling (19/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/DotMulti.java build 04-Dec-2025 14:58:40 J2S transpiling (20/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/End.java build 04-Dec-2025 14:58:40 J2S transpiling (21/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/FastBracket.java build 04-Dec-2025 14:58:40 J2S transpiling (22/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/FastMulti.java build 04-Dec-2025 14:58:40 J2S transpiling (23/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/FileRegex.java build 04-Dec-2025 14:58:40 J2S transpiling (24/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Group.java build 04-Dec-2025 14:58:40 J2S transpiling (25/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/LeftRule.java build 04-Dec-2025 14:58:40 J2S transpiling (26/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Multi.java build 04-Dec-2025 14:58:40 J2S transpiling (27/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/MultiMin.java build 04-Dec-2025 14:58:40 J2S transpiling (28/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Multi_stage2.java build 04-Dec-2025 14:58:40 J2S transpiling (29/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/NoPattern.java build 04-Dec-2025 14:58:40 J2S transpiling (30/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/NonDirFileRegex.java build 04-Dec-2025 14:58:40 J2S transpiling (31/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/NotImplementedError.java build 04-Dec-2025 14:58:40 J2S transpiling (32/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/NullPattern.java build 04-Dec-2025 14:58:40 J2S transpiling (33/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/NullRule.java build 04-Dec-2025 14:58:40 J2S transpiling (34/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Or.java build 04-Dec-2025 14:58:40 J2S transpiling (35/1253) 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/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/RegSyntax.java build 04-Dec-2025 14:58:41 J2S transpiling (48/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/RegSyntaxError.java build 04-Dec-2025 14:58:41 J2S transpiling (49/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Regex.java build 04-Dec-2025 14:58:42 J2S transpiling (50/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/RegexReader.java build 04-Dec-2025 14:58:42 J2S transpiling (51/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/RegexTokenizer.java build 04-Dec-2025 14:58:42 J2S transpiling (52/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/RegexWriter.java build 04-Dec-2025 14:58:42 >>>main found for com.stevesoft.pat.RegexWriter build 04-Dec-2025 14:58:42 J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/./build/jalviewjs/tmp/site_js/com_stevesoft_pat_RegexWriter.html build 04-Dec-2025 14:58:42 J2S transpiling (53/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/ReplaceRule.java build 04-Dec-2025 14:58:42 J2S transpiling (54/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Replacer.java build 04-Dec-2025 14:58:42 J2S transpiling (55/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/RightRule.java build 04-Dec-2025 14:58:42 J2S transpiling (56/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/Rthings.java build 04-Dec-2025 14:58:42 J2S transpiling (57/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/com/stevesoft/pat/RuleHolder.java build 04-Dec-2025 14:58:42 J2S transpiling (58/1253) 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04-Dec-2025 14:58:49 J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/./build/jalviewjs/tmp/site_js/jalview_bin_GetdownLauncherUpdate.html build 04-Dec-2025 14:58:49 J2S transpiling (249/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/bin/HiDPISetting.java build 04-Dec-2025 14:58:49 J2S transpiling (250/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/bin/Jalview.java build 04-Dec-2025 14:58:50 >>>main found for jalview.bin.Jalview build 04-Dec-2025 14:58:50 J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/./build/jalviewjs/tmp/site_js/jalview_bin_Jalview.html build 04-Dec-2025 14:58:50 J2S transpiling (251/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/bin/JalviewJS2.java build 04-Dec-2025 14:58:50 >>>main found for jalview.bin.JalviewJS2 build 04-Dec-2025 14:58:50 J2S creating 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transpiling (898/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/EmblFlatfileSource.java build 04-Dec-2025 14:59:08 J2S transpiling (899/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/EmblSource.java build 04-Dec-2025 14:59:08 J2S transpiling (900/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/EmblXmlSource.java build 04-Dec-2025 14:59:08 J2S transpiling (901/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/GeneDbSource.java build 04-Dec-2025 14:59:08 J2S transpiling (902/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/Pdb.java build 04-Dec-2025 14:59:08 J2S transpiling (903/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/Pfam.java build 04-Dec-2025 14:59:08 J2S transpiling (904/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/PfamFull.java build 04-Dec-2025 14:59:08 J2S transpiling (905/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/PfamSeed.java build 04-Dec-2025 14:59:08 J2S transpiling (906/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/Rfam.java build 04-Dec-2025 14:59:08 J2S transpiling (907/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/RfamFull.java build 04-Dec-2025 14:59:08 J2S transpiling (908/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/RfamSeed.java build 04-Dec-2025 14:59:08 J2S transpiling (909/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/TDBeacons.java build 04-Dec-2025 14:59:08 J2S transpiling (910/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/Uniprot.java build 04-Dec-2025 14:59:08 J2S transpiling (911/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/UniprotName.java build 04-Dec-2025 14:59:08 J2S transpiling (912/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/Xfam.java build 04-Dec-2025 14:59:08 J2S transpiling (913/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/ebi/EBIFetchClient.java build 04-Dec-2025 14:59:08 J2S transpiling (914/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/ebi/HmmerJSONProcessor.java build 04-Dec-2025 14:59:08 J2S transpiling (915/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/ebi/hmmerClient.java build 04-Dec-2025 14:59:08 >>>main found for jalview.ws.ebi.hmmerClient build 04-Dec-2025 14:59:08 J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/./build/jalviewjs/tmp/site_js/jalview_ws_ebi_hmmerClient.html build 04-Dec-2025 14:59:08 J2S transpiling (916/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/gui/AnnotationWsJob.java build 04-Dec-2025 14:59:08 J2S transpiling (917/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/gui/MsaWSJob.java build 04-Dec-2025 14:59:08 J2S transpiling (918/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/gui/MsaWSThread.java build 04-Dec-2025 14:59:08 J2S transpiling (919/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/gui/WsJob.java build 04-Dec-2025 14:59:08 J2S transpiling (920/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/io/mime/HttpContentHandler.java build 04-Dec-2025 14:59:08 J2S transpiling (921/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/io/mime/JalviewMimeContentHandler.java build 04-Dec-2025 14:59:08 J2S transpiling (922/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/io/mime/MimeTypes.java build 04-Dec-2025 14:59:08 J2S transpiling (923/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/Annotate3D.java build 04-Dec-2025 14:59:08 J2S transpiling (924/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/Discoverer.java build 04-Dec-2025 14:59:08 J2S transpiling (925/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/JPredClient.java build 04-Dec-2025 14:59:08 J2S transpiling (926/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/JPredThread.java build 04-Dec-2025 14:59:08 J2S transpiling (927/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/JWS1Thread.java build 04-Dec-2025 14:59:08 J2S transpiling (928/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/MsaWSClient.java build 04-Dec-2025 14:59:08 J2S transpiling (929/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/MsaWSThread.java build 04-Dec-2025 14:59:08 J2S transpiling (930/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/SeqSearchWSClient.java build 04-Dec-2025 14:59:08 J2S transpiling (931/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/SeqSearchWSThread.java build 04-Dec-2025 14:59:08 J2S transpiling (932/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/WS1Client.java build 04-Dec-2025 14:59:08 J2S transpiling (933/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/WSJob.java build 04-Dec-2025 14:59:08 J2S transpiling (934/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/AWS2Thread.java build 04-Dec-2025 14:59:08 J2S transpiling (935/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/JWs2Job.java build 04-Dec-2025 14:59:08 J2S transpiling (936/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/JabaParamStore.java build 04-Dec-2025 14:59:08 J2S transpiling (937/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/JabaPreset.java build 04-Dec-2025 14:59:08 J2S transpiling (938/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/JabaWsParamTest.java build 04-Dec-2025 14:59:08 >>>main found for jalview.ws.jws2.JabaWsParamTest build 04-Dec-2025 14:59:08 J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/./build/jalviewjs/tmp/site_js/jalview_ws_jws2_JabaWsParamTest.html build 04-Dec-2025 14:59:08 J2S transpiling (939/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/JabaWsServerQuery.java build 04-Dec-2025 14:59:10 J2S transpiling (940/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/Jws2Client.java build 04-Dec-2025 14:59:10 J2S transpiling (941/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/Jws2ClientFactory.java build 04-Dec-2025 14:59:10 J2S transpiling (942/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/Jws2Discoverer.java build 04-Dec-2025 14:59:10 J2S transpiling (943/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/MsaWSClient.java build 04-Dec-2025 14:59:10 J2S transpiling (944/1253) 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(Found 4 errors + 3202 warnings) Build done build 04-Dec-2025 14:59:13 Invoking 'Gradle Project Builder' on '/jalview'. build 04-Dec-2025 14:59:15 :jalviewjsTranspile (Thread[Execution worker for ':',5,main]) completed. Took 1 mins 27.408 secs. build 04-Dec-2025 14:59:15 :jalviewjsCopyTransferSiteJs (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:59:15 build 04-Dec-2025 14:59:15 > Task :jalviewjsCopyTransferSiteJs build 04-Dec-2025 14:59:15 Caching disabled for task ':jalviewjsCopyTransferSiteJs' because: build 04-Dec-2025 14:59:15 Build cache is disabled build 04-Dec-2025 14:59:15 Task ':jalviewjsCopyTransferSiteJs' is not up-to-date because: build 04-Dec-2025 14:59:15 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site has been removed. build 04-Dec-2025 14:59:15 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site/com_stevesoft_pat_RegexWriter.html has been removed. build 04-Dec-2025 14:59:15 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site/jalview_bin_AppletParams.html has been removed. build 04-Dec-2025 14:59:15 :jalviewjsCopyTransferSiteJs (Thread[Execution worker for ':',5,main]) completed. Took 0.402 secs. build 04-Dec-2025 14:59:15 :jalviewjsTransferUnzipLib (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:59:15 build 04-Dec-2025 14:59:15 > Task :jalviewjsTransferUnzipLib build 04-Dec-2025 14:59:15 Caching disabled for task ':jalviewjsTransferUnzipLib' because: build 04-Dec-2025 14:59:15 Build cache is disabled build 04-Dec-2025 14:59:15 Task ':jalviewjsTransferUnzipLib' is not up-to-date because: build 04-Dec-2025 14:59:15 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_lib has been removed. build 04-Dec-2025 14:59:15 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_lib/fr_orsay_lri_varna_applications_AlignmentDemo.html has been removed. build 04-Dec-2025 14:59:15 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_lib/fr_orsay_lri_varna_applications_fragseq_FragSeqGUI.html has been removed. build 04-Dec-2025 14:59:15 :jalviewjsTransferUnzipLib (Thread[Execution worker for ':',5,main]) completed. Took 0.562 secs. build 04-Dec-2025 14:59:15 :jalviewjsTransferUnzipSwingJs (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:59:16 build 04-Dec-2025 14:59:16 > Task :jalviewjsTransferUnzipSwingJs build 04-Dec-2025 14:59:16 Caching disabled for task ':jalviewjsTransferUnzipSwingJs' because: build 04-Dec-2025 14:59:16 Build cache is disabled build 04-Dec-2025 14:59:16 Task ':jalviewjsTransferUnzipSwingJs' is not up-to-date because: build 04-Dec-2025 14:59:16 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_swingjs has been removed. build 04-Dec-2025 14:59:16 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_swingjs/___j2sflags.htm has been removed. build 04-Dec-2025 14:59:16 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_swingjs/debug.log has been removed. build 04-Dec-2025 14:59:16 :jalviewjsTransferUnzipSwingJs (Thread[Execution worker for ':',5,main]) completed. Took 0.81 secs. build 04-Dec-2025 14:59:16 :jalviewjsTransferUnzipAllLibs (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:59:16 build 04-Dec-2025 14:59:16 > Task :jalviewjsTransferUnzipAllLibs build 04-Dec-2025 14:59:16 Skipping task ':jalviewjsTransferUnzipAllLibs' as it has no actions. build 04-Dec-2025 14:59:16 :jalviewjsTransferUnzipAllLibs (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 04-Dec-2025 14:59:16 :jalviewjsSyncAllLibs (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:59:18 build 04-Dec-2025 14:59:18 > Task :jalviewjsSyncAllLibs build 04-Dec-2025 14:59:18 Caching disabled for task ':jalviewjsSyncAllLibs' because: build 04-Dec-2025 14:59:18 Build cache is disabled build 04-Dec-2025 14:59:18 Task ':jalviewjsSyncAllLibs' is not up-to-date because: build 04-Dec-2025 14:59:18 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site/swingjs/j2s/javajs/async/Assets.js has changed. build 04-Dec-2025 14:59:18 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site/swingjs/j2s/javajs/async/Async.js has changed. build 04-Dec-2025 14:59:18 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site/swingjs/j2s/javajs/async/AsyncColorChooser.js has changed. build 04-Dec-2025 14:59:18 :jalviewjsSyncAllLibs (Thread[Execution worker for ':',5,main]) completed. Took 1.567 secs. build 04-Dec-2025 14:59:18 :copyResources (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:59:18 build 04-Dec-2025 14:59:18 > Task :copyResources UP-TO-DATE build 04-Dec-2025 14:59:18 Caching disabled for task ':copyResources' because: build 04-Dec-2025 14:59:18 Build cache is disabled build 04-Dec-2025 14:59:18 Skipping task ':copyResources' as it is up-to-date. build 04-Dec-2025 14:59:18 :copyResources (Thread[Execution worker for ':',5,main]) completed. Took 0.021 secs. build 04-Dec-2025 14:59:18 :createBuildProperties (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:59:18 build 04-Dec-2025 14:59:18 > Task :createBuildProperties build 04-Dec-2025 14:59:18 Caching disabled for task ':createBuildProperties' because: build 04-Dec-2025 14:59:18 Build cache is disabled build 04-Dec-2025 14:59:18 Task ':createBuildProperties' is not up-to-date because: build 04-Dec-2025 14:59:18 Value of input property 'comment' has changed for task ':createBuildProperties' build 04-Dec-2025 14:59:18 Value of input property 'properties' has changed for task ':createBuildProperties' build 04-Dec-2025 14:59:18 :createBuildProperties (Thread[Execution worker for ':',5,main]) completed. Took 0.002 secs. build 04-Dec-2025 14:59:18 :jalviewjsSyncBuildProperties (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:59:18 build 04-Dec-2025 14:59:18 > Task :jalviewjsSyncBuildProperties build 04-Dec-2025 14:59:18 Caching disabled for task ':jalviewjsSyncBuildProperties' because: build 04-Dec-2025 14:59:18 Build cache is disabled build 04-Dec-2025 14:59:18 Task ':jalviewjsSyncBuildProperties' is not up-to-date because: build 04-Dec-2025 14:59:18 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site/swingjs/j2s/.build_properties has been removed. build 04-Dec-2025 14:59:18 :jalviewjsSyncBuildProperties (Thread[Execution worker for ':',5,main]) completed. Took 0.116 secs. build 04-Dec-2025 14:59:18 :jalviewjsBuildAllCores (Thread[Execution worker for ':',5,main]) started. build 04-Dec-2025 14:59:20 build 04-Dec-2025 14:59:20 > Task :jalviewjsBuildAllCores build 04-Dec-2025 14:59:20 Execution optimizations have been disabled for task ':jalviewjsBuildAllCores' to ensure correctness due to the following reasons: build 04-Dec-2025 14:59:20 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_lib/swingjs/j2s'. Reason: Task ':jalviewjsBuildAllCores' uses this output of task ':jalviewjsTransferUnzipLib' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Dec-2025 14:59:20 Invalidating VFS because task ':jalviewjsBuildAllCores' failed validation build 04-Dec-2025 14:59:20 Caching disabled for task ':jalviewjsBuildAllCores' because: build 04-Dec-2025 14:59:20 Build cache is disabled build 04-Dec-2025 14:59:20 Task ':jalviewjsBuildAllCores' is not up-to-date because: build 04-Dec-2025 14:59:20 Incremental execution has been disabled to ensure correctness. Please consult deprecation warnings for more details. build 04-Dec-2025 14:59:20 Creating core for stevesoft... build 04-Dec-2025 14:59:20 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corestevesoft.js build 04-Dec-2025 14:59:20 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corestevesoft.z.js build 04-Dec-2025 14:59:20 build 04-Dec-2025 14:59:20 Running '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corestevesoft.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corestevesoft.z.js' build 04-Dec-2025 14:59:20 build 04-Dec-2025 14:59:20 Starting process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corestevesoft.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corestevesoft.z.js build 04-Dec-2025 14:59:20 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' build 04-Dec-2025 14:59:21 -- build 04-Dec-2025 14:59:21 Creating core for jvjmol... build 04-Dec-2025 14:59:21 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvjmol.js build 04-Dec-2025 14:59:21 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvjmol.z.js build 04-Dec-2025 14:59:21 build 04-Dec-2025 14:59:21 Running '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvjmol.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvjmol.z.js' build 04-Dec-2025 14:59:21 build 04-Dec-2025 14:59:21 Starting process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvjmol.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvjmol.z.js build 04-Dec-2025 14:59:21 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' build 04-Dec-2025 14:59:25 -- build 04-Dec-2025 14:59:25 Creating core for jalview... build 04-Dec-2025 14:59:25 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.js build 04-Dec-2025 14:59:25 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.z.js build 04-Dec-2025 14:59:25 build 04-Dec-2025 14:59:25 Running '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.z.js' build 04-Dec-2025 14:59:25 build 04-Dec-2025 14:59:25 Starting process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.z.js build 04-Dec-2025 14:59:25 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' error 04-Dec-2025 14:59:26 ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.js:10508: ERROR - Parse error. missing ) after argument list error 04-Dec-2025 14:59:26 }}, 1); error 04-Dec-2025 14:59:26 ^ error 04-Dec-2025 14:59:26 error 04-Dec-2025 14:59:26 1 error(s), 0 warning(s) build 04-Dec-2025 14:59:26 build 04-Dec-2025 14:59:26 > Task :jalviewjsBuildAllCores FAILED build 04-Dec-2025 14:59:26 :jalviewjsBuildAllCores (Thread[Execution worker for ':',5,main]) completed. Took 8.377 secs. error 04-Dec-2025 14:59:27 build 04-Dec-2025 14:59:27 build 04-Dec-2025 14:59:27 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 04-Dec-2025 14:59:27 build 04-Dec-2025 14:59:27 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 04-Dec-2025 14:59:27 build 04-Dec-2025 14:59:27 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 04-Dec-2025 14:59:27 build 04-Dec-2025 14:59:27 Execution optimizations have been disabled for 1 invalid unit(s) of work during this build to ensure correctness. build 04-Dec-2025 14:59:27 Please consult deprecation warnings for more details. build 04-Dec-2025 14:59:27 18 actionable tasks: 16 executed, 2 up-to-date error 04-Dec-2025 14:59:27 FAILURE: Build failed with an exception. error 04-Dec-2025 14:59:27 error 04-Dec-2025 14:59:27 * Where: error 04-Dec-2025 14:59:27 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build.gradle' line: 3944 error 04-Dec-2025 14:59:27 error 04-Dec-2025 14:59:27 * What went wrong: error 04-Dec-2025 14:59:27 Execution failed for task ':jalviewjsBuildAllCores'. error 04-Dec-2025 14:59:27 > Process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' finished with non-zero exit value 1 error 04-Dec-2025 14:59:27 error 04-Dec-2025 14:59:27 * Try: error 04-Dec-2025 14:59:27 > Run with --stacktrace option to get the stack trace. error 04-Dec-2025 14:59:27 > Run with --debug option to get more log output. error 04-Dec-2025 14:59:27 > Run with --scan to get full insights. error 04-Dec-2025 14:59:27 error 04-Dec-2025 14:59:27 * Get more help at https://help.gradle.org error 04-Dec-2025 14:59:27 error 04-Dec-2025 14:59:27 BUILD FAILED in 1m 54s simple 04-Dec-2025 14:59:27 simple 04-Dec-2025 14:59:27 Failing task since return code of [/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=DEVELOP-2-12 -PJAVA_VERSION=11 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/latest -Pbamboo_planKey=JB-GDC330 --info eclipse jalviewjsCreateJ2sSettings jalviewjs] was 1 while expected 0 simple 04-Dec-2025 14:59:27 Finished task 'JalviewJS ${bamboo.CHANNEL} release' with result: Failed simple 04-Dec-2025 14:59:27 Running post build plugin 'NCover Results Collector' simple 04-Dec-2025 14:59:27 Running post build plugin 'Artifact Copier' simple 04-Dec-2025 14:59:27 Publishing an artifact: develop_channel_executable_jar error 04-Dec-2025 14:59:27 Unable to publish artifact [develop_channel_executable_jar]: simple 04-Dec-2025 14:59:27 The artifact hasn't been successfully published after 20.03 ms simple 04-Dec-2025 14:59:27 Publishing an artifact: develop_jalview-js-site_tar error 04-Dec-2025 14:59:27 Unable to publish artifact [develop_jalview-js-site_tar]: simple 04-Dec-2025 14:59:27 The artifact hasn't been successfully published after 2.534 ms simple 04-Dec-2025 14:59:27 Publishing an artifact: getdown_develop_channel_tar error 04-Dec-2025 14:59:27 Unable to publish artifact [getdown_develop_channel_tar]: simple 04-Dec-2025 14:59:27 The artifact hasn't been successfully published after 3.195 ms simple 04-Dec-2025 14:59:27 Running post build plugin 'Artifactory Release Management Staging' simple 04-Dec-2025 14:59:27 Running post build plugin 'Artifactory Build Info Copier' simple 04-Dec-2025 14:59:27 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 04-Dec-2025 14:59:27 Running post build plugin 'npm Cache Cleanup' simple 04-Dec-2025 14:59:27 Running post build plugin 'Clover Results Collector' simple 04-Dec-2025 14:59:27 Running post build plugin 'Docker Container Cleanup' simple 04-Dec-2025 14:59:27 Finalising the build... simple 04-Dec-2025 14:59:27 Stopping timer. simple 04-Dec-2025 14:59:27 Build JB-GDC330-JOB1-7 completed. simple 04-Dec-2025 14:59:27 Running on server: post build plugin 'NCover Results Collector' simple 04-Dec-2025 14:59:27 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 04-Dec-2025 14:59:27 Running on server: post build plugin 'Clover Delta Calculator' simple 04-Dec-2025 14:59:27 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 04-Dec-2025 14:59:27 All post build plugins have finished simple 04-Dec-2025 14:59:27 Generating build results summary... simple 04-Dec-2025 14:59:27 Saving build results to disk... simple 04-Dec-2025 14:59:27 Logging substituted variables... simple 04-Dec-2025 14:59:27 Indexing build results... simple 04-Dec-2025 14:59:27 Finished building JB-GDC330-JOB1-7.