simple 05-Dec-2025 18:18:15 Build Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again - Default Job #10 (JB-GPC657-JOB1-10) started building on agent Default Agent simple 05-Dec-2025 18:18:15 simple 05-Dec-2025 18:18:15 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1 simple 05-Dec-2025 18:18:15 Executing build Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again - Default Job #10 (JB-GPC657-JOB1-10) simple 05-Dec-2025 18:18:15 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 05-Dec-2025 18:18:15 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1 simple 05-Dec-2025 18:18:15 Updating source code to revision: 93fb58cbe20343f44ca1822ba33a9713771dea50 simple 05-Dec-2025 18:18:15 Fetching 'refs/heads/patch/JAL-4606_again_and_again' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 05-Dec-2025 18:18:15 Checking out revision 93fb58cbe20343f44ca1822ba33a9713771dea50. simple 05-Dec-2025 18:18:15 Already on 'patch/JAL-4606_again_and_again' simple 05-Dec-2025 18:18:15 Updated source code to revision: 93fb58cbe20343f44ca1822ba33a9713771dea50 simple 05-Dec-2025 18:18:15 Finished task 'Checkout Default Repository' with result: Success simple 05-Dec-2025 18:18:15 Running pre-build action: VCS Version Collector simple 05-Dec-2025 18:18:15 Running pre-build action: Artifactory Release Staging command 05-Dec-2025 18:18:15 Substituting variable: ${bamboo.planKey} with JB-GPC657 simple 05-Dec-2025 18:18:15 Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 05-Dec-2025 18:18:15 Bamboo Artifactory Plugin version: 2.6.2 command 05-Dec-2025 18:18:15 Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again - Default Job #10 (JB-GPC657-JOB1-10)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC657 clean shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4606_again_and_again\nbamboo_dependency_parent_0=JB-GDB735-10\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4606_again_and_again\nbamboo_repository_revision_number=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC657-JOB1-10\nbamboo_repository_46498625_branch_name=patch/JAL-4606_again_and_again\nbamboo_repository_46498625_git_branch=patch/JAL-4606_again_and_again\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-GPC657-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GPC657-JOB1\nbamboo_shortPlanName=patch-JAL-4606_again_and_again\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=10\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-GPC657-JOB1-10\nbamboo_repository_46498625_name=Jalview Gitlab\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again\nbamboo_shortPlanKey=GPC657\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_buildTimeStamp=2025-12-05T18:18:15.276Z\nbamboo_repository_previous_revision_number=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_repository_git_branch=patch/JAL-4606_again_and_again\nbamboo_buildResultKey=JB-GPC657-JOB1-10\nbamboo_repository_branch_name=patch/JAL-4606_again_and_again\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498625_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_1_revision=93fb58cbe20343f44ca1822ba33a9713771dea50\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_repository_46498625_git_username=\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=patch/JAL-4606_again_and_again\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_repository_46498625_previous_revision_number=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46498625_revision_number=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_planRepository_branchDisplayName=patch/JAL-4606_again_and_again\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4606_again_and_again\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-46302819\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-GPC657-JOB1\nbamboo_planKey=JB-GPC657\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4606_again_and_again\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 05-Dec-2025 18:18:17 build 05-Dec-2025 18:18:17 > Configure project : build 05-Dec-2025 18:18:17 Using properties from file './utils/channels/default/channel_gradle.properties' build 05-Dec-2025 18:18:17 JALVIEW_VERSION is set to '2.11.5.1' build 05-Dec-2025 18:18:17 HEADLESS BUILD build 05-Dec-2025 18:18:17 J2S ENABLED build 05-Dec-2025 18:18:17 Using a BUILD profile. build 05-Dec-2025 18:18:17 eclipseDir exists build 05-Dec-2025 18:18:17 build 05-Dec-2025 18:18:17 > Task :clean build 05-Dec-2025 18:18:17 > Task :cleanPackageDir build 05-Dec-2025 18:18:17 > Task :copyHelp build 05-Dec-2025 18:18:18 > Task :buildIndices build 05-Dec-2025 18:18:18 > Task :copyResources build 05-Dec-2025 18:18:18 > Task :copyChannelResources build 05-Dec-2025 18:18:18 build 05-Dec-2025 18:18:18 > Task :createBuildProperties build 05-Dec-2025 18:18:18 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 05-Dec-2025 18:18:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:18 build 05-Dec-2025 18:18:18 > Task :buildResources build 05-Dec-2025 18:18:18 > Task :copyDocs build 05-Dec-2025 18:18:18 build 05-Dec-2025 18:18:18 > Task :convertMdFiles build 05-Dec-2025 18:18:18 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 05-Dec-2025 18:18:18 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/releaseprocess.html build 05-Dec-2025 18:18:18 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 05-Dec-2025 18:18:18 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/building.html build 05-Dec-2025 18:18:18 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/jalview-projects.html build 05-Dec-2025 18:18:19 build 05-Dec-2025 18:18:19 > Task :releasesTemplates build 05-Dec-2025 18:18:19 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 05-Dec-2025 18:18:19 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:19 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:19 Stripping rc/test/etc for 2_11_5_1 build 05-Dec-2025 18:18:19 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md build 05-Dec-2025 18:18:19 build 05-Dec-2025 18:18:19 > Task :prepare build 05-Dec-2025 18:18:21 build 05-Dec-2025 18:18:21 > Task :compileJava build 05-Dec-2025 18:18:21 Setting target compatibility to 11 error 05-Dec-2025 18:18:25 Note: Some input files use or override a deprecated API. error 05-Dec-2025 18:18:25 Note: Recompile with -Xlint:deprecation for details. error 05-Dec-2025 18:18:25 Note: Some input files use unchecked or unsafe operations. error 05-Dec-2025 18:18:25 Note: Recompile with -Xlint:unchecked for details. build 05-Dec-2025 18:18:25 build 05-Dec-2025 18:18:25 > Task :processResources build 05-Dec-2025 18:18:25 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 05-Dec-2025 18:18:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:25 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:25 build 05-Dec-2025 18:18:25 > Task :classes build 05-Dec-2025 18:18:26 build 05-Dec-2025 18:18:26 > Task :compileLinkCheck build 05-Dec-2025 18:18:26 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 05-Dec-2025 18:18:26 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:26 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:26 build 05-Dec-2025 18:18:26 > Task :linkCheck build 05-Dec-2025 18:18:26 Checking help file links build 05-Dec-2025 18:18:26 build 05-Dec-2025 18:18:26 Results: build 05-Dec-2025 18:18:26 161 distinct help targets build 05-Dec-2025 18:18:26 161 help mappings build 05-Dec-2025 18:18:26 0 invalid targets build 05-Dec-2025 18:18:26 31 unused targets build 05-Dec-2025 18:18:26 uniprotfetcher: html/features/uniprotsequencefetcher.html build 05-Dec-2025 18:18:26 overviewprefs: html/features/preferences.html#overview build 05-Dec-2025 18:18:26 cdnafeatures: html/features/codingfeatures.html build 05-Dec-2025 18:18:26 startupprefs: html/features/preferences.html#startup build 05-Dec-2025 18:18:26 ensemblfetch: html/features/ensemblsequencefetcher.html build 05-Dec-2025 18:18:26 io.modellerpir: html/io/modellerpir.html build 05-Dec-2025 18:18:26 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 05-Dec-2025 18:18:26 pdbmcviewer: html/features/pdbviewer.html build 05-Dec-2025 18:18:26 groovy.colours: html/features/groovy.html#groovyColours build 05-Dec-2025 18:18:26 seqmappings: html/features/seqmappings.html build 05-Dec-2025 18:18:26 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 05-Dec-2025 18:18:26 splitframe.mirrorfonts: html/features/splitView.html#mirror build 05-Dec-2025 18:18:26 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 05-Dec-2025 18:18:26 search: html/features/search.html build 05-Dec-2025 18:18:26 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 05-Dec-2025 18:18:26 alformats: html/io/fileformats.html build 05-Dec-2025 18:18:26 strucprefs: html/features/preferences.html#structure build 05-Dec-2025 18:18:26 siftsmapping: html/features/siftsmapping.html build 05-Dec-2025 18:18:26 chimera.annotxfer: html/features/chimera.html#annotxfer build 05-Dec-2025 18:18:26 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 05-Dec-2025 18:18:26 newkeys: html/features/newkeystrokes.html build 05-Dec-2025 18:18:26 importvcf.attribs: html/features/importvcf.html#attribs build 05-Dec-2025 18:18:26 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 05-Dec-2025 18:18:26 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 05-Dec-2025 18:18:26 jalarchive: html/features/jalarchive.html build 05-Dec-2025 18:18:26 newsreader: html/webServices/newsreader.html build 05-Dec-2025 18:18:26 jalviewcltool: html/features/commandline.html#script build 05-Dec-2025 18:18:26 popMenuAddref: html/menus/popupMenu.html#addrefannot build 05-Dec-2025 18:18:26 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 05-Dec-2025 18:18:26 paematrixformat: html/io/paematrixformat.html build 05-Dec-2025 18:18:26 overview: html/features/overview.html build 05-Dec-2025 18:18:26 0 invalid map urls build 05-Dec-2025 18:18:26 0 invalid image attributes build 05-Dec-2025 18:18:26 520 internal href links (120 with anchors) build 05-Dec-2025 18:18:26 0 invalid internal href links build 05-Dec-2025 18:18:26 0 invalid internal anchor links build 05-Dec-2025 18:18:26 112 external href links build 05-Dec-2025 18:18:26 External links not verified as internet not available build 05-Dec-2025 18:18:26 *** Success *** build 05-Dec-2025 18:18:27 build 05-Dec-2025 18:18:27 > Task :jar build 05-Dec-2025 18:18:27 > Task :syncJars build 05-Dec-2025 18:18:27 > Task :makeDist build 05-Dec-2025 18:18:34 > Task :shadowJar build 05-Dec-2025 18:18:34 build 05-Dec-2025 18:18:34 > Task :getdownImagesCopy build 05-Dec-2025 18:18:34 Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons: build 05-Dec-2025 18:18:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/utils/channels/default/images'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 05-Dec-2025 18:18:34 build 05-Dec-2025 18:18:34 > Task :getdownImagesProcess build 05-Dec-2025 18:18:34 > Task :getdownImages build 05-Dec-2025 18:18:34 > Task :getdownWebsiteBuild build 05-Dec-2025 18:18:36 build 05-Dec-2025 18:18:36 > Task :getdownDigest build 05-Dec-2025 18:18:36 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... error 05-Dec-2025 18:18:36 2025/12/05 18:18:35:084 WARNING Starting without install4j classes error 05-Dec-2025 18:18:36 2025/12/05 18:18:35:659 WARNING Starting without install4j classes build 05-Dec-2025 18:18:36 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 05-Dec-2025 18:18:36 build 05-Dec-2025 18:18:36 > Task :getdown build 05-Dec-2025 18:18:36 build 05-Dec-2025 18:18:36 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 05-Dec-2025 18:18:36 build 05-Dec-2025 18:18:36 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 05-Dec-2025 18:18:36 build 05-Dec-2025 18:18:36 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 05-Dec-2025 18:18:36 build 05-Dec-2025 18:18:36 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 05-Dec-2025 18:18:36 Please consult deprecation warnings for more details. build 05-Dec-2025 18:18:36 build 05-Dec-2025 18:18:36 BUILD SUCCESSFUL in 20s build 05-Dec-2025 18:18:36 22 actionable tasks: 22 executed simple 05-Dec-2025 18:18:36 Finished task 'Jalview distribution for Java 11' with result: Success command 05-Dec-2025 18:18:36 Substituting variable: ${bamboo.planKey} with JB-GPC657 simple 05-Dec-2025 18:18:36 Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 05-Dec-2025 18:18:36 Bamboo Artifactory Plugin version: 2.6.2 command 05-Dec-2025 18:18:36 Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again - Default Job #10 (JB-GPC657-JOB1-10)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -x clean -PCHANNEL=BUILD -PJAVA_VERSION=1.8 -Pbamboo_planKey=JB-GPC657 shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4606_again_and_again\nbamboo_dependency_parent_0=JB-GDB735-10\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4606_again_and_again\nbamboo_repository_revision_number=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC657-JOB1-10\nbamboo_repository_46498625_branch_name=patch/JAL-4606_again_and_again\nbamboo_repository_46498625_git_branch=patch/JAL-4606_again_and_again\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-GPC657-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GPC657-JOB1\nbamboo_shortPlanName=patch-JAL-4606_again_and_again\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=10\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-GPC657-JOB1-10\nbamboo_repository_46498625_name=Jalview Gitlab\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again\nbamboo_shortPlanKey=GPC657\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_buildTimeStamp=2025-12-05T18:18:15.276Z\nbamboo_repository_previous_revision_number=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_repository_git_branch=patch/JAL-4606_again_and_again\nbamboo_buildResultKey=JB-GPC657-JOB1-10\nbamboo_repository_branch_name=patch/JAL-4606_again_and_again\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - patch-JAL-4606_again_and_again - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498625_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_1_revision=93fb58cbe20343f44ca1822ba33a9713771dea50\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_repository_46498625_git_username=\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC657 clean shadowJar getdown\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=patch/JAL-4606_again_and_again\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_repository_46498625_previous_revision_number=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46498625_revision_number=93fb58cbe20343f44ca1822ba33a9713771dea50\nbamboo_planRepository_branchDisplayName=patch/JAL-4606_again_and_again\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4606_again_and_again\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-46302819\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-GPC657-JOB1\nbamboo_planKey=JB-GPC657\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4606_again_and_again\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 05-Dec-2025 18:18:37 build 05-Dec-2025 18:18:37 > Configure project : build 05-Dec-2025 18:18:37 Using properties from file './utils/channels/default/channel_gradle.properties' build 05-Dec-2025 18:18:37 JALVIEW_VERSION is set to '2.11.5.1' build 05-Dec-2025 18:18:37 HEADLESS BUILD build 05-Dec-2025 18:18:37 J2S ENABLED build 05-Dec-2025 18:18:37 Using a BUILD profile. build 05-Dec-2025 18:18:37 eclipseDir exists build 05-Dec-2025 18:18:37 build 05-Dec-2025 18:18:37 > Task :copyHelp UP-TO-DATE build 05-Dec-2025 18:18:38 > Task :buildIndices build 05-Dec-2025 18:18:38 > Task :copyResources UP-TO-DATE build 05-Dec-2025 18:18:38 > Task :copyChannelResources UP-TO-DATE build 05-Dec-2025 18:18:38 build 05-Dec-2025 18:18:38 > Task :createBuildProperties build 05-Dec-2025 18:18:38 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 05-Dec-2025 18:18:38 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:38 build 05-Dec-2025 18:18:38 > Task :buildResources build 05-Dec-2025 18:18:38 > Task :copyDocs build 05-Dec-2025 18:18:38 build 05-Dec-2025 18:18:38 > Task :convertMdFiles build 05-Dec-2025 18:18:38 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 05-Dec-2025 18:18:38 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/releaseprocess.html build 05-Dec-2025 18:18:38 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 05-Dec-2025 18:18:38 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/building.html build 05-Dec-2025 18:18:38 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/resources/doc_build/doc/jalview-projects.html build 05-Dec-2025 18:18:38 build 05-Dec-2025 18:18:38 > Task :releasesTemplates build 05-Dec-2025 18:18:38 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 05-Dec-2025 18:18:38 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:38 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:38 Stripping rc/test/etc for 2_11_5_1 build 05-Dec-2025 18:18:38 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md build 05-Dec-2025 18:18:38 build 05-Dec-2025 18:18:38 > Task :prepare build 05-Dec-2025 18:18:40 build 05-Dec-2025 18:18:40 > Task :compileJava build 05-Dec-2025 18:18:40 Setting target compatibility to 1.8 error 05-Dec-2025 18:18:44 Note: Some input files use or override a deprecated API. error 05-Dec-2025 18:18:44 Note: Recompile with -Xlint:deprecation for details. error 05-Dec-2025 18:18:44 Note: Some input files use unchecked or unsafe operations. error 05-Dec-2025 18:18:44 Note: Recompile with -Xlint:unchecked for details. build 05-Dec-2025 18:18:44 build 05-Dec-2025 18:18:44 > Task :processResources build 05-Dec-2025 18:18:44 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 05-Dec-2025 18:18:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:44 build 05-Dec-2025 18:18:44 > Task :classes build 05-Dec-2025 18:18:44 > Task :cleanPackageDir build 05-Dec-2025 18:18:45 build 05-Dec-2025 18:18:45 > Task :compileLinkCheck build 05-Dec-2025 18:18:45 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 05-Dec-2025 18:18:45 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:45 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-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 05-Dec-2025 18:18:45 build 05-Dec-2025 18:18:45 > Task :linkCheck build 05-Dec-2025 18:18:45 Checking help file links build 05-Dec-2025 18:18:45 build 05-Dec-2025 18:18:45 Results: build 05-Dec-2025 18:18:45 161 distinct help targets build 05-Dec-2025 18:18:45 161 help mappings build 05-Dec-2025 18:18:45 0 invalid targets build 05-Dec-2025 18:18:45 31 unused targets build 05-Dec-2025 18:18:45 uniprotfetcher: html/features/uniprotsequencefetcher.html build 05-Dec-2025 18:18:45 overviewprefs: html/features/preferences.html#overview build 05-Dec-2025 18:18:45 cdnafeatures: html/features/codingfeatures.html build 05-Dec-2025 18:18:45 startupprefs: html/features/preferences.html#startup build 05-Dec-2025 18:18:45 ensemblfetch: html/features/ensemblsequencefetcher.html build 05-Dec-2025 18:18:45 io.modellerpir: html/io/modellerpir.html build 05-Dec-2025 18:18:45 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 05-Dec-2025 18:18:45 pdbmcviewer: html/features/pdbviewer.html build 05-Dec-2025 18:18:45 groovy.colours: html/features/groovy.html#groovyColours build 05-Dec-2025 18:18:45 seqmappings: html/features/seqmappings.html build 05-Dec-2025 18:18:45 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 05-Dec-2025 18:18:45 splitframe.mirrorfonts: html/features/splitView.html#mirror build 05-Dec-2025 18:18:45 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 05-Dec-2025 18:18:45 search: html/features/search.html build 05-Dec-2025 18:18:45 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 05-Dec-2025 18:18:45 alformats: html/io/fileformats.html build 05-Dec-2025 18:18:45 strucprefs: html/features/preferences.html#structure build 05-Dec-2025 18:18:45 siftsmapping: html/features/siftsmapping.html build 05-Dec-2025 18:18:45 chimera.annotxfer: html/features/chimera.html#annotxfer build 05-Dec-2025 18:18:45 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 05-Dec-2025 18:18:45 newkeys: html/features/newkeystrokes.html build 05-Dec-2025 18:18:45 importvcf.attribs: html/features/importvcf.html#attribs build 05-Dec-2025 18:18:45 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 05-Dec-2025 18:18:45 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 05-Dec-2025 18:18:45 jalarchive: html/features/jalarchive.html build 05-Dec-2025 18:18:45 newsreader: html/webServices/newsreader.html build 05-Dec-2025 18:18:45 jalviewcltool: html/features/commandline.html#script build 05-Dec-2025 18:18:45 popMenuAddref: html/menus/popupMenu.html#addrefannot build 05-Dec-2025 18:18:45 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 05-Dec-2025 18:18:45 paematrixformat: html/io/paematrixformat.html build 05-Dec-2025 18:18:45 overview: html/features/overview.html build 05-Dec-2025 18:18:45 0 invalid map urls build 05-Dec-2025 18:18:45 0 invalid image attributes build 05-Dec-2025 18:18:45 520 internal href links (120 with anchors) build 05-Dec-2025 18:18:45 0 invalid internal href links build 05-Dec-2025 18:18:45 0 invalid internal anchor links build 05-Dec-2025 18:18:45 112 external href links build 05-Dec-2025 18:18:45 External links not verified as internet not available build 05-Dec-2025 18:18:45 *** Success *** build 05-Dec-2025 18:18:46 build 05-Dec-2025 18:18:46 > Task :jar build 05-Dec-2025 18:18:46 > Task :syncJars build 05-Dec-2025 18:18:46 > Task :makeDist build 05-Dec-2025 18:18:52 > Task :shadowJar build 05-Dec-2025 18:18:52 build 05-Dec-2025 18:18:52 > Task :getdownImagesCopy build 05-Dec-2025 18:18:52 Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons: build 05-Dec-2025 18:18:52 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/utils/channels/default/images'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 05-Dec-2025 18:18:52 build 05-Dec-2025 18:18:52 > Task :getdownImagesProcess build 05-Dec-2025 18:18:52 > Task :getdownImages build 05-Dec-2025 18:18:52 > Task :getdownWebsiteBuild build 05-Dec-2025 18:18:54 build 05-Dec-2025 18:18:54 > Task :getdownDigest build 05-Dec-2025 18:18:54 Generating digest file './build/website/docroot/getdown/default/1.8/digest.txt'... error 05-Dec-2025 18:18:54 2025/12/05 18:18:53:131 WARNING Starting without install4j classes error 05-Dec-2025 18:18:54 2025/12/05 18:18:53:647 WARNING Starting without install4j classes build 05-Dec-2025 18:18:54 Generating digest file './build/website/docroot/getdown/default/1.8/digest2.txt'... build 05-Dec-2025 18:18:54 build 05-Dec-2025 18:18:54 > Task :getdown build 05-Dec-2025 18:18:54 build 05-Dec-2025 18:18:54 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 05-Dec-2025 18:18:54 build 05-Dec-2025 18:18:54 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 05-Dec-2025 18:18:54 build 05-Dec-2025 18:18:54 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 05-Dec-2025 18:18:54 build 05-Dec-2025 18:18:54 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 05-Dec-2025 18:18:54 Please consult deprecation warnings for more details. build 05-Dec-2025 18:18:54 build 05-Dec-2025 18:18:54 BUILD SUCCESSFUL in 17s build 05-Dec-2025 18:18:54 21 actionable tasks: 18 executed, 3 up-to-date simple 05-Dec-2025 18:18:54 Finished task 'Jalview distribution for Java 8' with result: Success simple 05-Dec-2025 18:18:54 Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled simple 05-Dec-2025 18:18:54 Running post build plugin 'NCover Results Collector' simple 05-Dec-2025 18:18:54 Running post build plugin 'Artifact Copier' simple 05-Dec-2025 18:18:54 Publishing an artifact: Jalview executables simple 05-Dec-2025 18:18:54 Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 182.8 ms simple 05-Dec-2025 18:18:54 Publishing an artifact: install4j installers error 05-Dec-2025 18:18:54 Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/install4j does not exist. simple 05-Dec-2025 18:18:54 The artifact hasn't been successfully published after 209.8 μs simple 05-Dec-2025 18:18:54 Publishing an artifact: getdown-channel error 05-Dec-2025 18:18:54 Unable to publish artifact [getdown-channel]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/getdown/website does not exist. simple 05-Dec-2025 18:18:54 The artifact hasn't been successfully published after 40.42 μs simple 05-Dec-2025 18:18:54 Publishing an artifact: Jalview getdown launcher error 05-Dec-2025 18:18:54 Unable to publish artifact [Jalview getdown launcher]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/getdown/files does not exist. simple 05-Dec-2025 18:18:54 The artifact hasn't been successfully published after 29.33 μs simple 05-Dec-2025 18:18:54 Publishing an artifact: getdown build for website simple 05-Dec-2025 18:18:55 Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 268.4 ms simple 05-Dec-2025 18:18:55 Publishing an artifact: getdown build for archive error 05-Dec-2025 18:18:55 Unable to publish artifact [getdown build for archive]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC657-JOB1/build/website/docroot/old does not exist. simple 05-Dec-2025 18:18:55 The artifact hasn't been successfully published after 81.63 μs simple 05-Dec-2025 18:18:55 Running post build plugin 'Artifactory Release Management Staging' simple 05-Dec-2025 18:18:55 Running post build plugin 'Artifactory Build Info Copier' simple 05-Dec-2025 18:18:55 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 05-Dec-2025 18:18:55 Running post build plugin 'npm Cache Cleanup' simple 05-Dec-2025 18:18:55 Running post build plugin 'Clover Results Collector' simple 05-Dec-2025 18:18:55 Running post build plugin 'Docker Container Cleanup' simple 05-Dec-2025 18:18:55 Finalising the build... simple 05-Dec-2025 18:18:55 Stopping timer. simple 05-Dec-2025 18:18:55 Build JB-GPC657-JOB1-10 completed. simple 05-Dec-2025 18:18:55 Running on server: post build plugin 'NCover Results Collector' simple 05-Dec-2025 18:18:55 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 05-Dec-2025 18:18:55 Running on server: post build plugin 'Clover Delta Calculator' simple 05-Dec-2025 18:18:55 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 05-Dec-2025 18:18:55 All post build plugins have finished simple 05-Dec-2025 18:18:55 Generating build results summary... simple 05-Dec-2025 18:18:55 Saving build results to disk... simple 05-Dec-2025 18:18:55 Logging substituted variables... simple 05-Dec-2025 18:18:55 Indexing build results... simple 05-Dec-2025 18:18:55 Finished building JB-GPC657-JOB1-10.