simple 12-Feb-2026 01:56:50 Build Jalview Builds - Getdown Plan Channel - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Default Job #1 (JB-GPC669-JOB1-1) started building on agent Default Agent simple 12-Feb-2026 01:56:50 simple 12-Feb-2026 01:56:50 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1 simple 12-Feb-2026 01:56:50 Executing build Jalview Builds - Getdown Plan Channel - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Default Job #1 (JB-GPC669-JOB1-1) simple 12-Feb-2026 01:56:50 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 12-Feb-2026 01:56:50 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1 simple 12-Feb-2026 01:56:50 Updating source code to revision: 89c895478e2de885c6475780e1191e8b19fe1dff simple 12-Feb-2026 01:56:50 Fetching 'refs/heads/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 12-Feb-2026 01:56:50 Checking out revision 89c895478e2de885c6475780e1191e8b19fe1dff. simple 12-Feb-2026 01:56:50 Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/.git'. simple 12-Feb-2026 01:56:50 Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1'... simple 12-Feb-2026 01:56:50 done. simple 12-Feb-2026 01:56:56 Branch feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp set up to track remote branch feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp from origin. simple 12-Feb-2026 01:56:56 Switched to a new branch 'feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp' simple 12-Feb-2026 01:56:56 Updated source code to revision: 89c895478e2de885c6475780e1191e8b19fe1dff simple 12-Feb-2026 01:56:56 Finished task 'Checkout Default Repository' with result: Success simple 12-Feb-2026 01:56:56 Running pre-build action: VCS Version Collector simple 12-Feb-2026 01:56:57 Running pre-build action: Artifactory Release Staging command 12-Feb-2026 01:56:57 Substituting variable: ${bamboo.planKey} with JB-GPC669 simple 12-Feb-2026 01:56:57 Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 12-Feb-2026 01:56:57 Bamboo Artifactory Plugin version: 2.6.2 command 12-Feb-2026 01:56:57 Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Default Job #1 (JB-GPC669-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC669 clean shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_repository_48169024_name=Jalview Gitlab\nbamboo_planRepository_1_branchDisplayName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_repository_revision_number=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_repository_48169024_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169024_branch_name=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC669-JOB1-1\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-GPC669-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GPC669-JOB1\nbamboo_repository_48169024_git_username=\nbamboo_shortPlanName=feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_repository_48169024_git_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC669-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_48169024_revision_number=89c895478e2de885c6475780e1191e8b19fe1dff\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_shortPlanKey=GPC669\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=89c895478e2de885c6475780e1191e8b19fe1dff\nbamboo_buildTimeStamp=2026-02-12T01:56:50.263Z\nbamboo_repository_git_branch=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_buildResultKey=JB-GPC669-JOB1-1\nbamboo_repository_branch_name=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - feature-JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=89c895478e2de885c6475780e1191e8b19fe1dff\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_dependenciesDisabled=false\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=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\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-47972479\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_ManualBuildTriggerReason_userName=jprocter\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-GPC669-JOB1\nbamboo_planKey=JB-GPC669\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 12-Feb-2026 01:56:58 Starting a Gradle Daemon (subsequent builds will be faster) build 12-Feb-2026 01:57:05 build 12-Feb-2026 01:57:05 > Configure project : build 12-Feb-2026 01:57:05 Using properties from file './utils/channels/default/channel_gradle.properties' build 12-Feb-2026 01:57:05 JALVIEW_VERSION is set to '2.12.0' build 12-Feb-2026 01:57:05 HEADLESS BUILD build 12-Feb-2026 01:57:05 J2S ENABLED build 12-Feb-2026 01:57:05 Using a BUILD profile. build 12-Feb-2026 01:57:06 eclipseDir exists build 12-Feb-2026 01:57:06 build 12-Feb-2026 01:57:06 > Task :clean build 12-Feb-2026 01:57:06 > Task :cleanPackageDir UP-TO-DATE build 12-Feb-2026 01:57:07 > Task :copyHelp build 12-Feb-2026 01:57:09 > Task :buildIndices build 12-Feb-2026 01:57:09 > Task :copyResources build 12-Feb-2026 01:57:09 > Task :copyChannelResources build 12-Feb-2026 01:57:10 build 12-Feb-2026 01:57:10 > Task :createBuildProperties build 12-Feb-2026 01:57:10 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 12-Feb-2026 01:57:10 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-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 12-Feb-2026 01:57:10 build 12-Feb-2026 01:57:10 > Task :buildResources build 12-Feb-2026 01:57:10 > Task :copyDocs build 12-Feb-2026 01:57:10 build 12-Feb-2026 01:57:10 > Task :convertMdFiles build 12-Feb-2026 01:57:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 12-Feb-2026 01:57:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/build/resources/doc_build/doc/releaseprocess.html build 12-Feb-2026 01:57:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 12-Feb-2026 01:57:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/build/resources/doc_build/doc/JalviewJS-API.html build 12-Feb-2026 01:57:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/build/resources/doc_build/doc/building.html build 12-Feb-2026 01:57:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/build/resources/doc_build/doc/addingWebClient.html build 12-Feb-2026 01:57:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/build/resources/doc_build/doc/jalview-projects.html build 12-Feb-2026 01:57:10 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html build 12-Feb-2026 01:57:11 build 12-Feb-2026 01:57:11 > Task :releasesTemplates build 12-Feb-2026 01:57:11 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 12-Feb-2026 01:57:11 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-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 12-Feb-2026 01:57:11 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-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 12-Feb-2026 01:57:11 Stripping rc/test/etc for 2_12_0 build 12-Feb-2026 01:57:11 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/help/markdown/whatsnew/whatsnew-2_12_0.md build 12-Feb-2026 01:57:11 build 12-Feb-2026 01:57:11 > Task :prepare build 12-Feb-2026 01:57:14 build 12-Feb-2026 01:57:14 > Task :compileJava build 12-Feb-2026 01:57:14 Setting target compatibility to 11 error 12-Feb-2026 01:57:26 Note: Some input files use or override a deprecated API. error 12-Feb-2026 01:57:26 Note: Recompile with -Xlint:deprecation for details. error 12-Feb-2026 01:57:26 Note: Some input files use unchecked or unsafe operations. error 12-Feb-2026 01:57:26 Note: Recompile with -Xlint:unchecked for details. build 12-Feb-2026 01:57:30 build 12-Feb-2026 01:57:30 > Task :processResources build 12-Feb-2026 01:57:30 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 12-Feb-2026 01:57:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-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 12-Feb-2026 01:57:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-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 12-Feb-2026 01:57:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-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 12-Feb-2026 01:57:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-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 12-Feb-2026 01:57:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-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 12-Feb-2026 01:57:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-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 12-Feb-2026 01:57:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-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 12-Feb-2026 01:57:30 build 12-Feb-2026 01:57:30 > Task :classes build 12-Feb-2026 01:57:32 build 12-Feb-2026 01:57:32 > Task :compileLinkCheck build 12-Feb-2026 01:57:32 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 12-Feb-2026 01:57:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-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 12-Feb-2026 01:57:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-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 12-Feb-2026 01:57:34 build 12-Feb-2026 01:57:34 > Task :linkCheck build 12-Feb-2026 01:57:34 Checking help file links build 12-Feb-2026 01:57:34 build 12-Feb-2026 01:57:34 Results: build 12-Feb-2026 01:57:34 162 distinct help targets build 12-Feb-2026 01:57:34 162 help mappings build 12-Feb-2026 01:57:34 0 invalid targets build 12-Feb-2026 01:57:34 31 unused targets build 12-Feb-2026 01:57:34 uniprotfetcher: html/features/uniprotsequencefetcher.html build 12-Feb-2026 01:57:34 overviewprefs: html/features/preferences.html#overview build 12-Feb-2026 01:57:34 cdnafeatures: html/features/codingfeatures.html build 12-Feb-2026 01:57:34 startupprefs: html/features/preferences.html#startup build 12-Feb-2026 01:57:34 ensemblfetch: html/features/ensemblsequencefetcher.html build 12-Feb-2026 01:57:34 io.modellerpir: html/io/modellerpir.html build 12-Feb-2026 01:57:34 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 12-Feb-2026 01:57:34 pdbmcviewer: html/features/pdbviewer.html build 12-Feb-2026 01:57:34 groovy.colours: html/features/groovy.html#groovyColours build 12-Feb-2026 01:57:34 seqmappings: html/features/seqmappings.html build 12-Feb-2026 01:57:34 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 12-Feb-2026 01:57:34 splitframe.mirrorfonts: html/features/splitView.html#mirror build 12-Feb-2026 01:57:34 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 12-Feb-2026 01:57:34 search: html/features/search.html build 12-Feb-2026 01:57:34 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 12-Feb-2026 01:57:34 alformats: html/io/fileformats.html build 12-Feb-2026 01:57:34 strucprefs: html/features/preferences.html#structure build 12-Feb-2026 01:57:34 siftsmapping: html/features/siftsmapping.html build 12-Feb-2026 01:57:34 chimera.annotxfer: html/features/chimera.html#annotxfer build 12-Feb-2026 01:57:34 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 12-Feb-2026 01:57:34 newkeys: html/features/newkeystrokes.html build 12-Feb-2026 01:57:34 importvcf.attribs: html/features/importvcf.html#attribs build 12-Feb-2026 01:57:34 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 12-Feb-2026 01:57:34 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 12-Feb-2026 01:57:34 jalarchive: html/features/jalarchive.html build 12-Feb-2026 01:57:34 newsreader: html/webServices/newsreader.html build 12-Feb-2026 01:57:34 jalviewcltool: html/features/commandline.html#script build 12-Feb-2026 01:57:34 popMenuAddref: html/menus/popupMenu.html#addrefannot build 12-Feb-2026 01:57:34 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 12-Feb-2026 01:57:34 paematrixformat: html/io/paematrixformat.html build 12-Feb-2026 01:57:34 overview: html/features/overview.html build 12-Feb-2026 01:57:34 0 invalid map urls build 12-Feb-2026 01:57:34 0 invalid image attributes build 12-Feb-2026 01:57:34 520 internal href links (119 with anchors) build 12-Feb-2026 01:57:34 0 invalid internal href links build 12-Feb-2026 01:57:34 0 invalid internal anchor links build 12-Feb-2026 01:57:34 113 external href links build 12-Feb-2026 01:57:34 External links not verified as internet not available build 12-Feb-2026 01:57:34 *** Success *** build 12-Feb-2026 01:57:35 build 12-Feb-2026 01:57:35 > Task :jar build 12-Feb-2026 01:57:35 > Task :syncJars build 12-Feb-2026 01:57:35 > Task :makeDist build 12-Feb-2026 01:57:43 > Task :shadowJar build 12-Feb-2026 01:57:43 build 12-Feb-2026 01:57:43 > Task :getdownImagesCopy build 12-Feb-2026 01:57:43 Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons: build 12-Feb-2026 01:57:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-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 12-Feb-2026 01:57:44 build 12-Feb-2026 01:57:44 > Task :getdownImagesProcess build 12-Feb-2026 01:57:44 > Task :getdownImages build 12-Feb-2026 01:57:44 > Task :getdownWebsiteBuild build 12-Feb-2026 01:57:45 build 12-Feb-2026 01:57:45 > Task :getdownDigest error 12-Feb-2026 01:57:45 2026/02/12 01:57:44:625 WARNING Starting without install4j classes error 12-Feb-2026 01:57:45 2026/02/12 01:57:45:137 WARNING Starting without install4j classes build 12-Feb-2026 01:57:45 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 12-Feb-2026 01:57:45 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 12-Feb-2026 01:57:45 build 12-Feb-2026 01:57:45 > Task :getdown build 12-Feb-2026 01:57:45 build 12-Feb-2026 01:57:45 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 12-Feb-2026 01:57:45 build 12-Feb-2026 01:57:45 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 12-Feb-2026 01:57:45 build 12-Feb-2026 01:57:45 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 12-Feb-2026 01:57:45 build 12-Feb-2026 01:57:45 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 12-Feb-2026 01:57:45 Please consult deprecation warnings for more details. build 12-Feb-2026 01:57:45 build 12-Feb-2026 01:57:45 BUILD SUCCESSFUL in 48s build 12-Feb-2026 01:57:45 22 actionable tasks: 21 executed, 1 up-to-date simple 12-Feb-2026 01:57:46 Finished task 'Jalview distribution for Java 11' with result: Success simple 12-Feb-2026 01:57:46 Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled simple 12-Feb-2026 01:57:46 Running post build plugin 'NCover Results Collector' simple 12-Feb-2026 01:57:46 Running post build plugin 'Artifact Copier' simple 12-Feb-2026 01:57:46 Publishing an artifact: Jalview executables simple 12-Feb-2026 01:57:46 Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 148.0 ms simple 12-Feb-2026 01:57:46 Publishing an artifact: install4j installers error 12-Feb-2026 01:57:46 Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/build/install4j does not exist. simple 12-Feb-2026 01:57:46 The artifact hasn't been successfully published after 3.618 ms simple 12-Feb-2026 01:57:46 Publishing an artifact: getdown-channel error 12-Feb-2026 01:57:46 Unable to publish artifact [getdown-channel]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/getdown/website does not exist. simple 12-Feb-2026 01:57:46 The artifact hasn't been successfully published after 102.8 μs simple 12-Feb-2026 01:57:46 Publishing an artifact: Jalview getdown launcher error 12-Feb-2026 01:57:46 Unable to publish artifact [Jalview getdown launcher]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/getdown/files does not exist. simple 12-Feb-2026 01:57:46 The artifact hasn't been successfully published after 46.54 μs simple 12-Feb-2026 01:57:46 Publishing an artifact: getdown build for website simple 12-Feb-2026 01:57:46 Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 138.1 ms simple 12-Feb-2026 01:57:46 Publishing an artifact: getdown build for archive error 12-Feb-2026 01:57:46 Unable to publish artifact [getdown build for archive]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC669-JOB1/build/website/docroot/old does not exist. simple 12-Feb-2026 01:57:46 The artifact hasn't been successfully published after 127.8 μs simple 12-Feb-2026 01:57:46 Running post build plugin 'Artifactory Release Management Staging' simple 12-Feb-2026 01:57:46 Running post build plugin 'Artifactory Build Info Copier' simple 12-Feb-2026 01:57:46 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 12-Feb-2026 01:57:46 Running post build plugin 'npm Cache Cleanup' simple 12-Feb-2026 01:57:46 Running post build plugin 'Clover Results Collector' simple 12-Feb-2026 01:57:46 Running post build plugin 'Docker Container Cleanup' simple 12-Feb-2026 01:57:46 Finalising the build... simple 12-Feb-2026 01:57:46 Stopping timer. simple 12-Feb-2026 01:57:46 Build JB-GPC669-JOB1-1 completed. simple 12-Feb-2026 01:57:46 Running on server: post build plugin 'NCover Results Collector' simple 12-Feb-2026 01:57:46 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 12-Feb-2026 01:57:46 Running on server: post build plugin 'Clover Delta Calculator' simple 12-Feb-2026 01:57:46 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 12-Feb-2026 01:57:46 All post build plugins have finished simple 12-Feb-2026 01:57:46 Generating build results summary... simple 12-Feb-2026 01:57:46 Saving build results to disk... simple 12-Feb-2026 01:57:46 Logging substituted variables... simple 12-Feb-2026 01:57:46 Indexing build results... simple 12-Feb-2026 01:57:46 Finished building JB-GPC669-JOB1-1.