simple 26-Jul-2024 11:33:10 Build Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4386_generate_multiple_leaves_for_ss_sources - Default Job #7 (JB-GDL2-JOB1-7) started building on agent Default Agent simple 26-Jul-2024 11:33:10 simple 26-Jul-2024 11:33:10 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-JOB1 simple 26-Jul-2024 11:33:10 Executing build Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4386_generate_multiple_leaves_for_ss_sources - Default Job #7 (JB-GDL2-JOB1-7) simple 26-Jul-2024 11:33:10 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 26-Jul-2024 11:33:10 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-JOB1 simple 26-Jul-2024 11:33:10 Updating source code to revision: a92d9ee8c25e41770bf745b793262f9a7937893e simple 26-Jul-2024 11:33:10 Fetching 'refs/heads/spike/JAL-4386_generate_multiple_leaves_for_ss_sources' from 'http://source.jalview.org/git/jalview.git'. simple 26-Jul-2024 11:33:11 Checking out revision a92d9ee8c25e41770bf745b793262f9a7937893e. simple 26-Jul-2024 11:33:14 Previous HEAD position was 5e59e84... JAL-4392 check if we are rendering a ss-consensus logo *just once* per row simple 26-Jul-2024 11:33:14 Switched to branch 'spike/JAL-4386_generate_multiple_leaves_for_ss_sources' simple 26-Jul-2024 11:33:15 Your branch is behind 'origin/spike/JAL-4386_generate_multiple_leaves_for_ss_sources' by 237 commits, and can be fast-forwarded. simple 26-Jul-2024 11:33:15 (use "git pull" to update your local branch) simple 26-Jul-2024 11:33:19 Checking out files: 3% (7/219) simple 26-Jul-2024 11:33:19 Checking out files: 4% (9/219) simple 26-Jul-2024 11:33:19 Checking out files: 5% (11/219) simple 26-Jul-2024 11:33:19 Checking out files: 6% (14/219) simple 26-Jul-2024 11:33:19 Checking out files: 7% (16/219) simple 26-Jul-2024 11:33:19 Checking out files: 8% (18/219) simple 26-Jul-2024 11:33:19 Checking out files: 9% (20/219) simple 26-Jul-2024 11:33:19 Checking out files: 10% (22/219) simple 26-Jul-2024 11:33:19 Checking out files: 11% (25/219) simple 26-Jul-2024 11:33:19 Checking out files: 12% 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Collector simple 26-Jul-2024 11:33:21 Running pre-build action: Artifactory Release Staging command 26-Jul-2024 11:33:21 Substituting variable: ${bamboo.planKey} with JB-GDL2 simple 26-Jul-2024 11:33:21 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 26-Jul-2024 11:33:21 Bamboo Artifactory Plugin version: 2.6.2 command 26-Jul-2024 11:33:21 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4386_generate_multiple_leaves_for_ss_sources - Default Job #7 (JB-GDL2-JOB1-7)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL2 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_dependency_parent_0=JB-GDB596-7\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=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_repository_revision_number=a92d9ee8c25e41770bf745b793262f9a7937893e\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL2-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-GDL2-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL2-JOB1\nbamboo_shortPlanName=spike-JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=7\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_46497937_revision_number=a92d9ee8c25e41770bf745b793262f9a7937893e\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL2-JOB1-7\nbamboo_repository_46497937_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_shortPlanKey=GDL2\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a92d9ee8c25e41770bf745b793262f9a7937893e\nbamboo_buildTimeStamp=2024-07-26T11:33:10.753+01:00\nbamboo_repository_previous_revision_number=5e59e8410d369c7ee653f1442c28198d75efbb30\nbamboo_repository_git_branch=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_buildResultKey=JB-GDL2-JOB1-7\nbamboo_repository_branch_name=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4386_generate_multiple_leaves_for_ss_sources - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=a92d9ee8c25e41770bf745b793262f9a7937893e\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_repository_46497937_previous_revision_number=5e59e8410d369c7ee653f1442c28198d75efbb30\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_46497937_git_branch=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46497937_git_username=\nbamboo_planRepository_branch=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_repository_46497937_branch_name=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46497937_name=Jalview Git\nbamboo_planRepository_branchDisplayName=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\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-46301473\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=http://source.jalview.org/git/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-GDL2-JOB1\nbamboo_planKey=JB-GDL2\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 26-Jul-2024 11:33:23 build 26-Jul-2024 11:33:23 > Configure project : build 26-Jul-2024 11:33:23 Using properties from file './utils/channels/default/channel_gradle.properties' build 26-Jul-2024 11:33:23 JALVIEW_VERSION is set to '2.11.4.0' build 26-Jul-2024 11:33:23 HEADLESS BUILD build 26-Jul-2024 11:33:23 J2S ENABLED build 26-Jul-2024 11:33:23 Using a BUILD profile. build 26-Jul-2024 11:33:23 eclipseDir exists build 26-Jul-2024 11:33:23 build 26-Jul-2024 11:33:23 > Task :clean build 26-Jul-2024 11:33:23 > Task :cleanPackageDir build 26-Jul-2024 11:33:23 > Task :getdownImagesCopy build 26-Jul-2024 11:33:24 > Task :getdownImagesProcess build 26-Jul-2024 11:33:24 > Task :getdownImages build 26-Jul-2024 11:33:26 > Task :copyHelp build 26-Jul-2024 11:33:29 > Task :buildIndices build 26-Jul-2024 11:33:29 > Task :copyResources build 26-Jul-2024 11:33:29 > Task :copyChannelResources build 26-Jul-2024 11:33:29 build 26-Jul-2024 11:33:29 > Task :createBuildProperties build 26-Jul-2024 11:33:29 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 26-Jul-2024 11:33:29 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:29 build 26-Jul-2024 11:33:29 > Task :buildResources build 26-Jul-2024 11:33:29 > Task :copyDocs build 26-Jul-2024 11:33:29 build 26-Jul-2024 11:33:29 > Task :convertMdFiles build 26-Jul-2024 11:33:29 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 26-Jul-2024 11:33:29 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-JOB1/build/resources/doc_build/doc/releaseprocess.html build 26-Jul-2024 11:33:29 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 26-Jul-2024 11:33:29 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-JOB1/build/resources/doc_build/doc/building.html build 26-Jul-2024 11:33:29 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-JOB1/build/resources/doc_build/doc/jalview-projects.html build 26-Jul-2024 11:33:30 build 26-Jul-2024 11:33:30 > Task :releasesTemplates build 26-Jul-2024 11:33:30 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 26-Jul-2024 11:33:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:30 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:30 build 26-Jul-2024 11:33:30 > Task :prepare build 26-Jul-2024 11:33:32 build 26-Jul-2024 11:33:32 > Task :compileJava build 26-Jul-2024 11:33:32 Setting target compatibility to 11 error 26-Jul-2024 11:33:45 Note: Some input files use or override a deprecated API. error 26-Jul-2024 11:33:45 Note: Recompile with -Xlint:deprecation for details. error 26-Jul-2024 11:33:45 Note: Some input files use unchecked or unsafe operations. error 26-Jul-2024 11:33:45 Note: Recompile with -Xlint:unchecked for details. build 26-Jul-2024 11:33:46 build 26-Jul-2024 11:33:46 > Task :processResources build 26-Jul-2024 11:33:46 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 26-Jul-2024 11:33:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:46 build 26-Jul-2024 11:33:46 > Task :classes build 26-Jul-2024 11:33:47 build 26-Jul-2024 11:33:47 > Task :compileLinkCheck build 26-Jul-2024 11:33:47 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 26-Jul-2024 11:33:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-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 26-Jul-2024 11:33:47 build 26-Jul-2024 11:33:47 > Task :linkCheck build 26-Jul-2024 11:33:47 Checking help file links build 26-Jul-2024 11:33:47 build 26-Jul-2024 11:33:47 Results: build 26-Jul-2024 11:33:47 156 distinct help targets build 26-Jul-2024 11:33:47 156 help mappings build 26-Jul-2024 11:33:47 0 invalid targets build 26-Jul-2024 11:33:47 31 unused targets build 26-Jul-2024 11:33:47 uniprotfetcher: html/features/uniprotsequencefetcher.html build 26-Jul-2024 11:33:47 overviewprefs: html/features/preferences.html#overview build 26-Jul-2024 11:33:47 cdnafeatures: html/features/codingfeatures.html build 26-Jul-2024 11:33:47 startupprefs: html/features/preferences.html#startup build 26-Jul-2024 11:33:47 ensemblfetch: html/features/ensemblsequencefetcher.html build 26-Jul-2024 11:33:47 io.modellerpir: html/io/modellerpir.html build 26-Jul-2024 11:33:47 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 26-Jul-2024 11:33:47 pdbmcviewer: html/features/pdbviewer.html build 26-Jul-2024 11:33:47 groovy.colours: html/features/groovy.html#groovyColours build 26-Jul-2024 11:33:47 seqmappings: html/features/seqmappings.html build 26-Jul-2024 11:33:47 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 26-Jul-2024 11:33:47 splitframe.mirrorfonts: html/features/splitView.html#mirror build 26-Jul-2024 11:33:47 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 26-Jul-2024 11:33:47 search: html/features/search.html build 26-Jul-2024 11:33:47 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 26-Jul-2024 11:33:47 alformats: html/io/fileformats.html build 26-Jul-2024 11:33:47 strucprefs: html/features/preferences.html#structure build 26-Jul-2024 11:33:47 siftsmapping: html/features/siftsmapping.html build 26-Jul-2024 11:33:47 chimera.annotxfer: html/features/chimera.html#annotxfer build 26-Jul-2024 11:33:47 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 26-Jul-2024 11:33:47 newkeys: html/features/newkeystrokes.html build 26-Jul-2024 11:33:47 importvcf.attribs: html/features/importvcf.html#attribs build 26-Jul-2024 11:33:47 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 26-Jul-2024 11:33:47 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 26-Jul-2024 11:33:47 jalarchive: html/features/jalarchive.html build 26-Jul-2024 11:33:47 newsreader: html/webServices/newsreader.html build 26-Jul-2024 11:33:47 jalviewcltool: html/features/commandline.html#script build 26-Jul-2024 11:33:47 popMenuAddref: html/menus/popupMenu.html#addrefannot build 26-Jul-2024 11:33:47 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 26-Jul-2024 11:33:47 paematrixformat: html/io/paematrixformat.html build 26-Jul-2024 11:33:47 overview: html/features/overview.html build 26-Jul-2024 11:33:47 0 invalid map urls build 26-Jul-2024 11:33:47 0 invalid image attributes build 26-Jul-2024 11:33:47 482 internal href links (106 with anchors) build 26-Jul-2024 11:33:47 0 invalid internal href links build 26-Jul-2024 11:33:47 0 invalid internal anchor links build 26-Jul-2024 11:33:47 111 external href links build 26-Jul-2024 11:33:47 External links not verified as internet not available build 26-Jul-2024 11:33:47 *** Success *** build 26-Jul-2024 11:33:48 build 26-Jul-2024 11:33:48 > Task :jar build 26-Jul-2024 11:33:50 > Task :syncJars build 26-Jul-2024 11:33:50 > Task :makeDist build 26-Jul-2024 11:33:50 > Task :getdownWebsiteBuild build 26-Jul-2024 11:33:51 build 26-Jul-2024 11:33:51 > Task :getdownDigest build 26-Jul-2024 11:33:51 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... error 26-Jul-2024 11:33:51 2024/07/26 11:33:50:552 WARNING Starting without install4j classes error 26-Jul-2024 11:33:51 2024/07/26 11:33:51:071 WARNING Starting without install4j classes build 26-Jul-2024 11:33:51 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 26-Jul-2024 11:33:51 build 26-Jul-2024 11:33:51 > Task :getdown build 26-Jul-2024 11:33:51 build 26-Jul-2024 11:33:51 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 26-Jul-2024 11:33:51 build 26-Jul-2024 11:33:51 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 26-Jul-2024 11:33:51 build 26-Jul-2024 11:33:51 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 26-Jul-2024 11:33:51 build 26-Jul-2024 11:33:51 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 26-Jul-2024 11:33:51 Please consult deprecation warnings for more details. build 26-Jul-2024 11:33:51 build 26-Jul-2024 11:33:51 BUILD SUCCESSFUL in 30s build 26-Jul-2024 11:33:51 21 actionable tasks: 21 executed simple 26-Jul-2024 11:33:52 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 26-Jul-2024 11:33:52 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 26-Jul-2024 11:33:52 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4386_generate_multiple_leaves_for_ss_sources - Default Job #7 (JB-GDL2-JOB1-7)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL2-JOB1-7-ScriptBuildTask-4854348579877116407.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_dependency_parent_0=JB-GDB596-7\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_repository_revision_number=a92d9ee8c25e41770bf745b793262f9a7937893e\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL2-JOB1-7\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL2-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL2-JOB1\nbamboo_shortPlanName=spike-JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_planRepository_name=Jalview Git\nbamboo_buildNumber=7\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_46497937_revision_number=a92d9ee8c25e41770bf745b793262f9a7937893e\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL2-JOB1-7\nbamboo_repository_46497937_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_shortPlanKey=GDL2\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a92d9ee8c25e41770bf745b793262f9a7937893e\nbamboo_buildTimeStamp=2024-07-26T11:33:10.753+01:00\nbamboo_repository_previous_revision_number=5e59e8410d369c7ee653f1442c28198d75efbb30\nbamboo_repository_git_branch=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_buildResultKey=JB-GDL2-JOB1-7\nbamboo_repository_branch_name=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - spike-JAL-4386_generate_multiple_leaves_for_ss_sources - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=a92d9ee8c25e41770bf745b793262f9a7937893e\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_repository_46497937_previous_revision_number=5e59e8410d369c7ee653f1442c28198d75efbb30\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-GDL2 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_repository_46497937_git_branch=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46497937_git_username=\nbamboo_planRepository_branch=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_repository_46497937_branch_name=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46497937_name=Jalview Git\nbamboo_planRepository_branchDisplayName=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\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-46301473\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/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-GDL2-JOB1\nbamboo_planKey=JB-GDL2\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=spike/JAL-4386_generate_multiple_leaves_for_ss_sources\n simple 26-Jul-2024 11:33:52 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 26-Jul-2024 11:33:52 Running post build plugin 'NCover Results Collector' simple 26-Jul-2024 11:33:52 Running post build plugin 'Artifact Copier' simple 26-Jul-2024 11:33:52 Publishing an artifact: getdown simple 26-Jul-2024 11:33:52 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 238.5 ms simple 26-Jul-2024 11:33:52 Running post build plugin 'Artifactory Release Management Staging' simple 26-Jul-2024 11:33:52 Running post build plugin 'Artifactory Build Info Copier' simple 26-Jul-2024 11:33:52 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 26-Jul-2024 11:33:52 Running post build plugin 'npm Cache Cleanup' simple 26-Jul-2024 11:33:52 Running post build plugin 'Clover Results Collector' simple 26-Jul-2024 11:33:52 Running post build plugin 'Docker Container Cleanup' simple 26-Jul-2024 11:33:52 Finalising the build... simple 26-Jul-2024 11:33:52 Stopping timer. simple 26-Jul-2024 11:33:52 Build JB-GDL2-JOB1-7 completed. simple 26-Jul-2024 11:33:52 Running on server: post build plugin 'NCover Results Collector' simple 26-Jul-2024 11:33:52 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 26-Jul-2024 11:33:52 Running on server: post build plugin 'Clover Delta Calculator' simple 26-Jul-2024 11:33:52 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 26-Jul-2024 11:33:52 All post build plugins have finished simple 26-Jul-2024 11:33:52 Generating build results summary... simple 26-Jul-2024 11:33:52 Saving build results to disk... simple 26-Jul-2024 11:33:52 Logging substituted variables... simple 26-Jul-2024 11:33:52 Indexing build results... simple 26-Jul-2024 11:33:52 Finished building JB-GDL2-JOB1-7.