simple 07-Nov-2024 13:14:37 Build Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Default Job #2 (JB-GDL38-JOB1-2) started building on agent Default Agent simple 07-Nov-2024 13:14:37 simple 07-Nov-2024 13:14:37 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1 simple 07-Nov-2024 13:14:37 Executing build Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Default Job #2 (JB-GDL38-JOB1-2) simple 07-Nov-2024 13:14:37 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 07-Nov-2024 13:14:37 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1 simple 07-Nov-2024 13:14:37 Updating source code to revision: cfb973824e06936f2f3b2c4cf9605bd687896cf4 simple 07-Nov-2024 13:14:37 Fetching 'refs/heads/experiment/JAL-4386_experimental_string_to_colour_scheme_methods' from 'http://source.jalview.org/git/jalview.git'. simple 07-Nov-2024 13:14:38 Checking out revision cfb973824e06936f2f3b2c4cf9605bd687896cf4. simple 07-Nov-2024 13:14:38 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 07-Nov-2024 13:14:38 503c832..cfb9738 experiment/JAL-4386_experimental_string_to_colour_scheme_methods -> origin/experiment/JAL-4386_experimental_string_to_colour_scheme_methods simple 07-Nov-2024 13:14:38 e1ff67b..1c79fdc feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels simple 07-Nov-2024 13:14:40 Already on 'experiment/JAL-4386_experimental_string_to_colour_scheme_methods' simple 07-Nov-2024 13:14:40 Your branch is behind 'origin/experiment/JAL-4386_experimental_string_to_colour_scheme_methods' by 4 commits, and can be fast-forwarded. simple 07-Nov-2024 13:14:40 (use "git pull" to update your local branch) simple 07-Nov-2024 13:14:40 HEAD is now at cfb9738 JAL-4386 Fixed to the colour scheme ranges and application to the normal calculated tree simple 07-Nov-2024 13:14:40 Updated source code to revision: cfb973824e06936f2f3b2c4cf9605bd687896cf4 simple 07-Nov-2024 13:14:40 Finished task 'Checkout Default Repository' with result: Success simple 07-Nov-2024 13:14:40 Running pre-build action: VCS Version Collector simple 07-Nov-2024 13:14:40 Running pre-build action: Artifactory Release Staging command 07-Nov-2024 13:14:40 Substituting variable: ${bamboo.planKey} with JB-GDL38 simple 07-Nov-2024 13:14:40 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 07-Nov-2024 13:14:40 Bamboo Artifactory Plugin version: 2.6.2 command 07-Nov-2024 13:14:40 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Default Job #2 (JB-GDL38-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL38 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_dependency_parent_0=JB-GDB640-2\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=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_repository_revision_number=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nbamboo_repository_46498175_revision_number=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL38-JOB1-2\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-GDL38-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL38-JOB1\nbamboo_shortPlanName=experiment-JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=2\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL38-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_shortPlanKey=GDL38\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nbamboo_buildTimeStamp=2024-11-07T13:09:27.703Z\nbamboo_repository_previous_revision_number=503c83212e9779b412c999dc1d64d4e6c5e41cae\nbamboo_repository_git_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_buildResultKey=JB-GDL38-JOB1-2\nbamboo_repository_branch_name=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498175_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_name=Jalview Git\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_repository_46498175_name=Jalview Git\nbamboo_planRepository_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_repository_46498175_git_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\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-46301949\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_repository_46498175_branch_name=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\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-GDL38-JOB1\nbamboo_planKey=JB-GDL38\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498175_previous_revision_number=503c83212e9779b412c999dc1d64d4e6c5e41cae\nbamboo_repository_46498175_git_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 07-Nov-2024 13:14:41 build 07-Nov-2024 13:14:41 > Configure project : build 07-Nov-2024 13:14:41 Using properties from file './utils/channels/default/channel_gradle.properties' build 07-Nov-2024 13:14:41 JALVIEW_VERSION is set to '2.11.4.1' build 07-Nov-2024 13:14:41 HEADLESS BUILD build 07-Nov-2024 13:14:41 J2S ENABLED build 07-Nov-2024 13:14:41 Using a BUILD profile. build 07-Nov-2024 13:14:41 eclipseDir exists build 07-Nov-2024 13:14:41 build 07-Nov-2024 13:14:41 > Task :clean build 07-Nov-2024 13:14:41 > Task :cleanPackageDir build 07-Nov-2024 13:14:41 > Task :getdownImagesCopy build 07-Nov-2024 13:14:41 > Task :getdownImagesProcess build 07-Nov-2024 13:14:41 > Task :getdownImages build 07-Nov-2024 13:14:42 > Task :copyHelp build 07-Nov-2024 13:14:43 > Task :buildIndices build 07-Nov-2024 13:14:43 > Task :copyResources build 07-Nov-2024 13:14:43 > Task :copyChannelResources build 07-Nov-2024 13:14:43 build 07-Nov-2024 13:14:43 > Task :createBuildProperties build 07-Nov-2024 13:14:43 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 07-Nov-2024 13:14:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:43 build 07-Nov-2024 13:14:43 > Task :buildResources build 07-Nov-2024 13:14:43 > Task :copyDocs build 07-Nov-2024 13:14:43 build 07-Nov-2024 13:14:43 > Task :convertMdFiles build 07-Nov-2024 13:14:43 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 07-Nov-2024 13:14:43 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/doc_build/doc/releaseprocess.html build 07-Nov-2024 13:14:43 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 07-Nov-2024 13:14:43 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/doc_build/doc/building.html build 07-Nov-2024 13:14:43 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/doc_build/doc/jalview-projects.html build 07-Nov-2024 13:14:43 build 07-Nov-2024 13:14:43 > Task :releasesTemplates build 07-Nov-2024 13:14:43 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 07-Nov-2024 13:14:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:43 Stripping rc/test/etc for 2_11_4_1 build 07-Nov-2024 13:14:43 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_1.md build 07-Nov-2024 13:14:43 build 07-Nov-2024 13:14:43 > Task :prepare build 07-Nov-2024 13:14:45 build 07-Nov-2024 13:14:45 > Task :compileJava build 07-Nov-2024 13:14:45 Setting target compatibility to 11 error 07-Nov-2024 13:14:51 Note: Some input files use or override a deprecated API. error 07-Nov-2024 13:14:51 Note: Recompile with -Xlint:deprecation for details. error 07-Nov-2024 13:14:51 Note: Some input files use unchecked or unsafe operations. error 07-Nov-2024 13:14:51 Note: Recompile with -Xlint:unchecked for details. build 07-Nov-2024 13:14:51 build 07-Nov-2024 13:14:51 > Task :processResources build 07-Nov-2024 13:14:51 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 07-Nov-2024 13:14:51 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:51 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:51 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:51 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:51 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:51 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:51 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:51 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:51 build 07-Nov-2024 13:14:51 > Task :classes build 07-Nov-2024 13:14:53 build 07-Nov-2024 13:14:53 > Task :compileLinkCheck build 07-Nov-2024 13:14:53 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 07-Nov-2024 13:14:53 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:53 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:53 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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 07-Nov-2024 13:14:55 build 07-Nov-2024 13:14:55 > Task :linkCheck build 07-Nov-2024 13:14:55 Checking help file links build 07-Nov-2024 13:17:00 build 07-Nov-2024 13:17:00 Results: build 07-Nov-2024 13:17:00 159 distinct help targets build 07-Nov-2024 13:17:00 159 help mappings build 07-Nov-2024 13:17:00 0 invalid targets build 07-Nov-2024 13:17:00 32 unused targets build 07-Nov-2024 13:17:00 uniprotfetcher: html/features/uniprotsequencefetcher.html build 07-Nov-2024 13:17:00 overviewprefs: html/features/preferences.html#overview build 07-Nov-2024 13:17:00 cdnafeatures: html/features/codingfeatures.html build 07-Nov-2024 13:17:00 startupprefs: html/features/preferences.html#startup build 07-Nov-2024 13:17:00 ensemblfetch: html/features/ensemblsequencefetcher.html build 07-Nov-2024 13:17:00 io.modellerpir: html/io/modellerpir.html build 07-Nov-2024 13:17:00 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 07-Nov-2024 13:17:00 pdbmcviewer: html/features/pdbviewer.html build 07-Nov-2024 13:17:00 workingwithpae: html/features/paematrices.html build 07-Nov-2024 13:17:00 groovy.colours: html/features/groovy.html#groovyColours build 07-Nov-2024 13:17:00 seqmappings: html/features/seqmappings.html build 07-Nov-2024 13:17:00 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 07-Nov-2024 13:17:00 splitframe.mirrorfonts: html/features/splitView.html#mirror build 07-Nov-2024 13:17:00 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 07-Nov-2024 13:17:00 search: html/features/search.html build 07-Nov-2024 13:17:00 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 07-Nov-2024 13:17:00 alformats: html/io/fileformats.html build 07-Nov-2024 13:17:00 strucprefs: html/features/preferences.html#structure build 07-Nov-2024 13:17:00 siftsmapping: html/features/siftsmapping.html build 07-Nov-2024 13:17:00 chimera.annotxfer: html/features/chimera.html#annotxfer build 07-Nov-2024 13:17:00 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 07-Nov-2024 13:17:00 newkeys: html/features/newkeystrokes.html build 07-Nov-2024 13:17:00 importvcf.attribs: html/features/importvcf.html#attribs build 07-Nov-2024 13:17:00 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 07-Nov-2024 13:17:00 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 07-Nov-2024 13:17:00 jalarchive: html/features/jalarchive.html build 07-Nov-2024 13:17:00 newsreader: html/webServices/newsreader.html build 07-Nov-2024 13:17:00 jalviewcltool: html/features/commandline.html#script build 07-Nov-2024 13:17:00 popMenuAddref: html/menus/popupMenu.html#addrefannot build 07-Nov-2024 13:17:00 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 07-Nov-2024 13:17:00 paematrixformat: html/io/paematrixformat.html build 07-Nov-2024 13:17:00 overview: html/features/overview.html build 07-Nov-2024 13:17:00 0 invalid map urls build 07-Nov-2024 13:17:00 0 invalid image attributes build 07-Nov-2024 13:17:00 508 internal href links (110 with anchors) build 07-Nov-2024 13:17:00 0 invalid internal href links build 07-Nov-2024 13:17:00 0 invalid internal anchor links build 07-Nov-2024 13:17:00 113 external href links build 07-Nov-2024 13:17:00 External links not verified as internet not available build 07-Nov-2024 13:17:00 *** Success *** build 07-Nov-2024 13:17:01 build 07-Nov-2024 13:17:01 > Task :jar build 07-Nov-2024 13:17:01 > Task :syncJars build 07-Nov-2024 13:17:01 > Task :makeDist build 07-Nov-2024 13:17:02 > Task :getdownWebsiteBuild error 07-Nov-2024 13:17:03 2024/11/07 13:17:02:500 WARNING Starting without install4j classes error 07-Nov-2024 13:17:03 2024/11/07 13:17:03:063 WARNING Starting without install4j classes build 07-Nov-2024 13:17:03 build 07-Nov-2024 13:17:03 > Task :getdownDigest build 07-Nov-2024 13:17:03 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 07-Nov-2024 13:17:03 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 07-Nov-2024 13:17:03 build 07-Nov-2024 13:17:03 > Task :getdown build 07-Nov-2024 13:17:03 build 07-Nov-2024 13:17:03 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 07-Nov-2024 13:17:03 build 07-Nov-2024 13:17:03 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 07-Nov-2024 13:17:03 build 07-Nov-2024 13:17:03 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 07-Nov-2024 13:17:03 build 07-Nov-2024 13:17:03 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 07-Nov-2024 13:17:03 Please consult deprecation warnings for more details. build 07-Nov-2024 13:17:03 build 07-Nov-2024 13:17:03 BUILD SUCCESSFUL in 2m 23s build 07-Nov-2024 13:17:03 21 actionable tasks: 21 executed simple 07-Nov-2024 13:17:04 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 07-Nov-2024 13:17:04 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 07-Nov-2024 13:17:04 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Default Job #2 (JB-GDL38-JOB1-2)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL38-JOB1-2-ScriptBuildTask-3531866373606566889.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_dependency_parent_0=JB-GDB640-2\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_repository_revision_number=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nbamboo_repository_46498175_revision_number=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL38-JOB1-2\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL38-JOB1\nbamboo_shortPlanName=experiment-JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_planRepository_name=Jalview Git\nbamboo_buildNumber=2\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-GDL38-JOB1-2\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_shortPlanKey=GDL38\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nbamboo_buildTimeStamp=2024-11-07T13:09:27.703Z\nbamboo_repository_previous_revision_number=503c83212e9779b412c999dc1d64d4e6c5e41cae\nbamboo_repository_git_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_buildResultKey=JB-GDL38-JOB1-2\nbamboo_repository_branch_name=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=cfb973824e06936f2f3b2c4cf9605bd687896cf4\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498175_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_name=Jalview Git\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-GDL38 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46498175_name=Jalview Git\nbamboo_planRepository_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_repository_46498175_git_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\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-46301949\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_repository_46498175_branch_name=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\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-GDL38-JOB1\nbamboo_planKey=JB-GDL38\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498175_previous_revision_number=503c83212e9779b412c999dc1d64d4e6c5e41cae\nbamboo_repository_46498175_git_username=\nbamboo_planRepository_1_branchName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods\n simple 07-Nov-2024 13:17:04 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 07-Nov-2024 13:17:04 Running post build plugin 'NCover Results Collector' simple 07-Nov-2024 13:17:04 Running post build plugin 'Artifact Copier' simple 07-Nov-2024 13:17:04 Publishing an artifact: getdown simple 07-Nov-2024 13:17:04 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 98.74 ms simple 07-Nov-2024 13:17:04 Running post build plugin 'Artifactory Release Management Staging' simple 07-Nov-2024 13:17:04 Running post build plugin 'Artifactory Build Info Copier' simple 07-Nov-2024 13:17:04 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 07-Nov-2024 13:17:04 Running post build plugin 'npm Cache Cleanup' simple 07-Nov-2024 13:17:04 Running post build plugin 'Clover Results Collector' simple 07-Nov-2024 13:17:04 Running post build plugin 'Docker Container Cleanup' simple 07-Nov-2024 13:17:04 Finalising the build... simple 07-Nov-2024 13:17:04 Stopping timer. simple 07-Nov-2024 13:17:04 Build JB-GDL38-JOB1-2 completed. simple 07-Nov-2024 13:17:04 Running on server: post build plugin 'NCover Results Collector' simple 07-Nov-2024 13:17:04 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 07-Nov-2024 13:17:04 Running on server: post build plugin 'Clover Delta Calculator' simple 07-Nov-2024 13:17:04 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 07-Nov-2024 13:17:04 All post build plugins have finished simple 07-Nov-2024 13:17:04 Generating build results summary... simple 07-Nov-2024 13:17:04 Saving build results to disk... simple 07-Nov-2024 13:17:04 Logging substituted variables... simple 07-Nov-2024 13:17:04 Indexing build results... simple 07-Nov-2024 13:17:04 Finished building JB-GDL38-JOB1-2.