simple 29-Oct-2021 16:46:13 Build Jalview Builds - Getdown Plan Channel - feature-JAL-3851_rest_api_for_genome_browser - Default Job #1 (JB-GPC270-JOB1-1) started building on agent Default Agent simple 29-Oct-2021 16:46:13 simple 29-Oct-2021 16:46:13 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1 simple 29-Oct-2021 16:46:13 Executing build Jalview Builds - Getdown Plan Channel - feature-JAL-3851_rest_api_for_genome_browser - Default Job #1 (JB-GPC270-JOB1-1) simple 29-Oct-2021 16:46:13 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 29-Oct-2021 16:46:13 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1 simple 29-Oct-2021 16:46:13 Updating source code to revision: 5b6a0829691db987481f5b365799842a1935ab0a simple 29-Oct-2021 16:46:13 Fetching 'refs/heads/feature/JAL-3851_rest_api_for_genome_browser' from 'http://source.jalview.org/git/jalview.git'. simple 29-Oct-2021 16:46:13 Checking out revision 5b6a0829691db987481f5b365799842a1935ab0a. simple 29-Oct-2021 16:46:13 Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1/.git'. simple 29-Oct-2021 16:46:13 Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1'... simple 29-Oct-2021 16:46:13 done. simple 29-Oct-2021 16:46:27 Branch feature/JAL-3851_rest_api_for_genome_browser set up to track remote branch feature/JAL-3851_rest_api_for_genome_browser from origin. simple 29-Oct-2021 16:46:27 Switched to a new branch 'feature/JAL-3851_rest_api_for_genome_browser' simple 29-Oct-2021 16:46:27 Updated source code to revision: 5b6a0829691db987481f5b365799842a1935ab0a simple 29-Oct-2021 16:46:27 Finished task 'Checkout Default Repository' with result: Success simple 29-Oct-2021 16:46:27 Running pre-build action: VCS Version Collector simple 29-Oct-2021 16:46:27 Running pre-build action: Artifactory Release Staging command 29-Oct-2021 16:46:27 Substituting variable: ${bamboo.planKey} with JB-GPC270 simple 29-Oct-2021 16:46:27 Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 29-Oct-2021 16:46:27 Bamboo Artifactory Plugin version: 2.6.2 command 29-Oct-2021 16:46:27 Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - feature-JAL-3851_rest_api_for_genome_browser - Default Job #1 (JB-GPC270-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC270 clean makeDist shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-3851_rest_api_for_genome_browser\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=feature/JAL-3851_rest_api_for_genome_browser\nbamboo_repository_revision_number=5b6a0829691db987481f5b365799842a1935ab0a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC270-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-GPC270-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GPC270-JOB1\nbamboo_shortPlanName=feature-JAL-3851_rest_api_for_genome_browser\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\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-GPC270-JOB1-1\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - feature-JAL-3851_rest_api_for_genome_browser\nbamboo_shortPlanKey=GPC270\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=5b6a0829691db987481f5b365799842a1935ab0a\nbamboo_buildTimeStamp=2021-10-29T16:46:13.297+01:00\nbamboo_repository_27918466_git_branch=feature/JAL-3851_rest_api_for_genome_browser\nbamboo_repository_git_branch=feature/JAL-3851_rest_api_for_genome_browser\nbamboo_buildResultKey=JB-GPC270-JOB1-1\nbamboo_repository_branch_name=feature/JAL-3851_rest_api_for_genome_browser\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - feature-JAL-3851_rest_api_for_genome_browser - Default Job\nbamboo_repository_27918466_name=Jalview Git\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=5b6a0829691db987481f5b365799842a1935ab0a\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\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-3851_rest_api_for_genome_browser\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-3851_rest_api_for_genome_browser\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-3851_rest_api_for_genome_browser\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_repository_27918466_revision_number=5b6a0829691db987481f5b365799842a1935ab0a\nbamboo_plan_storageTag=plan-27623683\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_27918466_branch_name=feature/JAL-3851_rest_api_for_genome_browser\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_repository_27918466_git_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=Soares\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_repository_27918466_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1\nbamboo_planKey=JB-GPC270\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=feature/JAL-3851_rest_api_for_genome_browser\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 29-Oct-2021 16:46:29 build 29-Oct-2021 16:46:29 > Configure project : build 29-Oct-2021 16:46:29 Using properties from file './utils/channels/default/channel_gradle.properties' build 29-Oct-2021 16:46:29 HEADLESS BUILD build 29-Oct-2021 16:46:29 J2S ENABLED build 29-Oct-2021 16:46:29 Using a BUILD profile. build 29-Oct-2021 16:46:29 eclipseDir exists build 29-Oct-2021 16:46:30 build 29-Oct-2021 16:46:30 > Task :clean build 29-Oct-2021 16:46:30 > Task :cleanPackageDir UP-TO-DATE build 29-Oct-2021 16:46:30 > Task :copyHelp build 29-Oct-2021 16:46:32 > Task :buildIndices build 29-Oct-2021 16:46:32 > Task :copyResources build 29-Oct-2021 16:46:32 > Task :copyChannelResources build 29-Oct-2021 16:46:32 > Task :createBuildProperties build 29-Oct-2021 16:46:32 > Task :buildResources build 29-Oct-2021 16:46:32 > Task :copyDocs build 29-Oct-2021 16:46:32 build 29-Oct-2021 16:46:32 > Task :convertMdFiles build 29-Oct-2021 16:46:32 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1/build/resources/doc_build/doc/releaseprocess.html build 29-Oct-2021 16:46:32 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1/build/resources/doc_build/doc/building.html build 29-Oct-2021 16:46:32 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1/build/resources/doc_build/doc/api_specification.html build 29-Oct-2021 16:46:32 build 29-Oct-2021 16:46:32 > Task :prepare build 29-Oct-2021 16:46:34 build 29-Oct-2021 16:46:34 > Task :compileJava build 29-Oct-2021 16:46:34 Setting target compatibility to 11 error 29-Oct-2021 16:46:39 Note: Some input files use or override a deprecated API. error 29-Oct-2021 16:46:39 Note: Recompile with -Xlint:deprecation for details. error 29-Oct-2021 16:46:39 Note: Some input files use unchecked or unsafe operations. error 29-Oct-2021 16:46:39 Note: Recompile with -Xlint:unchecked for details. build 29-Oct-2021 16:46:44 build 29-Oct-2021 16:46:44 > Task :processResources build 29-Oct-2021 16:46:44 > Task :classes build 29-Oct-2021 16:46:47 > Task :compileLinkCheck build 29-Oct-2021 16:46:48 build 29-Oct-2021 16:46:48 > Task :linkCheck build 29-Oct-2021 16:46:48 Checking help file links build 29-Oct-2021 16:46:48 build 29-Oct-2021 16:46:48 Results: build 29-Oct-2021 16:46:48 138 distinct help targets build 29-Oct-2021 16:46:48 138 help mappings build 29-Oct-2021 16:46:48 0 invalid targets build 29-Oct-2021 16:46:48 24 unused targets build 29-Oct-2021 16:46:48 uniprotfetcher: html/features/uniprotsequencefetcher.html build 29-Oct-2021 16:46:48 overviewprefs: html/features/preferences.html#overview build 29-Oct-2021 16:46:48 cdnafeatures: html/features/codingfeatures.html build 29-Oct-2021 16:46:48 ensemblfetch: html/features/ensemblsequencefetcher.html build 29-Oct-2021 16:46:48 io.modellerpir: html/io/modellerpir.html build 29-Oct-2021 16:46:48 pdbmcviewer: html/features/pdbviewer.html build 29-Oct-2021 16:46:48 groovy.colours: html/features/groovy.html#groovyColours build 29-Oct-2021 16:46:48 seqmappings: html/features/seqmappings.html build 29-Oct-2021 16:46:48 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 29-Oct-2021 16:46:48 splitframe.mirrorfonts: html/features/splitView.html#mirror build 29-Oct-2021 16:46:48 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 29-Oct-2021 16:46:48 search: html/features/search.html build 29-Oct-2021 16:46:48 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 29-Oct-2021 16:46:48 alformats: html/io/fileformats.html build 29-Oct-2021 16:46:48 strucprefs: html/features/preferences.html#structure build 29-Oct-2021 16:46:48 siftsmapping: html/features/siftsmapping.html build 29-Oct-2021 16:46:48 chimera.annotxfer: html/features/chimera.html#annotxfer build 29-Oct-2021 16:46:48 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 29-Oct-2021 16:46:48 newkeys: html/features/newkeystrokes.html build 29-Oct-2021 16:46:48 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 29-Oct-2021 16:46:48 jalarchive: html/features/jalarchive.html build 29-Oct-2021 16:46:48 newsreader: html/webServices/newsreader.html build 29-Oct-2021 16:46:48 popMenuAddref: html/menus/popupMenu.html#addrefannot build 29-Oct-2021 16:46:48 overview: html/features/overview.html build 29-Oct-2021 16:46:48 0 invalid map urls build 29-Oct-2021 16:46:48 0 invalid image attributes build 29-Oct-2021 16:46:48 388 internal href links (74 with anchors) build 29-Oct-2021 16:46:48 0 invalid internal href links build 29-Oct-2021 16:46:48 0 invalid internal anchor links build 29-Oct-2021 16:46:48 87 external href links build 29-Oct-2021 16:46:48 External links not verified as internet not available build 29-Oct-2021 16:46:48 *** Success *** build 29-Oct-2021 16:46:49 build 29-Oct-2021 16:46:49 > Task :jar build 29-Oct-2021 16:46:49 > Task :syncJars build 29-Oct-2021 16:46:49 > Task :makeDist build 29-Oct-2021 16:46:58 > Task :shadowJar build 29-Oct-2021 16:46:58 > Task :getdownWebsite build 29-Oct-2021 16:47:00 build 29-Oct-2021 16:47:00 > Task :getdownDigest build 29-Oct-2021 16:47:00 Generating digest file './getdown/website/11/digest.txt'... build 29-Oct-2021 16:47:00 Generating digest file './getdown/website/11/digest2.txt'... build 29-Oct-2021 16:47:00 build 29-Oct-2021 16:47:00 > Task :getdown build 29-Oct-2021 16:47:00 build 29-Oct-2021 16:47:00 Deprecated Gradle features were used in this build, making it incompatible with Gradle 7.0. build 29-Oct-2021 16:47:00 Use '--warning-mode all' to show the individual deprecation warnings. build 29-Oct-2021 16:47:00 See https://docs.gradle.org/6.5.1/userguide/command_line_interface.html#sec:command_line_warnings build 29-Oct-2021 16:47:00 build 29-Oct-2021 16:47:00 BUILD SUCCESSFUL in 32s build 29-Oct-2021 16:47:00 19 actionable tasks: 18 executed, 1 up-to-date error 29-Oct-2021 16:47:00 2021/10/29 16:46:58:932 WARNING Starting without install4j classes error 29-Oct-2021 16:47:00 2021/10/29 16:46:59:669 WARNING Starting without install4j classes simple 29-Oct-2021 16:47:00 Finished task 'Jalview distribution for Java 11' with result: Success command 29-Oct-2021 16:47:00 Substituting variable: ${bamboo.planKey} with JB-GPC270 simple 29-Oct-2021 16:47:00 Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 29-Oct-2021 16:47:00 Bamboo Artifactory Plugin version: 2.6.2 command 29-Oct-2021 16:47:00 Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - feature-JAL-3851_rest_api_for_genome_browser - Default Job #1 (JB-GPC270-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -x clean -PCHANNEL=BUILD -PJAVA_VERSION=1.8 -Pbamboo_planKey=JB-GPC270 shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=feature/JAL-3851_rest_api_for_genome_browser\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=feature/JAL-3851_rest_api_for_genome_browser\nbamboo_repository_revision_number=5b6a0829691db987481f5b365799842a1935ab0a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC270-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-GPC270-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GPC270-JOB1\nbamboo_shortPlanName=feature-JAL-3851_rest_api_for_genome_browser\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\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-GPC270-JOB1-1\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - feature-JAL-3851_rest_api_for_genome_browser\nbamboo_shortPlanKey=GPC270\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=5b6a0829691db987481f5b365799842a1935ab0a\nbamboo_buildTimeStamp=2021-10-29T16:46:13.297+01:00\nbamboo_repository_27918466_git_branch=feature/JAL-3851_rest_api_for_genome_browser\nbamboo_repository_git_branch=feature/JAL-3851_rest_api_for_genome_browser\nbamboo_buildResultKey=JB-GPC270-JOB1-1\nbamboo_repository_branch_name=feature/JAL-3851_rest_api_for_genome_browser\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - feature-JAL-3851_rest_api_for_genome_browser - Default Job\nbamboo_repository_27918466_name=Jalview Git\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=5b6a0829691db987481f5b365799842a1935ab0a\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\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-GPC270 clean makeDist shadowJar getdown\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-3851_rest_api_for_genome_browser\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-3851_rest_api_for_genome_browser\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=feature/JAL-3851_rest_api_for_genome_browser\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_repository_27918466_revision_number=5b6a0829691db987481f5b365799842a1935ab0a\nbamboo_plan_storageTag=plan-27623683\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_repository_27918466_branch_name=feature/JAL-3851_rest_api_for_genome_browser\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_repository_27918466_git_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=Soares\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_repository_27918466_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1\nbamboo_planKey=JB-GPC270\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=feature/JAL-3851_rest_api_for_genome_browser\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 29-Oct-2021 16:47:02 build 29-Oct-2021 16:47:02 > Configure project : build 29-Oct-2021 16:47:02 Using properties from file './utils/channels/default/channel_gradle.properties' build 29-Oct-2021 16:47:02 HEADLESS BUILD build 29-Oct-2021 16:47:02 J2S ENABLED build 29-Oct-2021 16:47:02 Using a BUILD profile. build 29-Oct-2021 16:47:02 eclipseDir exists build 29-Oct-2021 16:47:02 build 29-Oct-2021 16:47:02 > Task :copyHelp UP-TO-DATE build 29-Oct-2021 16:47:04 > Task :buildIndices build 29-Oct-2021 16:47:04 > Task :copyResources UP-TO-DATE build 29-Oct-2021 16:47:04 > Task :copyChannelResources UP-TO-DATE build 29-Oct-2021 16:47:04 > Task :createBuildProperties build 29-Oct-2021 16:47:04 > Task :buildResources build 29-Oct-2021 16:47:04 > Task :copyDocs build 29-Oct-2021 16:47:04 build 29-Oct-2021 16:47:04 > Task :convertMdFiles build 29-Oct-2021 16:47:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1/build/resources/doc_build/doc/releaseprocess.html build 29-Oct-2021 16:47:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1/build/resources/doc_build/doc/building.html build 29-Oct-2021 16:47:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1/build/resources/doc_build/doc/api_specification.html build 29-Oct-2021 16:47:04 build 29-Oct-2021 16:47:04 > Task :prepare build 29-Oct-2021 16:47:06 build 29-Oct-2021 16:47:06 > Task :compileJava build 29-Oct-2021 16:47:06 Setting target compatibility to 1.8 error 29-Oct-2021 16:47:14 Note: Some input files use or override a deprecated API. error 29-Oct-2021 16:47:14 Note: Recompile with -Xlint:deprecation for details. error 29-Oct-2021 16:47:14 Note: Some input files use unchecked or unsafe operations. error 29-Oct-2021 16:47:14 Note: Recompile with -Xlint:unchecked for details. build 29-Oct-2021 16:47:15 build 29-Oct-2021 16:47:15 > Task :processResources build 29-Oct-2021 16:47:15 > Task :classes build 29-Oct-2021 16:47:15 > Task :cleanPackageDir build 29-Oct-2021 16:47:18 > Task :compileLinkCheck build 29-Oct-2021 16:47:19 build 29-Oct-2021 16:47:19 > Task :linkCheck build 29-Oct-2021 16:47:19 Checking help file links build 29-Oct-2021 16:47:19 build 29-Oct-2021 16:47:19 Results: build 29-Oct-2021 16:47:19 138 distinct help targets build 29-Oct-2021 16:47:19 138 help mappings build 29-Oct-2021 16:47:19 0 invalid targets build 29-Oct-2021 16:47:19 24 unused targets build 29-Oct-2021 16:47:19 uniprotfetcher: html/features/uniprotsequencefetcher.html build 29-Oct-2021 16:47:19 overviewprefs: html/features/preferences.html#overview build 29-Oct-2021 16:47:19 cdnafeatures: html/features/codingfeatures.html build 29-Oct-2021 16:47:19 ensemblfetch: html/features/ensemblsequencefetcher.html build 29-Oct-2021 16:47:19 io.modellerpir: html/io/modellerpir.html build 29-Oct-2021 16:47:19 pdbmcviewer: html/features/pdbviewer.html build 29-Oct-2021 16:47:19 groovy.colours: html/features/groovy.html#groovyColours build 29-Oct-2021 16:47:19 seqmappings: html/features/seqmappings.html build 29-Oct-2021 16:47:19 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 29-Oct-2021 16:47:19 splitframe.mirrorfonts: html/features/splitView.html#mirror build 29-Oct-2021 16:47:19 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 29-Oct-2021 16:47:19 search: html/features/search.html build 29-Oct-2021 16:47:19 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 29-Oct-2021 16:47:19 alformats: html/io/fileformats.html build 29-Oct-2021 16:47:19 strucprefs: html/features/preferences.html#structure build 29-Oct-2021 16:47:19 siftsmapping: html/features/siftsmapping.html build 29-Oct-2021 16:47:19 chimera.annotxfer: html/features/chimera.html#annotxfer build 29-Oct-2021 16:47:19 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 29-Oct-2021 16:47:19 newkeys: html/features/newkeystrokes.html build 29-Oct-2021 16:47:19 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 29-Oct-2021 16:47:19 jalarchive: html/features/jalarchive.html build 29-Oct-2021 16:47:19 newsreader: html/webServices/newsreader.html build 29-Oct-2021 16:47:19 popMenuAddref: html/menus/popupMenu.html#addrefannot build 29-Oct-2021 16:47:19 overview: html/features/overview.html build 29-Oct-2021 16:47:19 0 invalid map urls build 29-Oct-2021 16:47:19 0 invalid image attributes build 29-Oct-2021 16:47:19 388 internal href links (74 with anchors) build 29-Oct-2021 16:47:19 0 invalid internal href links build 29-Oct-2021 16:47:19 0 invalid internal anchor links build 29-Oct-2021 16:47:19 87 external href links build 29-Oct-2021 16:47:19 External links not verified as internet not available build 29-Oct-2021 16:47:19 *** Success *** build 29-Oct-2021 16:47:20 build 29-Oct-2021 16:47:20 > Task :jar build 29-Oct-2021 16:47:20 > Task :syncJars build 29-Oct-2021 16:47:20 > Task :makeDist build 29-Oct-2021 16:47:28 > Task :shadowJar build 29-Oct-2021 16:47:28 > Task :getdownWebsite build 29-Oct-2021 16:47:30 build 29-Oct-2021 16:47:30 > Task :getdownDigest build 29-Oct-2021 16:47:30 Generating digest file './getdown/website/1.8/digest.txt'... build 29-Oct-2021 16:47:30 Generating digest file './getdown/website/1.8/digest2.txt'... build 29-Oct-2021 16:47:30 build 29-Oct-2021 16:47:30 > Task :getdown build 29-Oct-2021 16:47:30 build 29-Oct-2021 16:47:30 Deprecated Gradle features were used in this build, making it incompatible with Gradle 7.0. build 29-Oct-2021 16:47:30 Use '--warning-mode all' to show the individual deprecation warnings. build 29-Oct-2021 16:47:30 See https://docs.gradle.org/6.5.1/userguide/command_line_interface.html#sec:command_line_warnings build 29-Oct-2021 16:47:30 build 29-Oct-2021 16:47:30 BUILD SUCCESSFUL in 29s build 29-Oct-2021 16:47:30 18 actionable tasks: 15 executed, 3 up-to-date error 29-Oct-2021 16:47:30 2021/10/29 16:47:28:661 WARNING Starting without install4j classes error 29-Oct-2021 16:47:30 2021/10/29 16:47:29:698 WARNING Starting without install4j classes simple 29-Oct-2021 16:47:30 Finished task 'Jalview distribution for Java 8' with result: Success simple 29-Oct-2021 16:47:30 Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled simple 29-Oct-2021 16:47:30 Running post build plugin 'NCover Results Collector' simple 29-Oct-2021 16:47:30 Running post build plugin 'Artifact Copier' simple 29-Oct-2021 16:47:30 Publishing an artifact: Jalview executables simple 29-Oct-2021 16:47:30 Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 230.7 ms simple 29-Oct-2021 16:47:30 Publishing an artifact: install4j installers error 29-Oct-2021 16:47:30 Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC270-JOB1/build/install4j does not exist. simple 29-Oct-2021 16:47:30 The artifact hasn't been successfully published after 213.6 μs simple 29-Oct-2021 16:47:30 Publishing an artifact: getdown-channel simple 29-Oct-2021 16:47:31 Finished publishing of artifact Shared artifact: [getdown-channel], pattern: [**/*] anchored at: [getdown/website] in 307.5 ms simple 29-Oct-2021 16:47:31 Publishing an artifact: Jalview getdown launcher simple 29-Oct-2021 16:47:31 Finished publishing of artifact Shared artifact: [Jalview getdown launcher], pattern: [**/*] anchored at: [getdown/files] in 26.20 ms simple 29-Oct-2021 16:47:31 Running post build plugin 'Artifactory Release Management Staging' simple 29-Oct-2021 16:47:31 Running post build plugin 'Artifactory Build Info Copier' simple 29-Oct-2021 16:47:31 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 29-Oct-2021 16:47:31 Running post build plugin 'npm Cache Cleanup' simple 29-Oct-2021 16:47:31 Running post build plugin 'Clover Results Collector' simple 29-Oct-2021 16:47:31 Running post build plugin 'Docker Container Cleanup' simple 29-Oct-2021 16:47:31 Finalising the build... simple 29-Oct-2021 16:47:31 Stopping timer. simple 29-Oct-2021 16:47:31 Build JB-GPC270-JOB1-1 completed. simple 29-Oct-2021 16:47:31 Running on server: post build plugin 'NCover Results Collector' simple 29-Oct-2021 16:47:31 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 29-Oct-2021 16:47:31 Running on server: post build plugin 'Clover Delta Calculator' simple 29-Oct-2021 16:47:31 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 29-Oct-2021 16:47:31 All post build plugins have finished simple 29-Oct-2021 16:47:31 Generating build results summary... simple 29-Oct-2021 16:47:31 Saving build results to disk... simple 29-Oct-2021 16:47:31 Logging substituted variables... simple 29-Oct-2021 16:47:31 Indexing build results... simple 29-Oct-2021 16:47:31 Finished building JB-GPC270-JOB1-1.