simple	05-Dec-2019 14:53:14	Build Jalview Builds - Getdown Plan Channel - alpha-JAL-3362_Jalview_212_alpha - Default Job #1 (JB-GPC73-JOB1-1) started building on agent Default Agent
simple	05-Dec-2019 14:53:14	
simple	05-Dec-2019 14:53:14	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1
simple	05-Dec-2019 14:53:14	Executing build Jalview Builds - Getdown Plan Channel - alpha-JAL-3362_Jalview_212_alpha - Default Job #1 (JB-GPC73-JOB1-1)
simple	05-Dec-2019 14:53:14	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	05-Dec-2019 14:53:14	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1
simple	05-Dec-2019 14:53:14	Updating source code to revision: 57b0dee0192a285d36bd698655e639978487a30a
simple	05-Dec-2019 14:53:14	Fetching 'refs/heads/alpha/JAL-3362_Jalview_212_alpha' from 'http://source.jalview.org/git/jalview.git'.
simple	05-Dec-2019 14:53:14	Checking out revision 57b0dee0192a285d36bd698655e639978487a30a.
simple	05-Dec-2019 14:53:14	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1/.git'.
simple	05-Dec-2019 14:53:14	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1'...
simple	05-Dec-2019 14:53:14	done.
simple	05-Dec-2019 14:53:35	Switched to a new branch 'alpha/JAL-3362_Jalview_212_alpha'
simple	05-Dec-2019 14:53:35	Branch alpha/JAL-3362_Jalview_212_alpha set up to track remote branch alpha/JAL-3362_Jalview_212_alpha from origin.
simple	05-Dec-2019 14:53:35	Updated source code to revision: 57b0dee0192a285d36bd698655e639978487a30a
simple	05-Dec-2019 14:53:35	Finished task 'Checkout Default Repository' with result: Success
simple	05-Dec-2019 14:53:35	Running pre-build action: VCS Version Collector
simple	05-Dec-2019 14:53:35	Running pre-build action: Artifactory Release Staging
command	05-Dec-2019 14:53:35	Substituting variable: ${bamboo.planKey} with JB-GPC73
simple	05-Dec-2019 14:53:35	Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	05-Dec-2019 14:53:35	Bamboo Artifactory Plugin version: 2.6.2
command	05-Dec-2019 14:53:35	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - alpha-JAL-3362_Jalview_212_alpha - Default Job #1 (JB-GPC73-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC73 clean makeDist shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=alpha/JAL-3362_Jalview_212_alpha\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=alpha/JAL-3362_Jalview_212_alpha\nbamboo_repository_revision_number=57b0dee0192a285d36bd698655e639978487a30a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC73-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/JB-GPC73-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GPC73-JOB1\nbamboo_repository_12157032_git_username=\nbamboo_capability_system_jdk_JDK_1_8_0_171=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64\nbamboo_shortPlanName=alpha-JAL-3362_Jalview_212_alpha\nbamboo_repository_12157032_branch_name=alpha/JAL-3362_Jalview_212_alpha\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_capability_system_jdk_OpenJDK_11_JRE_only=/home/bamboo/buildtools/jvm/jre11_x64_linux\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC73-JOB1-1\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_12157032_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - alpha-JAL-3362_Jalview_212_alpha\nbamboo_shortPlanKey=GPC73\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/OpenJDK11/jdk-11\nbamboo_planRepository_revision=57b0dee0192a285d36bd698655e639978487a30a\nbamboo_buildTimeStamp=2019-12-05T14:53:14.284Z\nbamboo_repository_12157032_revision_number=57b0dee0192a285d36bd698655e639978487a30a\nbamboo_repository_git_branch=alpha/JAL-3362_Jalview_212_alpha\nbamboo_buildResultKey=JB-GPC73-JOB1-1\nbamboo_repository_branch_name=alpha/JAL-3362_Jalview_212_alpha\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - alpha-JAL-3362_Jalview_212_alpha - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=57b0dee0192a285d36bd698655e639978487a30a\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nJAVA_HOME=/home/bamboo/buildtools/OpenJDK11/jdk-11/\nbamboo_dependenciesDisabled=false\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_repository_12157032_name=Jalview Git\nbamboo_planRepository_branch=alpha/JAL-3362_Jalview_212_alpha\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=alpha/JAL-3362_Jalview_212_alpha\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=alpha/JAL-3362_Jalview_212_alpha\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_capability_system_jdk_JDK=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64\nbamboo_plan_storageTag=plan-11960527\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_repository_12157032_git_branch=alpha/JAL-3362_Jalview_212_alpha\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_ManualBuildTriggerReason_userName=jprocter\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/JB-GPC73-JOB1\nbamboo_planKey=JB-GPC73\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_capability_system_jdk_JDK_1_8=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=alpha/JAL-3362_Jalview_212_alpha\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	05-Dec-2019 14:53:37	Starting a Gradle Daemon, 1 incompatible and 1 stopped Daemons could not be reused, use --status for details
build	05-Dec-2019 14:53:45	
build	05-Dec-2019 14:53:45	> Configure project :
build	05-Dec-2019 14:53:45	Using a BUILD profile. appbase=https://builds.jalview.org/browse/JB-GPC73/latest/artifact/shared/getdown-channel/11
build	05-Dec-2019 14:53:46	Setting target compatibility to 11
build	05-Dec-2019 14:53:46	Using projectFile /srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1/utils/install4j/jalview-installers-java11.install4j
build	05-Dec-2019 14:53:46	
build	05-Dec-2019 14:53:46	> Task :clean UP-TO-DATE
build	05-Dec-2019 14:53:46	> Task :cleanPackageDir UP-TO-DATE
build	05-Dec-2019 14:53:48	> Task :copyHelp
build	05-Dec-2019 14:53:51	> Task :buildIndices
build	05-Dec-2019 14:53:53	
build	05-Dec-2019 14:53:53	> Task :compileJava
build	05-Dec-2019 14:53:53	Setting target compatibility to 11
error	05-Dec-2019 14:54:10	Note: Some input files use or override a deprecated API.
error	05-Dec-2019 14:54:10	Note: Recompile with -Xlint:deprecation for details.
error	05-Dec-2019 14:54:10	Note: Some input files use unchecked or unsafe operations.
error	05-Dec-2019 14:54:10	Note: Recompile with -Xlint:unchecked for details.
build	05-Dec-2019 14:54:14	
build	05-Dec-2019 14:54:14	> Task :processResources
build	05-Dec-2019 14:54:14	> Task :classes
build	05-Dec-2019 14:54:14	> Task :setGitVals UP-TO-DATE
build	05-Dec-2019 14:54:15	> Task :createBuildProperties
build	05-Dec-2019 14:54:17	> Task :compileLinkCheck
build	05-Dec-2019 14:54:17	> Task :deleteBuildingHTML UP-TO-DATE
build	05-Dec-2019 14:54:18	> Task :convertBuildingMD
build	05-Dec-2019 14:54:18	> Task :syncDocs
build	05-Dec-2019 14:54:18	> Task :syncResources
build	05-Dec-2019 14:54:18	> Task :prepare
build	05-Dec-2019 14:54:19	
build	05-Dec-2019 14:54:19	> Task :linkCheck
build	05-Dec-2019 14:54:19	Checking help file links
build	05-Dec-2019 14:54:19	
build	05-Dec-2019 14:54:19	Results:
build	05-Dec-2019 14:54:19	136 distinct help targets
build	05-Dec-2019 14:54:19	136 help mappings
build	05-Dec-2019 14:54:19	0 invalid targets
build	05-Dec-2019 14:54:19	24 unused targets
build	05-Dec-2019 14:54:19	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	05-Dec-2019 14:54:19	    overviewprefs: html/features/preferences.html#overview
build	05-Dec-2019 14:54:19	    cdnafeatures: html/features/codingfeatures.html
build	05-Dec-2019 14:54:19	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	05-Dec-2019 14:54:19	    io.modellerpir: html/io/modellerpir.html
build	05-Dec-2019 14:54:19	    pdbmcviewer: html/features/pdbviewer.html
build	05-Dec-2019 14:54:19	    groovy.colours: html/features/groovy.html#groovyColours
build	05-Dec-2019 14:54:19	    seqmappings: html/features/seqmappings.html
build	05-Dec-2019 14:54:19	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	05-Dec-2019 14:54:19	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	05-Dec-2019 14:54:19	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	05-Dec-2019 14:54:19	    search: html/features/search.html
build	05-Dec-2019 14:54:19	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	05-Dec-2019 14:54:19	    alformats: html/io/fileformats.html
build	05-Dec-2019 14:54:19	    strucprefs: html/features/preferences.html#structure
build	05-Dec-2019 14:54:19	    siftsmapping: html/features/siftsmapping.html
build	05-Dec-2019 14:54:19	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	05-Dec-2019 14:54:19	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	05-Dec-2019 14:54:19	    newkeys: html/features/newkeystrokes.html
build	05-Dec-2019 14:54:19	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	05-Dec-2019 14:54:19	    jalarchive: html/features/jalarchive.html
build	05-Dec-2019 14:54:19	    newsreader: html/webServices/newsreader.html
build	05-Dec-2019 14:54:19	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	05-Dec-2019 14:54:19	    overview: html/features/overview.html
build	05-Dec-2019 14:54:19	0 invalid map urls
build	05-Dec-2019 14:54:19	0 invalid image attributes
build	05-Dec-2019 14:54:19	386 internal href links (72 with anchors)
build	05-Dec-2019 14:54:19	0 invalid internal href links
build	05-Dec-2019 14:54:19	0 invalid internal anchor links
build	05-Dec-2019 14:54:19	89 external href links
build	05-Dec-2019 14:54:19	External links not verified as internet not available
build	05-Dec-2019 14:54:19	*** Success ***
build	05-Dec-2019 14:54:20	
build	05-Dec-2019 14:54:20	> Task :jar
build	05-Dec-2019 14:54:21	> Task :syncJars
build	05-Dec-2019 14:54:21	> Task :makeDist
build	05-Dec-2019 14:54:30	> Task :shadowJar
build	05-Dec-2019 14:54:30	> Task :getdownWebsite
build	05-Dec-2019 14:54:32	
build	05-Dec-2019 14:54:32	> Task :getdownDigest
build	05-Dec-2019 14:54:32	Generating digest file './getdown/website/11/digest.txt'...
build	05-Dec-2019 14:54:32	Generating digest file './getdown/website/11/digest2.txt'...
build	05-Dec-2019 14:54:32	
build	05-Dec-2019 14:54:32	> Task :getdown
build	05-Dec-2019 14:54:32	
build	05-Dec-2019 14:54:32	BUILD SUCCESSFUL in 56s
build	05-Dec-2019 14:54:32	19 actionable tasks: 16 executed, 3 up-to-date
simple	05-Dec-2019 14:54:32	Finished task 'Jalview distribution for Java 11' with result: Success
command	05-Dec-2019 14:54:32	Substituting variable: ${bamboo.planKey} with JB-GPC73
simple	05-Dec-2019 14:54:32	Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	05-Dec-2019 14:54:32	Bamboo Artifactory Plugin version: 2.6.2
command	05-Dec-2019 14:54:32	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - alpha-JAL-3362_Jalview_212_alpha - Default Job #1 (JB-GPC73-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-GPC73 shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=alpha/JAL-3362_Jalview_212_alpha\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=alpha/JAL-3362_Jalview_212_alpha\nbamboo_repository_revision_number=57b0dee0192a285d36bd698655e639978487a30a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC73-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/JB-GPC73-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GPC73-JOB1\nbamboo_repository_12157032_git_username=\nbamboo_capability_system_jdk_JDK_1_8_0_171=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64\nbamboo_shortPlanName=alpha-JAL-3362_Jalview_212_alpha\nbamboo_repository_12157032_branch_name=alpha/JAL-3362_Jalview_212_alpha\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_capability_system_jdk_OpenJDK_11_JRE_only=/home/bamboo/buildtools/jvm/jre11_x64_linux\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC73-JOB1-1\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_repository_12157032_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel - alpha-JAL-3362_Jalview_212_alpha\nbamboo_shortPlanKey=GPC73\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/OpenJDK11/jdk-11\nbamboo_planRepository_revision=57b0dee0192a285d36bd698655e639978487a30a\nbamboo_buildTimeStamp=2019-12-05T14:53:14.284Z\nbamboo_repository_12157032_revision_number=57b0dee0192a285d36bd698655e639978487a30a\nbamboo_repository_git_branch=alpha/JAL-3362_Jalview_212_alpha\nbamboo_buildResultKey=JB-GPC73-JOB1-1\nbamboo_repository_branch_name=alpha/JAL-3362_Jalview_212_alpha\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - alpha-JAL-3362_Jalview_212_alpha - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=57b0dee0192a285d36bd698655e639978487a30a\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-GPC73 clean makeDist shadowJar getdown\nJAVA_HOME=/home/bamboo/buildtools/OpenJDK11/jdk-11/\nbamboo_dependenciesDisabled=false\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_repository_12157032_name=Jalview Git\nbamboo_planRepository_branch=alpha/JAL-3362_Jalview_212_alpha\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=alpha/JAL-3362_Jalview_212_alpha\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=alpha/JAL-3362_Jalview_212_alpha\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_capability_system_jdk_JDK=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64\nbamboo_plan_storageTag=plan-11960527\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_repository_12157032_git_branch=alpha/JAL-3362_Jalview_212_alpha\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_ManualBuildTriggerReason_userName=jprocter\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/JB-GPC73-JOB1\nbamboo_planKey=JB-GPC73\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_capability_system_jdk_JDK_1_8=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=alpha/JAL-3362_Jalview_212_alpha\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	05-Dec-2019 14:54:34	
build	05-Dec-2019 14:54:34	> Configure project :
build	05-Dec-2019 14:54:34	Using a BUILD profile. appbase=https://builds.jalview.org/browse/JB-GPC73/latest/artifact/shared/getdown-channel/1.8
build	05-Dec-2019 14:54:34	Setting target compatibility to 1.8
build	05-Dec-2019 14:54:34	Using projectFile /srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1/utils/install4j/jalview-installers-java1.8.install4j
build	05-Dec-2019 14:54:36	
build	05-Dec-2019 14:54:36	> Task :compileJava
build	05-Dec-2019 14:54:36	Setting target compatibility to 1.8
error	05-Dec-2019 14:54:48	Note: Some input files use or override a deprecated API.
error	05-Dec-2019 14:54:48	Note: Recompile with -Xlint:deprecation for details.
error	05-Dec-2019 14:54:48	Note: Some input files use unchecked or unsafe operations.
error	05-Dec-2019 14:54:48	Note: Recompile with -Xlint:unchecked for details.
build	05-Dec-2019 14:54:49	
build	05-Dec-2019 14:54:49	> Task :processResources UP-TO-DATE
build	05-Dec-2019 14:54:49	> Task :classes
build	05-Dec-2019 14:54:49	> Task :cleanPackageDir
build	05-Dec-2019 14:54:49	> Task :copyHelp UP-TO-DATE
build	05-Dec-2019 14:54:51	> Task :buildIndices
build	05-Dec-2019 14:54:51	> Task :setGitVals UP-TO-DATE
build	05-Dec-2019 14:54:51	> Task :createBuildProperties
build	05-Dec-2019 14:54:53	> Task :compileLinkCheck
build	05-Dec-2019 14:54:53	> Task :deleteBuildingHTML
build	05-Dec-2019 14:54:53	> Task :convertBuildingMD
build	05-Dec-2019 14:54:53	> Task :syncDocs UP-TO-DATE
build	05-Dec-2019 14:54:53	> Task :syncResources UP-TO-DATE
build	05-Dec-2019 14:54:53	> Task :prepare UP-TO-DATE
build	05-Dec-2019 14:54:54	
build	05-Dec-2019 14:54:54	> Task :linkCheck
build	05-Dec-2019 14:54:54	Checking help file links
build	05-Dec-2019 14:54:54	
build	05-Dec-2019 14:54:54	Results:
build	05-Dec-2019 14:54:54	136 distinct help targets
build	05-Dec-2019 14:54:54	136 help mappings
build	05-Dec-2019 14:54:54	0 invalid targets
build	05-Dec-2019 14:54:54	24 unused targets
build	05-Dec-2019 14:54:54	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	05-Dec-2019 14:54:54	    overviewprefs: html/features/preferences.html#overview
build	05-Dec-2019 14:54:54	    cdnafeatures: html/features/codingfeatures.html
build	05-Dec-2019 14:54:54	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	05-Dec-2019 14:54:54	    io.modellerpir: html/io/modellerpir.html
build	05-Dec-2019 14:54:54	    pdbmcviewer: html/features/pdbviewer.html
build	05-Dec-2019 14:54:54	    groovy.colours: html/features/groovy.html#groovyColours
build	05-Dec-2019 14:54:54	    seqmappings: html/features/seqmappings.html
build	05-Dec-2019 14:54:54	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	05-Dec-2019 14:54:54	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	05-Dec-2019 14:54:54	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	05-Dec-2019 14:54:54	    search: html/features/search.html
build	05-Dec-2019 14:54:54	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	05-Dec-2019 14:54:54	    alformats: html/io/fileformats.html
build	05-Dec-2019 14:54:54	    strucprefs: html/features/preferences.html#structure
build	05-Dec-2019 14:54:54	    siftsmapping: html/features/siftsmapping.html
build	05-Dec-2019 14:54:54	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	05-Dec-2019 14:54:54	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	05-Dec-2019 14:54:54	    newkeys: html/features/newkeystrokes.html
build	05-Dec-2019 14:54:54	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	05-Dec-2019 14:54:54	    jalarchive: html/features/jalarchive.html
build	05-Dec-2019 14:54:54	    newsreader: html/webServices/newsreader.html
build	05-Dec-2019 14:54:54	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	05-Dec-2019 14:54:54	    overview: html/features/overview.html
build	05-Dec-2019 14:54:54	0 invalid map urls
build	05-Dec-2019 14:54:54	0 invalid image attributes
build	05-Dec-2019 14:54:54	386 internal href links (72 with anchors)
build	05-Dec-2019 14:54:54	0 invalid internal href links
build	05-Dec-2019 14:54:54	0 invalid internal anchor links
build	05-Dec-2019 14:54:54	89 external href links
build	05-Dec-2019 14:54:54	External links not verified as internet not available
build	05-Dec-2019 14:54:54	*** Success ***
build	05-Dec-2019 14:54:56	
build	05-Dec-2019 14:54:56	> Task :jar
build	05-Dec-2019 14:54:56	> Task :syncJars
build	05-Dec-2019 14:54:56	> Task :makeDist
build	05-Dec-2019 14:55:04	> Task :shadowJar
build	05-Dec-2019 14:55:04	> Task :getdownWebsite
build	05-Dec-2019 14:55:06	
build	05-Dec-2019 14:55:06	> Task :getdownDigest
build	05-Dec-2019 14:55:06	Generating digest file './getdown/website/1.8/digest.txt'...
build	05-Dec-2019 14:55:06	Generating digest file './getdown/website/1.8/digest2.txt'...
build	05-Dec-2019 14:55:06	
build	05-Dec-2019 14:55:06	> Task :getdown
build	05-Dec-2019 14:55:06	
build	05-Dec-2019 14:55:06	BUILD SUCCESSFUL in 33s
build	05-Dec-2019 14:55:06	18 actionable tasks: 14 executed, 4 up-to-date
simple	05-Dec-2019 14:55:06	Finished task 'Jalview distribution for Java 8' with result: Success
simple	05-Dec-2019 14:55:06	Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled
simple	05-Dec-2019 14:55:06	Running post build plugin 'NCover Results Collector'
simple	05-Dec-2019 14:55:06	Running post build plugin 'Artifact Copier'
simple	05-Dec-2019 14:55:06	Publishing an artifact: Jalview executables
simple	05-Dec-2019 14:55:07	Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 264.8 ms
simple	05-Dec-2019 14:55:07	Publishing an artifact: install4j installers
error	05-Dec-2019 14:55:07	Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1/build/install4j does not exist.
simple	05-Dec-2019 14:55:07	The artifact hasn't been successfully published after 12.99 ms
simple	05-Dec-2019 14:55:07	Publishing an artifact: getdown-channel
simple	05-Dec-2019 14:55:07	Finished publishing of artifact Shared artifact: [getdown-channel], pattern: [**/*] anchored at: [getdown/website] in 584.2 ms
simple	05-Dec-2019 14:55:07	Publishing an artifact: Jalview getdown launcher
simple	05-Dec-2019 14:55:07	Finished publishing of artifact Shared artifact: [Jalview getdown launcher], pattern: [**/*] anchored at: [getdown/files] in 25.58 ms
simple	05-Dec-2019 14:55:07	Running post build plugin 'Artifactory Release Management Staging'
simple	05-Dec-2019 14:55:07	Running post build plugin 'Artifactory Build Info Copier'
simple	05-Dec-2019 14:55:07	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	05-Dec-2019 14:55:07	Running post build plugin 'npm Cache Cleanup'
simple	05-Dec-2019 14:55:07	Running post build plugin 'Clover Results Collector'
simple	05-Dec-2019 14:55:07	Running post build plugin 'Docker Container Cleanup'
simple	05-Dec-2019 14:55:07	Finalising the build...
simple	05-Dec-2019 14:55:07	Stopping timer.
simple	05-Dec-2019 14:55:07	Build JB-GPC73-JOB1-1 completed.
simple	05-Dec-2019 14:55:07	Running on server: post build plugin 'NCover Results Collector'
simple	05-Dec-2019 14:55:07	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	05-Dec-2019 14:55:07	Running on server: post build plugin 'Clover Delta Calculator'
simple	05-Dec-2019 14:55:07	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	05-Dec-2019 14:55:07	All post build plugins have finished
simple	05-Dec-2019 14:55:07	Generating build results summary...
simple	05-Dec-2019 14:55:07	Saving build results to disk...
simple	05-Dec-2019 14:55:07	Logging substituted variables...
simple	05-Dec-2019 14:55:07	Indexing build results...
simple	05-Dec-2019 14:55:07	Finished building JB-GPC73-JOB1-1.