Build: #1 was successful
Job: Default Job was successful
Build log
The build generated 226 lines of output. Download or view full build log
| 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 |
| 05-Dec-2019 14:53:14 | |
| 05-Dec-2019 14:53:14 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1 |
| 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) |
| 05-Dec-2019 14:53:14 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 05-Dec-2019 14:53:14 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1 |
| 05-Dec-2019 14:53:14 | Updating source code to revision: 57b0dee0192a285d36bd698655e639978487a30a |
| 05-Dec-2019 14:53:14 | Fetching 'refs/heads/alpha/JAL-3362_Jalview_212_alpha' from 'http://source.jalview.org/git/jalview.git'. |
| 05-Dec-2019 14:53:14 | Checking out revision 57b0dee0192a285d36bd698655e639978487a30a. |
| 05-Dec-2019 14:53:14 | Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1/.git'. |
| 05-Dec-2019 14:53:14 | Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1'... |
| 05-Dec-2019 14:53:14 | done. |
| 05-Dec-2019 14:53:35 | Switched to a new branch 'alpha/JAL-3362_Jalview_212_alpha' |
| 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. |
| 05-Dec-2019 14:53:35 | Updated source code to revision: 57b0dee0192a285d36bd698655e639978487a30a |
| 05-Dec-2019 14:53:35 | Finished task 'Checkout Default Repository' with result: Success |
| 05-Dec-2019 14:53:35 | Running pre-build action: VCS Version Collector |
| 05-Dec-2019 14:53:35 | Running pre-build action: Artifactory Release Staging |
| 05-Dec-2019 14:53:35 | Substituting variable: ${bamboo.planKey} with JB-GPC73 |
| 05-Dec-2019 14:53:35 | Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 05-Dec-2019 14:53:35 | Bamboo Artifactory Plugin version: 2.6.2 |
| 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)' ... running command line: /home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC73 clean makeDist shadowJar getdown ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=alpha/JAL-3362_Jalview_212_alpha bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=alpha/JAL-3362_Jalview_212_alpha bamboo_repository_revision_number=57b0dee0192a285d36bd698655e639978487a30a bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC73-JOB1-1 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GPC73-JOB1 bamboo_repository_12157032_git_username= bamboo_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 bamboo_shortPlanName=alpha-JAL-3362_Jalview_212_alpha bamboo_repository_12157032_branch_name=alpha/JAL-3362_Jalview_212_alpha bamboo_planRepository_name=Jalview Git LOGNAME=bamboo bamboo_buildNumber=1 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_capability_system_jdk_OpenJDK_11_JRE_only=/home/bamboo/buildtools/jvm/jre11_x64_linux bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC73-JOB1-1 bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_repository_12157032_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_agentId=196609 bamboo_planName=Jalview Builds - Getdown Plan Channel - alpha-JAL-3362_Jalview_212_alpha bamboo_shortPlanKey=GPC73 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/OpenJDK11/jdk-11 bamboo_planRepository_revision=57b0dee0192a285d36bd698655e639978487a30a bamboo_buildTimeStamp=2019-12-05T14:53:14.284Z bamboo_repository_12157032_revision_number=57b0dee0192a285d36bd698655e639978487a30a bamboo_repository_git_branch=alpha/JAL-3362_Jalview_212_alpha bamboo_buildResultKey=JB-GPC73-JOB1-1 bamboo_repository_branch_name=alpha/JAL-3362_Jalview_212_alpha bamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - alpha-JAL-3362_Jalview_212_alpha - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=57b0dee0192a285d36bd698655e639978487a30a SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Git JAVA_HOME=/home/bamboo/buildtools/OpenJDK11/jdk-11/ bamboo_dependenciesDisabled=false LANG=en_GB.UTF-8 bamboo_buildFailed=false bamboo_repository_12157032_name=Jalview Git bamboo_planRepository_branch=alpha/JAL-3362_Jalview_212_alpha bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_branchDisplayName=alpha/JAL-3362_Jalview_212_alpha bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=alpha/JAL-3362_Jalview_212_alpha _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr bamboo_capability_system_jdk_JDK=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64 bamboo_plan_storageTag=plan-11960527 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_repository_12157032_git_branch=alpha/JAL-3362_Jalview_212_alpha bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_ManualBuildTriggerReason_userName=jprocter bamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1 bamboo_planKey=JB-GPC73 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= bamboo_capability_system_jdk_JDK_1_8=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64 HOME=/home/bamboo bamboo_planRepository_1_branchName=alpha/JAL-3362_Jalview_212_alpha PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 05-Dec-2019 14:53:37 | Starting a Gradle Daemon, 1 incompatible and 1 stopped Daemons could not be reused, use --status for details |
| 05-Dec-2019 14:53:45 | |
| 05-Dec-2019 14:53:45 | > Configure project : |
| 05-Dec-2019 14:53:45 | Using a BUILD profile. appbase=https://builds.jalview.org/browse/JB-GPC73/latest/artifact/shared/getdown-channel/11 |
| 05-Dec-2019 14:53:46 | Setting target compatibility to 11 |
| 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 |
| 05-Dec-2019 14:53:46 | |
| 05-Dec-2019 14:53:46 | > Task :clean UP-TO-DATE |
| 05-Dec-2019 14:53:46 | > Task :cleanPackageDir UP-TO-DATE |
| 05-Dec-2019 14:53:48 | > Task :copyHelp |
| 05-Dec-2019 14:53:51 | > Task :buildIndices |
| 05-Dec-2019 14:53:53 | |
| 05-Dec-2019 14:53:53 | > Task :compileJava |
| 05-Dec-2019 14:53:53 | Setting target compatibility to 11 |
| 05-Dec-2019 14:54:10 | Note: Some input files use or override a deprecated API. |
| 05-Dec-2019 14:54:10 | Note: Recompile with -Xlint:deprecation for details. |
| 05-Dec-2019 14:54:10 | Note: Some input files use unchecked or unsafe operations. |
| 05-Dec-2019 14:54:10 | Note: Recompile with -Xlint:unchecked for details. |
| 05-Dec-2019 14:54:14 | |
| 05-Dec-2019 14:54:14 | > Task :processResources |
| 05-Dec-2019 14:54:14 | > Task :classes |
| 05-Dec-2019 14:54:14 | > Task :setGitVals UP-TO-DATE |
| 05-Dec-2019 14:54:15 | > Task :createBuildProperties |
| 05-Dec-2019 14:54:17 | > Task :compileLinkCheck |
| 05-Dec-2019 14:54:17 | > Task :deleteBuildingHTML UP-TO-DATE |
| 05-Dec-2019 14:54:18 | > Task :convertBuildingMD |
| 05-Dec-2019 14:54:18 | > Task :syncDocs |
| 05-Dec-2019 14:54:18 | > Task :syncResources |
| 05-Dec-2019 14:54:18 | > Task :prepare |
| 05-Dec-2019 14:54:19 | |
| 05-Dec-2019 14:54:19 | > Task :linkCheck |
| 05-Dec-2019 14:54:19 | Checking help file links |
| 05-Dec-2019 14:54:19 | |
| 05-Dec-2019 14:54:19 | Results: |
| 05-Dec-2019 14:54:19 | 136 distinct help targets |
| 05-Dec-2019 14:54:19 | 136 help mappings |
| 05-Dec-2019 14:54:19 | 0 invalid targets |
| 05-Dec-2019 14:54:19 | 24 unused targets |
| 05-Dec-2019 14:54:19 | uniprotfetcher: html/features/uniprotsequencefetcher.html |
| 05-Dec-2019 14:54:19 | overviewprefs: html/features/preferences.html#overview |
| 05-Dec-2019 14:54:19 | cdnafeatures: html/features/codingfeatures.html |
| 05-Dec-2019 14:54:19 | ensemblfetch: html/features/ensemblsequencefetcher.html |
| 05-Dec-2019 14:54:19 | io.modellerpir: html/io/modellerpir.html |
| 05-Dec-2019 14:54:19 | pdbmcviewer: html/features/pdbviewer.html |
| 05-Dec-2019 14:54:19 | groovy.colours: html/features/groovy.html#groovyColours |
| 05-Dec-2019 14:54:19 | seqmappings: html/features/seqmappings.html |
| 05-Dec-2019 14:54:19 | uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts |
| 05-Dec-2019 14:54:19 | splitframe.mirrorfonts: html/features/splitView.html#mirror |
| 05-Dec-2019 14:54:19 | subtMatrices.pam250: html/calculations/scorematrices.html#pam250 |
| 05-Dec-2019 14:54:19 | search: html/features/search.html |
| 05-Dec-2019 14:54:19 | viewingpdbs.reps: html/features/viewingpdbs.html#viewreps |
| 05-Dec-2019 14:54:19 | alformats: html/io/fileformats.html |
| 05-Dec-2019 14:54:19 | strucprefs: html/features/preferences.html#structure |
| 05-Dec-2019 14:54:19 | siftsmapping: html/features/siftsmapping.html |
| 05-Dec-2019 14:54:19 | chimera.annotxfer: html/features/chimera.html#annotxfer |
| 05-Dec-2019 14:54:19 | pdbfts: html/features/pdbsequencefetcher.html#pdbfts |
| 05-Dec-2019 14:54:19 | newkeys: html/features/newkeystrokes.html |
| 05-Dec-2019 14:54:19 | seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature |
| 05-Dec-2019 14:54:19 | jalarchive: html/features/jalarchive.html |
| 05-Dec-2019 14:54:19 | newsreader: html/webServices/newsreader.html |
| 05-Dec-2019 14:54:19 | popMenuAddref: html/menus/popupMenu.html#addrefannot |
| 05-Dec-2019 14:54:19 | overview: html/features/overview.html |
| 05-Dec-2019 14:54:19 | 0 invalid map urls |
| 05-Dec-2019 14:54:19 | 0 invalid image attributes |
| 05-Dec-2019 14:54:19 | 386 internal href links (72 with anchors) |
| 05-Dec-2019 14:54:19 | 0 invalid internal href links |
| 05-Dec-2019 14:54:19 | 0 invalid internal anchor links |
| 05-Dec-2019 14:54:19 | 89 external href links |
| 05-Dec-2019 14:54:19 | External links not verified as internet not available |
| 05-Dec-2019 14:54:19 | *** Success *** |
| 05-Dec-2019 14:54:20 | |
| 05-Dec-2019 14:54:20 | > Task :jar |
| 05-Dec-2019 14:54:21 | > Task :syncJars |
| 05-Dec-2019 14:54:21 | > Task :makeDist |
| 05-Dec-2019 14:54:30 | > Task :shadowJar |
| 05-Dec-2019 14:54:30 | > Task :getdownWebsite |
| 05-Dec-2019 14:54:32 | |
| 05-Dec-2019 14:54:32 | > Task :getdownDigest |
| 05-Dec-2019 14:54:32 | Generating digest file './getdown/website/11/digest.txt'... |
| 05-Dec-2019 14:54:32 | Generating digest file './getdown/website/11/digest2.txt'... |
| 05-Dec-2019 14:54:32 | |
| 05-Dec-2019 14:54:32 | > Task :getdown |
| 05-Dec-2019 14:54:32 | |
| 05-Dec-2019 14:54:32 | BUILD SUCCESSFUL in 56s |
| 05-Dec-2019 14:54:32 | 19 actionable tasks: 16 executed, 3 up-to-date |
| 05-Dec-2019 14:54:32 | Finished task 'Jalview distribution for Java 11' with result: Success |
| 05-Dec-2019 14:54:32 | Substituting variable: ${bamboo.planKey} with JB-GPC73 |
| 05-Dec-2019 14:54:32 | Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 05-Dec-2019 14:54:32 | Bamboo Artifactory Plugin version: 2.6.2 |
| 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)' ... running command line: /home/bamboo/buildtools/gradle/bin/gradle -x test -x clean -PCHANNEL=BUILD -PJAVA_VERSION=1.8 -Pbamboo_planKey=JB-GPC73 shadowJar getdown ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=alpha/JAL-3362_Jalview_212_alpha bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=alpha/JAL-3362_Jalview_212_alpha bamboo_repository_revision_number=57b0dee0192a285d36bd698655e639978487a30a bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC73-JOB1-1 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GPC73-JOB1 bamboo_repository_12157032_git_username= bamboo_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 bamboo_shortPlanName=alpha-JAL-3362_Jalview_212_alpha bamboo_repository_12157032_branch_name=alpha/JAL-3362_Jalview_212_alpha bamboo_planRepository_name=Jalview Git LOGNAME=bamboo bamboo_buildNumber=1 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_capability_system_jdk_OpenJDK_11_JRE_only=/home/bamboo/buildtools/jvm/jre11_x64_linux bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC73-JOB1-1 bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_repository_12157032_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_agentId=196609 bamboo_planName=Jalview Builds - Getdown Plan Channel - alpha-JAL-3362_Jalview_212_alpha bamboo_shortPlanKey=GPC73 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/OpenJDK11/jdk-11 bamboo_planRepository_revision=57b0dee0192a285d36bd698655e639978487a30a bamboo_buildTimeStamp=2019-12-05T14:53:14.284Z bamboo_repository_12157032_revision_number=57b0dee0192a285d36bd698655e639978487a30a bamboo_repository_git_branch=alpha/JAL-3362_Jalview_212_alpha bamboo_buildResultKey=JB-GPC73-JOB1-1 bamboo_repository_branch_name=alpha/JAL-3362_Jalview_212_alpha bamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - alpha-JAL-3362_Jalview_212_alpha - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=57b0dee0192a285d36bd698655e639978487a30a SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Git bamboo_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 JAVA_HOME=/home/bamboo/buildtools/OpenJDK11/jdk-11/ bamboo_dependenciesDisabled=false LANG=en_GB.UTF-8 bamboo_buildFailed=false bamboo_repository_12157032_name=Jalview Git bamboo_planRepository_branch=alpha/JAL-3362_Jalview_212_alpha bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_branchDisplayName=alpha/JAL-3362_Jalview_212_alpha bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=alpha/JAL-3362_Jalview_212_alpha _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr bamboo_capability_system_jdk_JDK=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64 bamboo_plan_storageTag=plan-11960527 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_repository_12157032_git_branch=alpha/JAL-3362_Jalview_212_alpha bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_ManualBuildTriggerReason_userName=jprocter bamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/JB-GPC73-JOB1 bamboo_planKey=JB-GPC73 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= bamboo_capability_system_jdk_JDK_1_8=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64 HOME=/home/bamboo bamboo_planRepository_1_branchName=alpha/JAL-3362_Jalview_212_alpha PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 05-Dec-2019 14:54:34 | |
| 05-Dec-2019 14:54:34 | > Configure project : |
| 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 |
| 05-Dec-2019 14:54:34 | Setting target compatibility to 1.8 |
| 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 |
| 05-Dec-2019 14:54:36 | |
| 05-Dec-2019 14:54:36 | > Task :compileJava |
| 05-Dec-2019 14:54:36 | Setting target compatibility to 1.8 |
| 05-Dec-2019 14:54:48 | Note: Some input files use or override a deprecated API. |
| 05-Dec-2019 14:54:48 | Note: Recompile with -Xlint:deprecation for details. |
| 05-Dec-2019 14:54:48 | Note: Some input files use unchecked or unsafe operations. |
| 05-Dec-2019 14:54:48 | Note: Recompile with -Xlint:unchecked for details. |
| 05-Dec-2019 14:54:49 | |
| 05-Dec-2019 14:54:49 | > Task :processResources UP-TO-DATE |
| 05-Dec-2019 14:54:49 | > Task :classes |
| 05-Dec-2019 14:54:49 | > Task :cleanPackageDir |
| 05-Dec-2019 14:54:49 | > Task :copyHelp UP-TO-DATE |
| 05-Dec-2019 14:54:51 | > Task :buildIndices |
| 05-Dec-2019 14:54:51 | > Task :setGitVals UP-TO-DATE |
| 05-Dec-2019 14:54:51 | > Task :createBuildProperties |
| 05-Dec-2019 14:54:53 | > Task :compileLinkCheck |
| 05-Dec-2019 14:54:53 | > Task :deleteBuildingHTML |
| 05-Dec-2019 14:54:53 | > Task :convertBuildingMD |
| 05-Dec-2019 14:54:53 | > Task :syncDocs UP-TO-DATE |
| 05-Dec-2019 14:54:53 | > Task :syncResources UP-TO-DATE |
| 05-Dec-2019 14:54:53 | > Task :prepare UP-TO-DATE |
| 05-Dec-2019 14:54:54 | |
| 05-Dec-2019 14:54:54 | > Task :linkCheck |
| 05-Dec-2019 14:54:54 | Checking help file links |
| 05-Dec-2019 14:54:54 | |
| 05-Dec-2019 14:54:54 | Results: |
| 05-Dec-2019 14:54:54 | 136 distinct help targets |
| 05-Dec-2019 14:54:54 | 136 help mappings |
| 05-Dec-2019 14:54:54 | 0 invalid targets |
| 05-Dec-2019 14:54:54 | 24 unused targets |
| 05-Dec-2019 14:54:54 | uniprotfetcher: html/features/uniprotsequencefetcher.html |
| 05-Dec-2019 14:54:54 | overviewprefs: html/features/preferences.html#overview |
| 05-Dec-2019 14:54:54 | cdnafeatures: html/features/codingfeatures.html |
| 05-Dec-2019 14:54:54 | ensemblfetch: html/features/ensemblsequencefetcher.html |
| 05-Dec-2019 14:54:54 | io.modellerpir: html/io/modellerpir.html |
| 05-Dec-2019 14:54:54 | pdbmcviewer: html/features/pdbviewer.html |
| 05-Dec-2019 14:54:54 | groovy.colours: html/features/groovy.html#groovyColours |
| 05-Dec-2019 14:54:54 | seqmappings: html/features/seqmappings.html |
| 05-Dec-2019 14:54:54 | uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts |
| 05-Dec-2019 14:54:54 | splitframe.mirrorfonts: html/features/splitView.html#mirror |
| 05-Dec-2019 14:54:54 | subtMatrices.pam250: html/calculations/scorematrices.html#pam250 |
| 05-Dec-2019 14:54:54 | search: html/features/search.html |
| 05-Dec-2019 14:54:54 | viewingpdbs.reps: html/features/viewingpdbs.html#viewreps |
| 05-Dec-2019 14:54:54 | alformats: html/io/fileformats.html |
| 05-Dec-2019 14:54:54 | strucprefs: html/features/preferences.html#structure |
| 05-Dec-2019 14:54:54 | siftsmapping: html/features/siftsmapping.html |
| 05-Dec-2019 14:54:54 | chimera.annotxfer: html/features/chimera.html#annotxfer |
| 05-Dec-2019 14:54:54 | pdbfts: html/features/pdbsequencefetcher.html#pdbfts |
| 05-Dec-2019 14:54:54 | newkeys: html/features/newkeystrokes.html |
| 05-Dec-2019 14:54:54 | seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature |
| 05-Dec-2019 14:54:54 | jalarchive: html/features/jalarchive.html |
| 05-Dec-2019 14:54:54 | newsreader: html/webServices/newsreader.html |
| 05-Dec-2019 14:54:54 | popMenuAddref: html/menus/popupMenu.html#addrefannot |
| 05-Dec-2019 14:54:54 | overview: html/features/overview.html |
| 05-Dec-2019 14:54:54 | 0 invalid map urls |
| 05-Dec-2019 14:54:54 | 0 invalid image attributes |
| 05-Dec-2019 14:54:54 | 386 internal href links (72 with anchors) |
| 05-Dec-2019 14:54:54 | 0 invalid internal href links |
| 05-Dec-2019 14:54:54 | 0 invalid internal anchor links |
| 05-Dec-2019 14:54:54 | 89 external href links |
| 05-Dec-2019 14:54:54 | External links not verified as internet not available |
| 05-Dec-2019 14:54:54 | *** Success *** |
| 05-Dec-2019 14:54:56 | |
| 05-Dec-2019 14:54:56 | > Task :jar |
| 05-Dec-2019 14:54:56 | > Task :syncJars |
| 05-Dec-2019 14:54:56 | > Task :makeDist |
| 05-Dec-2019 14:55:04 | > Task :shadowJar |
| 05-Dec-2019 14:55:04 | > Task :getdownWebsite |
| 05-Dec-2019 14:55:06 | |
| 05-Dec-2019 14:55:06 | > Task :getdownDigest |
| 05-Dec-2019 14:55:06 | Generating digest file './getdown/website/1.8/digest.txt'... |
| 05-Dec-2019 14:55:06 | Generating digest file './getdown/website/1.8/digest2.txt'... |
| 05-Dec-2019 14:55:06 | |
| 05-Dec-2019 14:55:06 | > Task :getdown |
| 05-Dec-2019 14:55:06 | |
| 05-Dec-2019 14:55:06 | BUILD SUCCESSFUL in 33s |
| 05-Dec-2019 14:55:06 | 18 actionable tasks: 14 executed, 4 up-to-date |
| 05-Dec-2019 14:55:06 | Finished task 'Jalview distribution for Java 8' with result: Success |
| 05-Dec-2019 14:55:06 | Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled |
| 05-Dec-2019 14:55:06 | Running post build plugin 'NCover Results Collector' |
| 05-Dec-2019 14:55:06 | Running post build plugin 'Artifact Copier' |
| 05-Dec-2019 14:55:06 | Publishing an artifact: Jalview executables |
| 05-Dec-2019 14:55:07 | Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 264.8 ms |
| 05-Dec-2019 14:55:07 | Publishing an artifact: install4j installers |
| 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. |
| 05-Dec-2019 14:55:07 | The artifact hasn't been successfully published after 12.99 ms |
| 05-Dec-2019 14:55:07 | Publishing an artifact: getdown-channel |
| 05-Dec-2019 14:55:07 | Finished publishing of artifact Shared artifact: [getdown-channel], pattern: [**/*] anchored at: [getdown/website] in 584.2 ms |
| 05-Dec-2019 14:55:07 | Publishing an artifact: Jalview getdown launcher |
| 05-Dec-2019 14:55:07 | Finished publishing of artifact Shared artifact: [Jalview getdown launcher], pattern: [**/*] anchored at: [getdown/files] in 25.58 ms |
| 05-Dec-2019 14:55:07 | Running post build plugin 'Artifactory Release Management Staging' |
| 05-Dec-2019 14:55:07 | Running post build plugin 'Artifactory Build Info Copier' |
| 05-Dec-2019 14:55:07 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 05-Dec-2019 14:55:07 | Running post build plugin 'npm Cache Cleanup' |
| 05-Dec-2019 14:55:07 | Running post build plugin 'Clover Results Collector' |
| 05-Dec-2019 14:55:07 | Running post build plugin 'Docker Container Cleanup' |
| 05-Dec-2019 14:55:07 | Finalising the build... |
| 05-Dec-2019 14:55:07 | Stopping timer. |
| 05-Dec-2019 14:55:07 | Build JB-GPC73-JOB1-1 completed. |
| 05-Dec-2019 14:55:07 | Running on server: post build plugin 'NCover Results Collector' |
| 05-Dec-2019 14:55:07 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 05-Dec-2019 14:55:07 | Running on server: post build plugin 'Clover Delta Calculator' |
| 05-Dec-2019 14:55:07 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 05-Dec-2019 14:55:07 | All post build plugins have finished |
| 05-Dec-2019 14:55:07 | Generating build results summary... |
| 05-Dec-2019 14:55:07 | Saving build results to disk... |
| 05-Dec-2019 14:55:07 | Logging substituted variables... |
| 05-Dec-2019 14:55:07 | Indexing build results... |
| 05-Dec-2019 14:55:07 | Finished building JB-GPC73-JOB1-1. |