simple	06-Jul-2020 17:04:06	Build Jalview Builds - Gradle build with getdown and install4j - bug-JAL-3628_Unable_to_save_update_to_existing_file_in_Windows - Default Job #3 (JB-JGP14-JOB1-3) started building on agent Default Agent
simple	06-Jul-2020 17:04:06	
simple	06-Jul-2020 17:04:06	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1
simple	06-Jul-2020 17:04:06	Executing build Jalview Builds - Gradle build with getdown and install4j - bug-JAL-3628_Unable_to_save_update_to_existing_file_in_Windows - Default Job #3 (JB-JGP14-JOB1-3)
simple	06-Jul-2020 17:04:06	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	06-Jul-2020 17:04:06	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1
simple	06-Jul-2020 17:04:06	Updating source code to revision: 06d91fe495898df93fd6fcdc305f304cf9f3aa16
simple	06-Jul-2020 17:04:06	Fetching 'refs/heads/bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows' from 'http://source.jalview.org/git/jalview.git'.
simple	06-Jul-2020 17:04:07	Checking out revision 06d91fe495898df93fd6fcdc305f304cf9f3aa16.
simple	06-Jul-2020 17:04:08	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164
simple	06-Jul-2020 17:04:08	   1de3658..06d91fe  bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows -> origin/bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows
simple	06-Jul-2020 17:04:08	Already on 'bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows'
simple	06-Jul-2020 17:04:08	Your branch is behind 'origin/bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows' by 2 commits, and can be fast-forwarded.
simple	06-Jul-2020 17:04:08	  (use "git pull" to update your local branch)
simple	06-Jul-2020 17:04:08	HEAD is now at 06d91fe Merge branch 'bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows' of https://source.jalview.org/git/jalview into bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows
simple	06-Jul-2020 17:04:08	Updated source code to revision: 06d91fe495898df93fd6fcdc305f304cf9f3aa16
simple	06-Jul-2020 17:04:08	Finished task 'Checkout Default Repository' with result: Success
simple	06-Jul-2020 17:04:08	Running pre-build action: VCS Version Collector
simple	06-Jul-2020 17:04:08	Running pre-build action: Artifactory Release Staging
command	06-Jul-2020 17:04:08	Substituting variable: ${bamboo.planKey} with JB-JGP14
simple	06-Jul-2020 17:04:08	Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	06-Jul-2020 17:04:08	Bamboo Artifactory Plugin version: 2.6.2
command	06-Jul-2020 17:04:08	Beginning to execute external process for build 'Jalview Builds - Gradle build with getdown and install4j - bug-JAL-3628_Unable_to_save_update_to_existing_file_in_Windows - Default Job #3 (JB-JGP14-JOB1-3)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PJAVA_VERSION=11 -PCHANNEL=BUILD -Pbamboo_planKey=JB-JGP14 clean makeDist shadowJar getdown installers\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows\nbamboo_repository_revision_number=06d91fe495898df93fd6fcdc305f304cf9f3aa16\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-JGP14-JOB1-3\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_24707116_name=Jalview Git\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-JGP14-JOB1\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=bug-JAL-3628_Unable_to_save_update_to_existing_file_in_Windows\nbamboo_repository_24707116_revision_number=06d91fe495898df93fd6fcdc305f304cf9f3aa16\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=3\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-JGP14-JOB1-3\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - 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build	06-Jul-2020 17:04:09	
build	06-Jul-2020 17:04:09	> Configure project :
build	06-Jul-2020 17:04:09	HEADLESS BUILD
build	06-Jul-2020 17:04:09	Using a BUILD profile.
build	06-Jul-2020 17:04:10	
build	06-Jul-2020 17:04:10	> Task :clean
build	06-Jul-2020 17:04:10	> Task :cleanPackageDir
build	06-Jul-2020 17:04:10	> Task :copyHelp
build	06-Jul-2020 17:04:11	> Task :buildIndices
build	06-Jul-2020 17:04:13	
build	06-Jul-2020 17:04:13	> Task :compileJava
build	06-Jul-2020 17:04:13	Setting target compatibility to 11
error	06-Jul-2020 17:04:17	Note: Some input files use or override a deprecated API.
error	06-Jul-2020 17:04:17	Note: Recompile with -Xlint:deprecation for details.
error	06-Jul-2020 17:04:17	Note: Some input files use unchecked or unsafe operations.
error	06-Jul-2020 17:04:17	Note: Recompile with -Xlint:unchecked for details.
build	06-Jul-2020 17:04:17	
build	06-Jul-2020 17:04:17	> Task :processResources
build	06-Jul-2020 17:04:17	> Task :classes
build	06-Jul-2020 17:04:17	> Task :setGitVals UP-TO-DATE
build	06-Jul-2020 17:04:17	> Task :createBuildProperties
build	06-Jul-2020 17:04:18	> Task :compileLinkCheck
build	06-Jul-2020 17:04:18	> Task :cleanBuildingHTML UP-TO-DATE
build	06-Jul-2020 17:04:19	> Task :convertBuildingMD
build	06-Jul-2020 17:04:19	> Task :syncDocs
build	06-Jul-2020 17:04:19	> Task :syncResources
build	06-Jul-2020 17:04:19	> Task :prepare
build	06-Jul-2020 17:04:19	
build	06-Jul-2020 17:04:19	> Task :linkCheck
build	06-Jul-2020 17:04:19	Checking help file links
build	06-Jul-2020 17:04:19	
build	06-Jul-2020 17:04:19	Results:
build	06-Jul-2020 17:04:19	138 distinct help targets
build	06-Jul-2020 17:04:19	138 help mappings
build	06-Jul-2020 17:04:19	0 invalid targets
build	06-Jul-2020 17:04:19	24 unused targets
build	06-Jul-2020 17:04:19	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	06-Jul-2020 17:04:19	    overviewprefs: html/features/preferences.html#overview
build	06-Jul-2020 17:04:19	    cdnafeatures: html/features/codingfeatures.html
build	06-Jul-2020 17:04:19	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	06-Jul-2020 17:04:19	    io.modellerpir: html/io/modellerpir.html
build	06-Jul-2020 17:04:19	    pdbmcviewer: html/features/pdbviewer.html
build	06-Jul-2020 17:04:19	    groovy.colours: html/features/groovy.html#groovyColours
build	06-Jul-2020 17:04:19	    seqmappings: html/features/seqmappings.html
build	06-Jul-2020 17:04:19	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	06-Jul-2020 17:04:19	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	06-Jul-2020 17:04:19	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	06-Jul-2020 17:04:19	    search: html/features/search.html
build	06-Jul-2020 17:04:19	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	06-Jul-2020 17:04:19	    alformats: html/io/fileformats.html
build	06-Jul-2020 17:04:19	    strucprefs: html/features/preferences.html#structure
build	06-Jul-2020 17:04:19	    siftsmapping: html/features/siftsmapping.html
build	06-Jul-2020 17:04:19	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	06-Jul-2020 17:04:19	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	06-Jul-2020 17:04:19	    newkeys: html/features/newkeystrokes.html
build	06-Jul-2020 17:04:19	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	06-Jul-2020 17:04:19	    jalarchive: html/features/jalarchive.html
build	06-Jul-2020 17:04:19	    newsreader: html/webServices/newsreader.html
build	06-Jul-2020 17:04:19	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	06-Jul-2020 17:04:19	    overview: html/features/overview.html
build	06-Jul-2020 17:04:19	0 invalid map urls
build	06-Jul-2020 17:04:19	0 invalid image attributes
build	06-Jul-2020 17:04:19	386 internal href links (74 with anchors)
build	06-Jul-2020 17:04:19	0 invalid internal href links
build	06-Jul-2020 17:04:19	0 invalid internal anchor links
build	06-Jul-2020 17:04:19	87 external href links
build	06-Jul-2020 17:04:19	External links not verified as internet not available
build	06-Jul-2020 17:04:19	*** Success ***
build	06-Jul-2020 17:04:20	
build	06-Jul-2020 17:04:20	> Task :jar
build	06-Jul-2020 17:04:21	> Task :syncJars
build	06-Jul-2020 17:04:21	> Task :makeDist
build	06-Jul-2020 17:04:27	> Task :shadowJar
build	06-Jul-2020 17:04:27	> Task :getdownWebsite
build	06-Jul-2020 17:04:28	
build	06-Jul-2020 17:04:28	> Task :getdownDigest
build	06-Jul-2020 17:04:28	Generating digest file './getdown/website/11/digest.txt'...
build	06-Jul-2020 17:04:28	Generating digest file './getdown/website/11/digest2.txt'...
build	06-Jul-2020 17:04:28	
build	06-Jul-2020 17:04:28	> Task :getdown
error	06-Jul-2020 17:04:28	2020/07/06 17:04:27:543 WARNING Starting without install4j classes
error	06-Jul-2020 17:04:28	2020/07/06 17:04:28:038 WARNING Starting without install4j classes
build	06-Jul-2020 17:04:28	> Task :copyInstall4jTemplate
build	06-Jul-2020 17:04:30	
build	06-Jul-2020 17:04:30	> Task :installers
build	06-Jul-2020 17:04:30	Using projectFile /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/utils/install4j/jalview-install4j-conf.install4j
build	06-Jul-2020 17:04:32	install4j version 8.0.5 (build 8155), built on 2020-03-16
build	06-Jul-2020 17:04:32	Using Java 1.8.0_252 from /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.252.b09-2.el7_8.x86_64/jre
build	06-Jul-2020 17:04:32	Registered to Jalview, University of Dundee
build	06-Jul-2020 17:04:32	
build	06-Jul-2020 17:04:32	Loading config file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/utils/install4j/jalview-install4j-conf.install4j
build	06-Jul-2020 17:04:33	Creating media file 'Windows x64 EXE Installer':
build	06-Jul-2020 17:04:33	  Collecting files:
build	06-Jul-2020 17:04:33	  [WARNING] The version of the bundled JRE is too low. It should be at least 11!
build	06-Jul-2020 17:04:33	  Compiling launchers:
build	06-Jul-2020 17:04:33	    Compiling launcher 'Jalview Launcher':
build	06-Jul-2020 17:04:33	      Generating VM options file jalview.vmoptions.
build	06-Jul-2020 17:04:33	  Creating media file: 
build	06-Jul-2020 17:04:33	    Using custom installer icon: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/utils/install4j/../../resources/images/jalview_logos.ico
build	06-Jul-2020 17:04:35	    Zipping custom code & resources JAR file
build	06-Jul-2020 17:04:35	    Identifying components
build	06-Jul-2020 17:04:35	    Adding JRE (jre-11-windows-x64.tar.gz)
build	06-Jul-2020 17:04:35	    Shrinking runtime
build	06-Jul-2020 17:04:36	  
build	06-Jul-2020 17:04:36	Creating media file 'macOS Disk Image':
build	06-Jul-2020 17:04:36	  Collecting files:
build	06-Jul-2020 17:04:36	  Compiling launchers:
build	06-Jul-2020 17:04:36	    Compiling launcher 'Jalview Launcher':
build	06-Jul-2020 17:04:36	      Generating VM options file vmoptions.txt.
build	06-Jul-2020 17:04:36	  Creating media file: 
build	06-Jul-2020 17:04:36	    Identifying components
build	06-Jul-2020 17:04:36	      Shrinking runtime
build	06-Jul-2020 17:04:37	  
build	06-Jul-2020 17:04:37	Creating media file 'Linux x64 Shell Installer':
build	06-Jul-2020 17:04:37	  Collecting files:
build	06-Jul-2020 17:04:37	  [WARNING] The version of the bundled JRE is too low. It should be at least 11!
build	06-Jul-2020 17:04:37	  Compiling launchers:
build	06-Jul-2020 17:04:37	    Compiling launcher 'Jalview Launcher':
build	06-Jul-2020 17:04:37	      Generating launcher script file
build	06-Jul-2020 17:04:37	      Generating VM options file .i4j_external_735/jalview.vmoptions.
build	06-Jul-2020 17:04:37	  Creating media file: 
build	06-Jul-2020 17:04:37	    Generating launcher script file
build	06-Jul-2020 17:04:37	    Zipping custom code & resources JAR file
build	06-Jul-2020 17:04:37	    Identifying components
build	06-Jul-2020 17:04:37	    Adding JRE (jre-11-linux-x64.tar.gz)
build	06-Jul-2020 17:04:37	    Shrinking runtime
build	06-Jul-2020 17:04:38	  
build	06-Jul-2020 17:04:38	Creating media file 'Unix .tar.gz Archive':
build	06-Jul-2020 17:04:38	  Collecting files:
build	06-Jul-2020 17:04:38	  Compiling launchers:
build	06-Jul-2020 17:04:38	    Compiling launcher 'Jalview Launcher':
build	06-Jul-2020 17:04:38	      Generating launcher script file
build	06-Jul-2020 17:04:38	      Generating VM options file .i4j_external_735/jalview.vmoptions.
build	06-Jul-2020 17:04:38	  Creating media file: 
build	06-Jul-2020 17:04:38	    Identifying components
build	06-Jul-2020 17:04:38	      Shrinking runtime
build	06-Jul-2020 17:04:38	  
build	06-Jul-2020 17:04:38	Creating media file 'Unix Shell Installer':
build	06-Jul-2020 17:04:38	  Collecting files:
build	06-Jul-2020 17:04:38	  Compiling launchers:
build	06-Jul-2020 17:04:38	    Compiling launcher 'Jalview Launcher':
build	06-Jul-2020 17:04:38	      Generating launcher script file
build	06-Jul-2020 17:04:38	      Generating VM options file .i4j_external_735/jalview.vmoptions.
build	06-Jul-2020 17:04:38	  Creating media file: 
build	06-Jul-2020 17:04:38	    Generating launcher script file
build	06-Jul-2020 17:04:39	    Zipping custom code & resources JAR file
build	06-Jul-2020 17:04:39	    Identifying components
build	06-Jul-2020 17:04:39	    Shrinking runtime
build	06-Jul-2020 17:04:39	  
build	06-Jul-2020 17:04:39	Compressing 5 media files with 4 threads:
build	06-Jul-2020 17:04:55	
build	06-Jul-2020 17:04:55	Compressed media file 'macOS Disk Image':
build	06-Jul-2020 17:04:55	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/11
build	06-Jul-2020 17:04:56	  The name of the media file is Jalview_Build-2_11_1_0-macos-java_11.dmg.
build	06-Jul-2020 17:04:56	  The size of the media file is 82.0 MB
build	06-Jul-2020 17:04:58	
build	06-Jul-2020 17:04:58	Compressed media file 'Unix .tar.gz Archive':
build	06-Jul-2020 17:04:58	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/11
build	06-Jul-2020 17:04:58	  The name of the media file is jalview_build-2_11_1_0-unix-java_11.tar.gz.
build	06-Jul-2020 17:04:58	  The size of the media file is 44.7 MB
build	06-Jul-2020 17:05:04	
build	06-Jul-2020 17:05:04	Compressed media file 'Unix Shell Installer':
build	06-Jul-2020 17:05:04	  Compressing files
build	06-Jul-2020 17:05:04	  Applying LZMA compression
build	06-Jul-2020 17:05:04	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/11
build	06-Jul-2020 17:05:04	  The name of the media file is jalview_build-2_11_1_0-unix-java_11.sh.
build	06-Jul-2020 17:05:04	  The size of the media file is 40.1 MB
build	06-Jul-2020 17:05:07	
build	06-Jul-2020 17:05:07	Compressed media file 'Windows x64 EXE Installer':
build	06-Jul-2020 17:05:07	  Compressing files
build	06-Jul-2020 17:05:07	  Applying LZMA compression
build	06-Jul-2020 17:05:07	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/11
build	06-Jul-2020 17:05:07	  The name of the media file is Jalview_Build-2_11_1_0-windows-x64-java_11.exe.
build	06-Jul-2020 17:05:07	  The size of the media file is 81.0 MB
build	06-Jul-2020 17:05:07	
build	06-Jul-2020 17:05:07	Compressed media file 'Linux x64 Shell Installer':
build	06-Jul-2020 17:05:07	  Compressing files
build	06-Jul-2020 17:05:07	  Applying LZMA compression
build	06-Jul-2020 17:05:07	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/11
build	06-Jul-2020 17:05:07	  The name of the media file is jalview_build-2_11_1_0-linux_x64-java_11.sh.
build	06-Jul-2020 17:05:07	  The size of the media file is 79.8 MB
build	06-Jul-2020 17:05:07	Writing md5sums.
build	06-Jul-2020 17:05:07	Writing sha256sums.
build	06-Jul-2020 17:05:07	Writing updates.xml.
build	06-Jul-2020 17:05:07	Please upload updates.xml to https://www.jalview.org/install4j/updates.xml
build	06-Jul-2020 17:05:07	and upload all generated media files to the same directory.
build	06-Jul-2020 17:05:07	
build	06-Jul-2020 17:05:07	Build completed in 35.4 seconds.
build	06-Jul-2020 17:05:08	
build	06-Jul-2020 17:05:08	BUILD SUCCESSFUL in 1m 0s
build	06-Jul-2020 17:05:08	21 actionable tasks: 20 executed, 1 up-to-date
simple	06-Jul-2020 17:05:09	Finished task 'Jalview distribution for Java 11' with result: Success
command	06-Jul-2020 17:05:09	Substituting variable: ${bamboo.planKey} with JB-JGP14
simple	06-Jul-2020 17:05:09	Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	06-Jul-2020 17:05:09	Bamboo Artifactory Plugin version: 2.6.2
command	06-Jul-2020 17:05:09	Beginning to execute external process for build 'Jalview Builds - Gradle build with getdown and install4j - bug-JAL-3628_Unable_to_save_update_to_existing_file_in_Windows - Default Job #3 (JB-JGP14-JOB1-3)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -x clean -PJAVA_VERSION=1.8 -PCHANNEL=BUILD -Pbamboo_planKey=JB-JGP14 shadowJar getdown installers\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows\nbamboo_repository_revision_number=06d91fe495898df93fd6fcdc305f304cf9f3aa16\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-JGP14-JOB1-3\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_24707116_name=Jalview Git\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-JGP14-JOB1\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=bug-JAL-3628_Unable_to_save_update_to_existing_file_in_Windows\nbamboo_repository_24707116_revision_number=06d91fe495898df93fd6fcdc305f304cf9f3aa16\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=3\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-JGP14-JOB1-3\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - 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build	06-Jul-2020 17:05:11	
build	06-Jul-2020 17:05:11	> Configure project :
build	06-Jul-2020 17:05:11	HEADLESS BUILD
build	06-Jul-2020 17:05:11	Using a BUILD profile.
build	06-Jul-2020 17:05:13	
build	06-Jul-2020 17:05:13	> Task :compileJava
build	06-Jul-2020 17:05:13	Setting target compatibility to 1.8
error	06-Jul-2020 17:05:17	Note: Some input files use or override a deprecated API.
error	06-Jul-2020 17:05:17	Note: Recompile with -Xlint:deprecation for details.
error	06-Jul-2020 17:05:17	Note: Some input files use unchecked or unsafe operations.
error	06-Jul-2020 17:05:17	Note: Recompile with -Xlint:unchecked for details.
build	06-Jul-2020 17:05:17	
build	06-Jul-2020 17:05:17	> Task :processResources UP-TO-DATE
build	06-Jul-2020 17:05:17	> Task :classes
build	06-Jul-2020 17:05:17	> Task :cleanPackageDir
build	06-Jul-2020 17:05:17	> Task :copyHelp UP-TO-DATE
build	06-Jul-2020 17:05:18	> Task :buildIndices
build	06-Jul-2020 17:05:18	> Task :setGitVals UP-TO-DATE
build	06-Jul-2020 17:05:18	> Task :createBuildProperties
build	06-Jul-2020 17:05:19	> Task :compileLinkCheck
build	06-Jul-2020 17:05:19	> Task :cleanBuildingHTML
build	06-Jul-2020 17:05:20	> Task :convertBuildingMD
build	06-Jul-2020 17:05:20	> Task :syncDocs UP-TO-DATE
build	06-Jul-2020 17:05:20	> Task :syncResources UP-TO-DATE
build	06-Jul-2020 17:05:20	> Task :prepare UP-TO-DATE
build	06-Jul-2020 17:05:21	
build	06-Jul-2020 17:05:21	> Task :linkCheck
build	06-Jul-2020 17:05:21	Checking help file links
build	06-Jul-2020 17:05:21	
build	06-Jul-2020 17:05:21	Results:
build	06-Jul-2020 17:05:21	138 distinct help targets
build	06-Jul-2020 17:05:21	138 help mappings
build	06-Jul-2020 17:05:21	0 invalid targets
build	06-Jul-2020 17:05:21	24 unused targets
build	06-Jul-2020 17:05:21	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	06-Jul-2020 17:05:21	    overviewprefs: html/features/preferences.html#overview
build	06-Jul-2020 17:05:21	    cdnafeatures: html/features/codingfeatures.html
build	06-Jul-2020 17:05:21	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	06-Jul-2020 17:05:21	    io.modellerpir: html/io/modellerpir.html
build	06-Jul-2020 17:05:21	    pdbmcviewer: html/features/pdbviewer.html
build	06-Jul-2020 17:05:21	    groovy.colours: html/features/groovy.html#groovyColours
build	06-Jul-2020 17:05:21	    seqmappings: html/features/seqmappings.html
build	06-Jul-2020 17:05:21	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	06-Jul-2020 17:05:21	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	06-Jul-2020 17:05:21	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	06-Jul-2020 17:05:21	    search: html/features/search.html
build	06-Jul-2020 17:05:21	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	06-Jul-2020 17:05:21	    alformats: html/io/fileformats.html
build	06-Jul-2020 17:05:21	    strucprefs: html/features/preferences.html#structure
build	06-Jul-2020 17:05:21	    siftsmapping: html/features/siftsmapping.html
build	06-Jul-2020 17:05:21	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	06-Jul-2020 17:05:21	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	06-Jul-2020 17:05:21	    newkeys: html/features/newkeystrokes.html
build	06-Jul-2020 17:05:21	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	06-Jul-2020 17:05:21	    jalarchive: html/features/jalarchive.html
build	06-Jul-2020 17:05:21	    newsreader: html/webServices/newsreader.html
build	06-Jul-2020 17:05:21	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	06-Jul-2020 17:05:21	    overview: html/features/overview.html
build	06-Jul-2020 17:05:21	0 invalid map urls
build	06-Jul-2020 17:05:21	0 invalid image attributes
build	06-Jul-2020 17:05:21	386 internal href links (74 with anchors)
build	06-Jul-2020 17:05:21	0 invalid internal href links
build	06-Jul-2020 17:05:21	0 invalid internal anchor links
build	06-Jul-2020 17:05:21	87 external href links
build	06-Jul-2020 17:05:21	External links not verified as internet not available
build	06-Jul-2020 17:05:21	*** Success ***
build	06-Jul-2020 17:05:21	
build	06-Jul-2020 17:05:21	> Task :jar
build	06-Jul-2020 17:05:22	> Task :syncJars
build	06-Jul-2020 17:05:22	> Task :makeDist
build	06-Jul-2020 17:05:27	> Task :shadowJar
build	06-Jul-2020 17:05:27	> Task :getdownWebsite
build	06-Jul-2020 17:05:28	
build	06-Jul-2020 17:05:28	> Task :getdownDigest
build	06-Jul-2020 17:05:28	Generating digest file './getdown/website/1.8/digest.txt'...
build	06-Jul-2020 17:05:28	Generating digest file './getdown/website/1.8/digest2.txt'...
error	06-Jul-2020 17:05:28	2020/07/06 17:05:27:589 WARNING Starting without install4j classes
error	06-Jul-2020 17:05:28	2020/07/06 17:05:28:034 WARNING Starting without install4j classes
build	06-Jul-2020 17:05:28	
build	06-Jul-2020 17:05:28	> Task :getdown
build	06-Jul-2020 17:05:28	> Task :copyInstall4jTemplate UP-TO-DATE
build	06-Jul-2020 17:05:30	
build	06-Jul-2020 17:05:30	> Task :installers
build	06-Jul-2020 17:05:30	Using projectFile /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/utils/install4j/jalview-install4j-conf.install4j
build	06-Jul-2020 17:05:30	install4j version 8.0.5 (build 8155), built on 2020-03-16
build	06-Jul-2020 17:05:30	Using Java 1.8.0_252 from /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.252.b09-2.el7_8.x86_64/jre
build	06-Jul-2020 17:05:30	Registered to Jalview, University of Dundee
build	06-Jul-2020 17:05:30	
build	06-Jul-2020 17:05:30	Loading config file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/utils/install4j/jalview-install4j-conf.install4j
build	06-Jul-2020 17:05:31	Creating media file 'Windows x64 EXE Installer':
build	06-Jul-2020 17:05:31	  Collecting files:
build	06-Jul-2020 17:05:31	  [WARNING] The version of the bundled JRE is too low. It should be at least 1.8!
build	06-Jul-2020 17:05:31	  Compiling launchers:
build	06-Jul-2020 17:05:31	    Compiling launcher 'Jalview Launcher':
build	06-Jul-2020 17:05:31	      Generating VM options file jalview.vmoptions.
build	06-Jul-2020 17:05:31	  Creating media file: 
build	06-Jul-2020 17:05:31	    Using custom installer icon: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/utils/install4j/../../resources/images/jalview_logos.ico
build	06-Jul-2020 17:05:33	    Zipping custom code & resources JAR file
build	06-Jul-2020 17:05:33	    Identifying components
build	06-Jul-2020 17:05:33	    Adding JRE (jre-8-windows-x64.tar.gz)
build	06-Jul-2020 17:05:33	    Shrinking runtime
build	06-Jul-2020 17:05:34	  
build	06-Jul-2020 17:05:34	Creating media file 'macOS Disk Image':
build	06-Jul-2020 17:05:34	  Collecting files:
build	06-Jul-2020 17:05:34	  Compiling launchers:
build	06-Jul-2020 17:05:34	    Compiling launcher 'Jalview Launcher':
build	06-Jul-2020 17:05:34	      Generating VM options file vmoptions.txt.
build	06-Jul-2020 17:05:34	  Creating media file: 
build	06-Jul-2020 17:05:34	    Identifying components
build	06-Jul-2020 17:05:34	      Shrinking runtime
build	06-Jul-2020 17:05:35	  
build	06-Jul-2020 17:05:35	Creating media file 'Linux x64 Shell Installer':
build	06-Jul-2020 17:05:35	  Collecting files:
build	06-Jul-2020 17:05:35	  [WARNING] The version of the bundled JRE is too low. It should be at least 1.8!
build	06-Jul-2020 17:05:35	  Compiling launchers:
build	06-Jul-2020 17:05:35	    Compiling launcher 'Jalview Launcher':
build	06-Jul-2020 17:05:35	      Generating launcher script file
build	06-Jul-2020 17:05:35	      Generating VM options file .i4j_external_735/jalview.vmoptions.
build	06-Jul-2020 17:05:35	  Creating media file: 
build	06-Jul-2020 17:05:35	    Generating launcher script file
build	06-Jul-2020 17:05:35	    Zipping custom code & resources JAR file
build	06-Jul-2020 17:05:35	    Identifying components
build	06-Jul-2020 17:05:35	    Adding JRE (jre-8-linux-x64.tar.gz)
build	06-Jul-2020 17:05:35	    Shrinking runtime
build	06-Jul-2020 17:05:36	  
build	06-Jul-2020 17:05:36	Creating media file 'Unix .tar.gz Archive':
build	06-Jul-2020 17:05:36	  Collecting files:
build	06-Jul-2020 17:05:36	  Compiling launchers:
build	06-Jul-2020 17:05:36	    Compiling launcher 'Jalview Launcher':
build	06-Jul-2020 17:05:36	      Generating launcher script file
build	06-Jul-2020 17:05:36	      Generating VM options file .i4j_external_735/jalview.vmoptions.
build	06-Jul-2020 17:05:36	  Creating media file: 
build	06-Jul-2020 17:05:36	    Identifying components
build	06-Jul-2020 17:05:36	      Shrinking runtime
build	06-Jul-2020 17:05:36	  
build	06-Jul-2020 17:05:36	Creating media file 'Unix Shell Installer':
build	06-Jul-2020 17:05:36	  Collecting files:
build	06-Jul-2020 17:05:36	  Compiling launchers:
build	06-Jul-2020 17:05:36	    Compiling launcher 'Jalview Launcher':
build	06-Jul-2020 17:05:36	      Generating launcher script file
build	06-Jul-2020 17:05:36	      Generating VM options file .i4j_external_735/jalview.vmoptions.
build	06-Jul-2020 17:05:36	  Creating media file: 
build	06-Jul-2020 17:05:36	    Generating launcher script file
build	06-Jul-2020 17:05:37	    Zipping custom code & resources JAR file
build	06-Jul-2020 17:05:37	    Identifying components
build	06-Jul-2020 17:05:37	    Shrinking runtime
build	06-Jul-2020 17:05:37	  
build	06-Jul-2020 17:05:37	Compressing 5 media files with 4 threads:
build	06-Jul-2020 17:05:52	
build	06-Jul-2020 17:05:52	Compressed media file 'macOS Disk Image':
build	06-Jul-2020 17:05:52	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/1.8
build	06-Jul-2020 17:05:52	  The name of the media file is Jalview_Build-2_11_1_0-macos-java_8.dmg.
build	06-Jul-2020 17:05:52	  The size of the media file is 75.7 MB
build	06-Jul-2020 17:05:55	
build	06-Jul-2020 17:05:55	Compressed media file 'Unix .tar.gz Archive':
build	06-Jul-2020 17:05:55	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/1.8
build	06-Jul-2020 17:05:55	  The name of the media file is jalview_build-2_11_1_0-unix-java_8.tar.gz.
build	06-Jul-2020 17:05:55	  The size of the media file is 38.4 MB
build	06-Jul-2020 17:05:58	
build	06-Jul-2020 17:05:58	Compressed media file 'Unix Shell Installer':
build	06-Jul-2020 17:05:58	  Compressing files
build	06-Jul-2020 17:05:58	  Applying LZMA compression
build	06-Jul-2020 17:05:58	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/1.8
build	06-Jul-2020 17:05:58	  The name of the media file is jalview_build-2_11_1_0-unix-java_8.sh.
build	06-Jul-2020 17:05:58	  The size of the media file is 34.1 MB
build	06-Jul-2020 17:06:00	
build	06-Jul-2020 17:06:00	Compressed media file 'Linux x64 Shell Installer':
build	06-Jul-2020 17:06:00	  Compressing files
build	06-Jul-2020 17:06:00	  Applying LZMA compression
build	06-Jul-2020 17:06:00	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/1.8
build	06-Jul-2020 17:06:00	  The name of the media file is jalview_build-2_11_1_0-linux_x64-java_8.sh.
build	06-Jul-2020 17:06:00	  The size of the media file is 73.1 MB
build	06-Jul-2020 17:06:00	
build	06-Jul-2020 17:06:00	Compressed media file 'Windows x64 EXE Installer':
build	06-Jul-2020 17:06:00	  Compressing files
build	06-Jul-2020 17:06:00	  Applying LZMA compression
build	06-Jul-2020 17:06:00	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/1.8
build	06-Jul-2020 17:06:00	  The name of the media file is Jalview_Build-2_11_1_0-windows-x64-java_8.exe.
build	06-Jul-2020 17:06:00	  The size of the media file is 71.6 MB
build	06-Jul-2020 17:06:00	Writing md5sums.
build	06-Jul-2020 17:06:00	Writing sha256sums.
build	06-Jul-2020 17:06:00	Writing updates.xml.
build	06-Jul-2020 17:06:00	Please upload updates.xml to https://www.jalview.org/install4j/updates.xml
build	06-Jul-2020 17:06:00	and upload all generated media files to the same directory.
build	06-Jul-2020 17:06:00	
build	06-Jul-2020 17:06:00	Build completed in 31.2 seconds.
build	06-Jul-2020 17:06:01	
build	06-Jul-2020 17:06:01	BUILD SUCCESSFUL in 52s
build	06-Jul-2020 17:06:01	20 actionable tasks: 15 executed, 5 up-to-date
simple	06-Jul-2020 17:06:02	Finished task 'Jalview distribution for Java 8' with result: Success
simple	06-Jul-2020 17:06:02	Running post build plugin 'NCover Results Collector'
simple	06-Jul-2020 17:06:02	Running post build plugin 'Artifact Copier'
simple	06-Jul-2020 17:06:02	Publishing an artifact: Jalview getdown launcher
simple	06-Jul-2020 17:06:02	Finished publishing of artifact Shared artifact: [Jalview getdown launcher], pattern: [**/*] anchored at: [getdown/files] in 39.42 ms
simple	06-Jul-2020 17:06:02	Publishing an artifact: getdown-channel
simple	06-Jul-2020 17:06:02	Finished publishing of artifact Shared artifact: [getdown-channel], pattern: [**/*] anchored at: [getdown/website] in 242.1 ms
simple	06-Jul-2020 17:06:02	Publishing an artifact: install4j installers
simple	06-Jul-2020 17:06:04	Finished publishing of artifact Shared artifact: [install4j installers], pattern: [**/*] anchored at: [build/install4j] in 2.012 s
simple	06-Jul-2020 17:06:04	Publishing an artifact: Jalview executables
simple	06-Jul-2020 17:06:04	Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 332.4 ms
simple	06-Jul-2020 17:06:04	Running post build plugin 'Artifactory Release Management Staging'
simple	06-Jul-2020 17:06:04	Running post build plugin 'Artifactory Build Info Copier'
simple	06-Jul-2020 17:06:04	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	06-Jul-2020 17:06:04	Running post build plugin 'npm Cache Cleanup'
simple	06-Jul-2020 17:06:04	Running post build plugin 'Clover Results Collector'
simple	06-Jul-2020 17:06:04	Running post build plugin 'Docker Container Cleanup'
simple	06-Jul-2020 17:06:04	Finalising the build...
simple	06-Jul-2020 17:06:04	Stopping timer.
simple	06-Jul-2020 17:06:04	Build JB-JGP14-JOB1-3 completed.
simple	06-Jul-2020 17:06:04	Running on server: post build plugin 'NCover Results Collector'
simple	06-Jul-2020 17:06:04	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	06-Jul-2020 17:06:04	Running on server: post build plugin 'Clover Delta Calculator'
simple	06-Jul-2020 17:06:04	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	06-Jul-2020 17:06:04	All post build plugins have finished
simple	06-Jul-2020 17:06:04	Generating build results summary...
simple	06-Jul-2020 17:06:04	Saving build results to disk...
simple	06-Jul-2020 17:06:04	Logging substituted variables...
simple	06-Jul-2020 17:06:04	Indexing build results...
simple	06-Jul-2020 17:06:04	Finished building JB-JGP14-JOB1-3.