simple	25-Mar-2019 08:58:51	Build Jalview Builds - jalview develop java11 build - Default Job #79 (JB-JDJB-JOB1-79) started building on agent Default Agent
simple	25-Mar-2019 08:58:51	
simple	25-Mar-2019 08:58:51	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDJB-JOB1
simple	25-Mar-2019 08:58:51	Executing build Jalview Builds - jalview develop java11 build - Default Job #79 (JB-JDJB-JOB1-79)
simple	25-Mar-2019 08:58:51	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	25-Mar-2019 08:58:51	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDJB-JOB1
simple	25-Mar-2019 08:58:51	Updating source code to revision: 522aa7882efafa14cc70163537863aec89ba0cc1
simple	25-Mar-2019 08:58:51	Fetching 'refs/heads/develop' from 'http://source.jalview.org/git/jalview.git'.
simple	25-Mar-2019 08:58:51	Checking out revision 522aa7882efafa14cc70163537863aec89ba0cc1.
simple	25-Mar-2019 08:58:51	error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object!
simple	25-Mar-2019 08:58:51	error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object!
simple	25-Mar-2019 08:58:51	error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object!
simple	25-Mar-2019 08:58:51	error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object!
simple	25-Mar-2019 08:58:51	error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object!
simple	25-Mar-2019 08:58:51	error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object!
simple	25-Mar-2019 08:58:51	error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object!
simple	25-Mar-2019 08:58:51	error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object!
simple	25-Mar-2019 08:58:51	error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object!
simple	25-Mar-2019 08:58:51	error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object!
simple	25-Mar-2019 08:58:51	error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object!
simple	25-Mar-2019 08:58:51	error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object!
simple	25-Mar-2019 08:58:52	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164
simple	25-Mar-2019 08:58:52	   2aaeed3..522aa78  develop    -> origin/develop
simple	25-Mar-2019 08:58:52	 * [new branch]      Jalview-JS/20190123 -> origin/Jalview-JS/20190123
simple	25-Mar-2019 08:58:52	 * [new branch]      feature/JAL-3187linkedFeatures -> origin/feature/JAL-3187linkedFeatures
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object!
simple	25-Mar-2019 08:58:52	error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object!
simple	25-Mar-2019 08:58:52	Already on 'develop'
simple	25-Mar-2019 08:58:52	Your branch is behind 'origin/develop' by 1 commit, and can be fast-forwarded.
simple	25-Mar-2019 08:58:52	  (use "git pull" to update your local branch)
simple	25-Mar-2019 08:58:52	HEAD is now at 522aa78 JAL-3127 scripts updated for method signature change
simple	25-Mar-2019 08:58:52	Updated source code to revision: 522aa7882efafa14cc70163537863aec89ba0cc1
simple	25-Mar-2019 08:58:52	Finished task 'Checkout Default Repository' with result: Success
simple	25-Mar-2019 08:58:52	Running pre-build action: VCS Version Collector
simple	25-Mar-2019 08:58:52	Running pre-build action: Artifactory Release Staging
simple	25-Mar-2019 08:58:52	Starting task 'j11 Ant build' of type 'com.atlassian.bamboo.plugins.ant:task.builder.ant'
command	25-Mar-2019 08:58:52	Beginning to execute external process for build 'Jalview Builds - jalview develop java11 build - Default Job #79 (JB-JDJB-JOB1-79)'\n ... running command line: \n/home/bamboo/buildtools/j11/ant-j11/bin/ant -Djava.io.tmpdir=/home/bamboo/latest/temp/JB-JDJB-JOB1 -f build-j11.xml clean build\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDJB-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_repository_6258708_git_branch=develop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=522aa7882efafa14cc70163537863aec89ba0cc1\nbamboo_repository_6258708_name=Jalview Git\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-JDJB-JOB1-79\nbamboo_repository_6258708_revision_number=522aa7882efafa14cc70163537863aec89ba0cc1\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDJB-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-JDJB-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=jalview develop java11 build\nbamboo_planRepository_name=Jalview Git\nbamboo_buildNumber=79\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-JDJB-JOB1-79\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - jalview develop java11 build\nbamboo_shortPlanKey=JDJB\nbamboo_repository_6258708_git_username=\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jvm/jdk11_x64_linux\nbamboo_planRepository_revision=522aa7882efafa14cc70163537863aec89ba0cc1\nbamboo_buildTimeStamp=2019-03-25T08:58:51.174Z\nbamboo_repository_previous_revision_number=2aaeed34a80cf782d2ea57a74bb5aa0880ee2aa1\nbamboo_planRepository_previousRevision=2aaeed34a80cf782d2ea57a74bb5aa0880ee2aa1\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-JDJB-JOB1-79\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - jalview develop java11 build - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=522aa7882efafa14cc70163537863aec89ba0cc1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nJAVA_HOME=/home/bamboo/buildtools/jvm/jdk11_x64_linux\nbamboo_repository_6258708_previous_revision_number=2aaeed34a80cf782d2ea57a74bb5aa0880ee2aa1\nbamboo_buildFailed=false\nANT_HOME=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_branch=develop\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=2aaeed34a80cf782d2ea57a74bb5aa0880ee2aa1\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\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-6062119\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\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr\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-JDJB-JOB1\nbamboo_planKey=JB-JDJB\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\nbamboo_repository_6258708_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_6258708_branch_name=develop\nbamboo_planRepository_1_branchName=develop\nPATH=/home/bamboo/buildtools/jvm/jdk11_x64_linux/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	25-Mar-2019 08:58:53	Buildfile: build-j11.xml does not exist!
error	25-Mar-2019 08:58:53	Build failed
simple	25-Mar-2019 08:58:53	Failing task since return code of [/home/bamboo/buildtools/j11/ant-j11/bin/ant -Djava.io.tmpdir=/home/bamboo/latest/temp/JB-JDJB-JOB1 -f build-j11.xml clean build] was 1 while expected 0
simple	25-Mar-2019 08:58:53	Finished task 'j11 Ant build' with result: Failed
simple	25-Mar-2019 08:58:53	Starting task 'build' of type 'com.atlassian.bamboo.plugins.ant:task.builder.ant'
command	25-Mar-2019 08:58:53	Beginning to execute external process for build 'Jalview Builds - jalview develop java11 build - Default Job #79 (JB-JDJB-JOB1-79)'\n ... running command line: \n/home/bamboo/buildtools/j11/ant-j11/bin/ant -Djava.io.tmpdir=/home/bamboo/latest/temp/JB-JDJB-JOB1 -f build-j11.xml makedist\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDJB-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_repository_6258708_git_branch=develop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=522aa7882efafa14cc70163537863aec89ba0cc1\nbamboo_repository_6258708_name=Jalview Git\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-JDJB-JOB1-79\nbamboo_repository_6258708_revision_number=522aa7882efafa14cc70163537863aec89ba0cc1\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDJB-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-JDJB-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=jalview develop java11 build\nbamboo_planRepository_name=Jalview Git\nbamboo_buildNumber=79\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-JDJB-JOB1-79\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - jalview develop java11 build\nbamboo_shortPlanKey=JDJB\nbamboo_repository_6258708_git_username=\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jvm/jdk11_x64_linux\nbamboo_planRepository_revision=522aa7882efafa14cc70163537863aec89ba0cc1\nbamboo_buildTimeStamp=2019-03-25T08:58:51.174Z\nbamboo_repository_previous_revision_number=2aaeed34a80cf782d2ea57a74bb5aa0880ee2aa1\nbamboo_planRepository_previousRevision=2aaeed34a80cf782d2ea57a74bb5aa0880ee2aa1\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-JDJB-JOB1-79\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - jalview develop java11 build - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=522aa7882efafa14cc70163537863aec89ba0cc1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nJAVA_HOME=/home/bamboo/buildtools/jvm/jdk11_x64_linux\nbamboo_repository_6258708_previous_revision_number=2aaeed34a80cf782d2ea57a74bb5aa0880ee2aa1\nbamboo_build_commandline_com_atlassian_bamboo_plugins_ant_task_builder_ant_5=/home/bamboo/buildtools/j11/ant-j11/bin/ant -Djava.io.tmpdir=/home/bamboo/latest/temp/JB-JDJB-JOB1 -f build-j11.xml clean build\nbamboo_buildFailed=true\nANT_HOME=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_branch=develop\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=2aaeed34a80cf782d2ea57a74bb5aa0880ee2aa1\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\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-6062119\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\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr\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-JDJB-JOB1\nbamboo_planKey=JB-JDJB\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\nbamboo_repository_6258708_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_6258708_branch_name=develop\nbamboo_planRepository_1_branchName=develop\nPATH=/home/bamboo/buildtools/jvm/jdk11_x64_linux/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	25-Mar-2019 08:58:53	Buildfile: build-j11.xml does not exist!
error	25-Mar-2019 08:58:53	Build failed
simple	25-Mar-2019 08:58:53	Failing task since return code of [/home/bamboo/buildtools/j11/ant-j11/bin/ant -Djava.io.tmpdir=/home/bamboo/latest/temp/JB-JDJB-JOB1 -f build-j11.xml makedist] was 1 while expected 0
simple	25-Mar-2019 08:58:53	Finished task 'build' with result: Failed
simple	25-Mar-2019 08:58:53	Running post build plugin 'NCover Results Collector'
simple	25-Mar-2019 08:58:53	Running post build plugin 'Artifact Copier'
simple	25-Mar-2019 08:58:53	Publishing an artifact: Clover Report (System)
error	25-Mar-2019 08:58:53	Unable to publish artifact [Clover Report (System)]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDJB-JOB1/clover does not exist.
simple	25-Mar-2019 08:58:53	The artifact hasn't been successfully published after 203.9 μs
simple	25-Mar-2019 08:58:53	Publishing an artifact: jalview-jars
error	25-Mar-2019 08:58:53	Unable to publish artifact [jalview-jars]: 
simple	25-Mar-2019 08:58:53	The artifact hasn't been successfully published after 26.85 ms
simple	25-Mar-2019 08:58:53	Running post build plugin 'Artifactory Release Management Staging'
simple	25-Mar-2019 08:58:53	Running post build plugin 'Artifactory Build Info Copier'
simple	25-Mar-2019 08:58:53	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	25-Mar-2019 08:58:53	Running post build plugin 'npm Cache Cleanup'
simple	25-Mar-2019 08:58:53	Running post build plugin 'Clover Results Collector'
error	25-Mar-2019 08:58:53	Failed to execute plugin 'Clover Results Collector' with error: No file matches the specified pattern:clover/jalviewX/clover.xml in [/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDJB-JOB1]
simple	25-Mar-2019 08:58:53	Running post build plugin 'Docker Container Cleanup'
simple	25-Mar-2019 08:58:53	Finalising the build...
simple	25-Mar-2019 08:58:53	Stopping timer.
simple	25-Mar-2019 08:58:53	Build JB-JDJB-JOB1-79 completed.
simple	25-Mar-2019 08:58:53	Running on server: post build plugin 'NCover Results Collector'
simple	25-Mar-2019 08:58:53	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	25-Mar-2019 08:58:53	Running on server: post build plugin 'Clover Delta Calculator'
simple	25-Mar-2019 08:58:53	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	25-Mar-2019 08:58:53	All post build plugins have finished
simple	25-Mar-2019 08:58:53	Generating build results summary...
simple	25-Mar-2019 08:58:53	Saving build results to disk...
simple	25-Mar-2019 08:58:53	Logging substituted variables...
simple	25-Mar-2019 08:58:53	Indexing build results...
simple	25-Mar-2019 08:58:53	Finished building JB-JDJB-JOB1-79.