simple 09-Jun-2020 10:58:36 Build Jalview Builds - Gradle build with getdown and install4j - Default Job #24 (JB-JGP-JOB1-24) started building on agent Default Agent simple 09-Jun-2020 10:58:36 simple 09-Jun-2020 10:58:36 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP-JOB1 simple 09-Jun-2020 10:58:36 Executing build Jalview Builds - Gradle build with getdown and install4j - Default Job #24 (JB-JGP-JOB1-24) simple 09-Jun-2020 10:58:36 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 09-Jun-2020 10:58:36 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP-JOB1 simple 09-Jun-2020 10:58:36 Updating source code to revision: 8939be9b96e7e3f7e836037b972ddce75fa4a17e simple 09-Jun-2020 10:58:36 Fetching 'refs/heads/develop' from 'http://source.jalview.org/git/jalview.git'. simple 09-Jun-2020 10:58:36 Checking out revision 8939be9b96e7e3f7e836037b972ddce75fa4a17e. simple 09-Jun-2020 10:58:38 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 09-Jun-2020 10:58:38 77745a4..8939be9 develop -> origin/develop simple 09-Jun-2020 10:58:38 * [new branch] JAL-3253-applet-SwingJS-omnibus -> origin/JAL-3253-applet-SwingJS-omnibus simple 09-Jun-2020 10:58:38 * [new branch] JAL-3253_applet_omnibus-BH -> origin/JAL-3253_applet_omnibus-BH simple 09-Jun-2020 10:58:38 * [new branch] Jalview-JS/JAL-3253-applet -> origin/Jalview-JS/JAL-3253-applet simple 09-Jun-2020 10:58:38 b2761fa..c844fbd Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e -> origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e simple 09-Jun-2020 10:58:38 b61fb78..b89316f Jalview-JS/develop -> origin/Jalview-JS/develop simple 09-Jun-2020 10:58:38 * [new branch] Jalview-JS/develop.JAL-3445-BSML-reader -> origin/Jalview-JS/develop.JAL-3445-BSML-reader simple 09-Jun-2020 10:58:38 * [new branch] Jalview-JS/develop.JAL-3446.SequenceFeatureAsync -> origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync simple 09-Jun-2020 10:58:38 * [new branch] Jalview-JS/develop.JAL-3446.ctrlDown -> origin/Jalview-JS/develop.JAL-3446.ctrlDown simple 09-Jun-2020 10:58:38 * [new branch] Jalview-JS/update_java2script -> origin/Jalview-JS/update_java2script simple 09-Jun-2020 10:58:38 * [new branch] alpha/merge_212_JalviewJS_2112 -> origin/alpha/merge_212_JalviewJS_2112 simple 09-Jun-2020 10:58:38 * [new branch] blocker/JAL-3611_space_character_in_jalview_install_path -> origin/blocker/JAL-3611_space_character_in_jalview_install_path simple 09-Jun-2020 10:58:38 * [new branch] bug/JAL-3529_uniprotidsinstockholm -> origin/bug/JAL-3529_uniprotidsinstockholm simple 09-Jun-2020 10:58:38 * [new branch] bug/JAL-3541_cloverReport_gradle_task_fails -> origin/bug/JAL-3541_cloverReport_gradle_task_fails simple 09-Jun-2020 10:58:38 * [new branch] bug/JAL-3541_clover_as_javaexec -> origin/bug/JAL-3541_clover_as_javaexec simple 09-Jun-2020 10:58:38 * [new branch] bug/JAL-3567virtualFeatureCoordinates -> origin/bug/JAL-3567virtualFeatureCoordinates simple 09-Jun-2020 10:58:38 * [new branch] bug/JAL-3574filterByPOS -> origin/bug/JAL-3574filterByPOS simple 09-Jun-2020 10:58:38 * [new branch] bug/JAL-3609_HiDPI_in_Linux -> origin/bug/JAL-3609_HiDPI_in_Linux simple 09-Jun-2020 10:58:38 * [new branch] bug/JAL-3613emblCDSTracking -> origin/bug/JAL-3613emblCDSTracking simple 09-Jun-2020 10:58:38 * [new branch] 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 09-Jun-2020 10:58:38 * [new branch] feature/JAL-3551Pymol -> origin/feature/JAL-3551Pymol simple 09-Jun-2020 10:58:38 * [new branch] feature/JAL-3624siftsInJS -> origin/feature/JAL-3624siftsInJS simple 09-Jun-2020 10:58:38 * [new branch] features/JAL-3638_jumptonextindel -> origin/features/JAL-3638_jumptonextindel simple 09-Jun-2020 10:58:38 * [new branch] features/JAL-3641_phredfromfastq -> origin/features/JAL-3641_phredfromfastq simple 09-Jun-2020 10:58:38 * [new branch] features/JAL-518_justify_seqs_in_region -> origin/features/JAL-518_justify_seqs_in_region simple 09-Jun-2020 10:58:38 * [new branch] improvement/JAL-3289_new_launch_screens -> origin/improvement/JAL-3289_new_launch_screens simple 09-Jun-2020 10:58:38 * [new branch] merge/Jalview-JS_develop_with_develop_build.gradle_gradle.properties_utils_install4j -> origin/merge/Jalview-JS_develop_with_develop_build.gradle_gradle.properties_utils_install4j simple 09-Jun-2020 10:58:38 * [new branch] patch/JAL-3626_gradle_refinementsfrom2111 -> origin/patch/JAL-3626_gradle_refinementsfrom2111 simple 09-Jun-2020 10:58:38 * [new branch] releases/Release_2_11_1_Branch -> origin/releases/Release_2_11_1_Branch simple 09-Jun-2020 10:58:38 * [new branch] story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window -> origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window simple 09-Jun-2020 10:58:38 * [new branch] task/JAL-3608_property_set_laf_and_tests -> origin/task/JAL-3608_property_set_laf_and_tests simple 09-Jun-2020 10:58:38 * [new branch] task/JAL-3609_HiDPI_support_in_java -> origin/task/JAL-3609_HiDPI_support_in_java simple 09-Jun-2020 10:58:38 * [new branch] testing/JAL-3577_jalviewversion_autoset -> origin/testing/JAL-3577_jalviewversion_autoset simple 09-Jun-2020 10:58:38 * [new branch] testing/JAL-3577_jalviewversion_autoset_fixed -> origin/testing/JAL-3577_jalviewversion_autoset_fixed simple 09-Jun-2020 10:58:38 * [new branch] trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker -> origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker simple 09-Jun-2020 10:58:38 * [new tag] Release_2_11_1_0 -> Release_2_11_1_0 simple 09-Jun-2020 10:58:38 Already on 'develop' simple 09-Jun-2020 10:58:38 Your branch is behind 'origin/develop' by 1039 commits, and can be fast-forwarded. simple 09-Jun-2020 10:58:38 (use "git pull" to update your local branch) simple 09-Jun-2020 10:58:39 HEAD is now at 8939be9 JAL-3446 new Jmol 15.1.3 jar added to j11lib, old j11lib Jmol-14.29.17-no_netscape.jar removed simple 09-Jun-2020 10:58:39 Updated source code to revision: 8939be9b96e7e3f7e836037b972ddce75fa4a17e simple 09-Jun-2020 10:58:39 Finished task 'Checkout Default Repository' with result: Success simple 09-Jun-2020 10:58:39 Running pre-build action: VCS Version Collector simple 09-Jun-2020 10:58:39 Running pre-build action: Artifactory Release Staging command 09-Jun-2020 10:58:39 Substituting variable: ${bamboo.planKey} with JB-JGP simple 09-Jun-2020 10:58:39 Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 09-Jun-2020 10:58:39 Bamboo Artifactory Plugin version: 2.6.2 command 09-Jun-2020 10:58:39 Beginning to execute external process for build 'Jalview Builds - Gradle build with getdown and install4j - Default Job #24 (JB-JGP-JOB1-24)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PJAVA_VERSION=11 -PCHANNEL=BUILD -Pbamboo_planKey=JB-JGP clean makeDist shadowJar getdown installers\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=8939be9b96e7e3f7e836037b972ddce75fa4a17e\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-JGP-JOB1-24\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-JGP-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=Gradle build with getdown and install4j\nbamboo_repository_6258691_git_branch=develop\nbamboo_repository_6258691_branch_name=develop\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=24\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-JGP-JOB1-24\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle build with getdown and install4j\nbamboo_repository_6258691_git_username=\nbamboo_shortPlanKey=JGP\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/OpenJDK11/jdk-11\nbamboo_planRepository_revision=8939be9b96e7e3f7e836037b972ddce75fa4a17e\nbamboo_repository_6258691_name=Jalview Git\nbamboo_buildTimeStamp=2020-06-09T10:58:36.036+01:00\nbamboo_repository_previous_revision_number=77745a47387bb12c3e4dea8bbec8ff38499571f2\nbamboo_planRepository_previousRevision=77745a47387bb12c3e4dea8bbec8ff38499571f2\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-JGP-JOB1-24\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Gradle build with getdown and install4j - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=8939be9b96e7e3f7e836037b972ddce75fa4a17e\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_6258691_previous_revision_number=77745a47387bb12c3e4dea8bbec8ff38499571f2\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_planRepository_branch=develop\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=77745a47387bb12c3e4dea8bbec8ff38499571f2\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\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-6062085\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_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_ManualBuildTriggerReason_userName=Soares\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_repository_6258691_revision_number=8939be9b96e7e3f7e836037b972ddce75fa4a17e\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP-JOB1\nbamboo_planKey=JB-JGP\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_6258691_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 09-Jun-2020 10:58:41 build 09-Jun-2020 10:58:41 > Configure project : build 09-Jun-2020 10:58:41 HEADLESS BUILD build 09-Jun-2020 10:58:41 J2S ENABLED build 09-Jun-2020 10:58:41 Using a BUILD profile. build 09-Jun-2020 10:58:41 eclipseDir exists build 09-Jun-2020 10:58:41 build 09-Jun-2020 10:58:41 > Task :clean build 09-Jun-2020 10:58:41 > Task :cleanPackageDir build 09-Jun-2020 10:58:42 > Task :copyHelp build 09-Jun-2020 10:58:43 > Task :buildIndices build 09-Jun-2020 10:58:45 build 09-Jun-2020 10:58:45 > Task :compileJava build 09-Jun-2020 10:58:45 Setting target compatibility to 11 command 09-Jun-2020 10:58:49 Request to stop 'JB-JGP-JOB1-24' received from Soares simple 09-Jun-2020 10:58:50 Exception executing command "/home/bamboo/buildtools/gradle/bin/gradle -x test -PJAVA_VERSION=11 -PCHANNEL=BUILD -Pbamboo_planKey=JB-JGP clean makeDist shadowJar getdown installers Interrupted while waiting for process to finishcom.atlassian.utils.process.ProcessException: Interrupted while waiting for process to finish simple 09-Jun-2020 10:58:50 Failing task since return code of [/home/bamboo/buildtools/gradle/bin/gradle -x test -PJAVA_VERSION=11 -PCHANNEL=BUILD -Pbamboo_planKey=JB-JGP clean makeDist shadowJar getdown installers] was 143 while expected 0 simple 09-Jun-2020 10:58:50 Finished task 'Jalview distribution for Java 11' with result: Failed simple 09-Jun-2020 10:58:50 Running post build plugin 'NCover Results Collector' simple 09-Jun-2020 10:58:50 Running post build plugin 'Artifact Copier' simple 09-Jun-2020 10:58:50 Publishing an artifact: Jalview getdown launcher simple 09-Jun-2020 10:58:50 Finished publishing of artifact Shared artifact: [Jalview getdown launcher], pattern: [**/*] anchored at: [getdown/files] in 194.4 ms simple 09-Jun-2020 10:58:50 Publishing an artifact: getdown-channel simple 09-Jun-2020 10:58:51 Finished publishing of artifact Shared artifact: [getdown-channel], pattern: [**/*] anchored at: [getdown/website] in 1.225 s simple 09-Jun-2020 10:58:51 Publishing an artifact: install4j installers error 09-Jun-2020 10:58:51 Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP-JOB1/build/install4j does not exist. simple 09-Jun-2020 10:58:51 The artifact hasn't been successfully published after 212.8 μs simple 09-Jun-2020 10:58:51 Publishing an artifact: Jalview executables error 09-Jun-2020 10:58:51 Unable to publish artifact [Jalview executables]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP-JOB1/build/libs does not exist. simple 09-Jun-2020 10:58:51 The artifact hasn't been successfully published after 72.63 μs simple 09-Jun-2020 10:58:51 Running post build plugin 'Artifactory Release Management Staging' simple 09-Jun-2020 10:58:51 Running post build plugin 'Artifactory Build Info Copier' simple 09-Jun-2020 10:58:51 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 09-Jun-2020 10:58:51 Running post build plugin 'npm Cache Cleanup' simple 09-Jun-2020 10:58:51 Running post build plugin 'Clover Results Collector' simple 09-Jun-2020 10:58:51 Running post build plugin 'Docker Container Cleanup' simple 09-Jun-2020 10:58:51 Finalising the build... simple 09-Jun-2020 10:58:51 Stopping timer. simple 09-Jun-2020 10:58:51 Build JB-JGP-JOB1-24 completed. simple 09-Jun-2020 10:58:51 Running on server: post build plugin 'NCover Results Collector' simple 09-Jun-2020 10:58:51 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 09-Jun-2020 10:58:51 Running on server: post build plugin 'Clover Delta Calculator' simple 09-Jun-2020 10:58:51 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 09-Jun-2020 10:58:51 All post build plugins have finished simple 09-Jun-2020 10:58:51 Generating build results summary... simple 09-Jun-2020 10:58:51 Saving build results to disk... simple 09-Jun-2020 10:58:51 Logging substituted variables... simple 09-Jun-2020 10:58:51 Indexing build results... simple 09-Jun-2020 10:58:51 Finished building JB-JGP-JOB1-24.