simple 12-Jan-2021 00:55:55 Build Jalview Builds - Gradle JalviewJS Build - Jalview-JS-develop - Default Job #182 (JB-GJB0-JOB1-182) started building on agent Default Agent simple 12-Jan-2021 00:55:55 simple 12-Jan-2021 00:55:55 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 simple 12-Jan-2021 00:55:55 Executing build Jalview Builds - Gradle JalviewJS Build - Jalview-JS-develop - Default Job #182 (JB-GJB0-JOB1-182) simple 12-Jan-2021 00:55:55 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 12-Jan-2021 00:55:55 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 simple 12-Jan-2021 00:55:55 Updating source code to revision: 650bca3ef095d09a5354240e7d2bafb6fc524122 simple 12-Jan-2021 00:55:55 Fetching 'refs/heads/Jalview-JS/develop' from 'http://source.jalview.org/git/jalview.git'. simple 12-Jan-2021 00:55:55 Checking out revision 650bca3ef095d09a5354240e7d2bafb6fc524122. simple 12-Jan-2021 00:55:56 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 12-Jan-2021 00:55:56 54f6fe3..650bca3 Jalview-JS/develop -> origin/Jalview-JS/develop simple 12-Jan-2021 00:55:56 * [new branch] JAL-3416_different_look_and_feel_on_linux -> origin/JAL-3416_different_look_and_feel_on_linux simple 12-Jan-2021 00:55:56 fc90b2a..4512cdb bug/JAL-3761_locateInFromTo -> origin/bug/JAL-3761_locateInFromTo simple 12-Jan-2021 00:55:56 * [new branch] bug/JAL-3788_autoOverviewClustal -> origin/bug/JAL-3788_autoOverviewClustal simple 12-Jan-2021 00:55:56 2ea1b35..5d501d5 develop -> origin/develop simple 12-Jan-2021 00:55:56 013c011..cfb482f feature/JAL-1713_overviewInProject -> origin/feature/JAL-1713_overviewInProject simple 12-Jan-2021 00:55:56 22bb2df..812efb5 feature/JAL-3117_overviewFocusAlignment -> origin/feature/JAL-3117_overviewFocusAlignment simple 12-Jan-2021 00:55:56 * [new branch] improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text -> origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text simple 12-Jan-2021 00:55:56 * [new branch] merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services -> origin/merge/Jalview-JS/develop_feature/JAL-3690_callback-based-web-services simple 12-Jan-2021 00:55:56 * [new branch] patch/JAL-3794_X_is_a_dna_rna_base_too -> origin/patch/JAL-3794_X_is_a_dna_rna_base_too simple 12-Jan-2021 00:55:56 * [new branch] task/JAL-3789_configurable_j2s_file_for_headless_transpile -> origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile simple 12-Jan-2021 00:55:56 * [new branch] task/JAL-3789_configurable_j2s_file_for_headless_transpile_with_official_swingjs -> origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile_with_official_swingjs simple 12-Jan-2021 00:55:56 * [new tag] Develop-2_11_2_0-d20201214 -> Develop-2_11_2_0-d20201214 simple 12-Jan-2021 00:55:56 * [new tag] Develop-2_11_2_0-d20201215 -> Develop-2_11_2_0-d20201215 simple 12-Jan-2021 00:55:57 Already on 'Jalview-JS/develop' simple 12-Jan-2021 00:55:57 Your branch is behind 'origin/Jalview-JS/develop' by 2 commits, and can be fast-forwarded. simple 12-Jan-2021 00:55:57 (use "git pull" to update your local branch) simple 12-Jan-2021 00:55:58 HEAD is now at 650bca3 JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle simple 12-Jan-2021 00:55:58 Updated source code to revision: 650bca3ef095d09a5354240e7d2bafb6fc524122 simple 12-Jan-2021 00:55:58 Finished task 'Checkout Default Repository' with result: Success simple 12-Jan-2021 00:55:58 Running pre-build action: VCS Version Collector simple 12-Jan-2021 00:55:58 Running pre-build action: Artifactory Release Staging simple 12-Jan-2021 00:55:58 Starting task 'JalviewJS build site and distributable tar' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 12-Jan-2021 00:55:58 Bamboo Artifactory Plugin version: 2.6.2 command 12-Jan-2021 00:55:58 Beginning to execute external process for build 'Jalview Builds - Gradle JalviewJS Build - Jalview-JS-develop - Default Job #182 (JB-GJB0-JOB1-182)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PJAVA_VERSION=11 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/jee-2019-12 --info clean eclipse jalviewjsCreateJ2sSettings jalviewjs jalviewjsSiteTar\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=Jalview-JS/develop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=Jalview-JS/develop\nbamboo_repository_revision_number=650bca3ef095d09a5354240e7d2bafb6fc524122\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GJB0-JOB1-182\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-GJB0-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GJB0-JOB1\nbamboo_shortPlanName=Jalview-JS-develop\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_repository_12156997_git_branch=Jalview-JS/develop\nbamboo_buildNumber=182\nbamboo_repository_12156997_name=Jalview Git\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GJB0-JOB1-182\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle JalviewJS Build - Jalview-JS-develop\nbamboo_shortPlanKey=GJB0\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=650bca3ef095d09a5354240e7d2bafb6fc524122\nbamboo_buildTimeStamp=2021-01-12T00:55:55.820Z\nbamboo_repository_previous_revision_number=54f6fe32b978af0932428981a56c9960b0df44a7\nbamboo_planRepository_previousRevision=54f6fe32b978af0932428981a56c9960b0df44a7\nbamboo_repository_git_branch=Jalview-JS/develop\nbamboo_buildResultKey=JB-GJB0-JOB1-182\nbamboo_repository_branch_name=Jalview-JS/develop\nbamboo_buildPlanName=Jalview Builds - Gradle JalviewJS Build - Jalview-JS-develop - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=650bca3ef095d09a5354240e7d2bafb6fc524122\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_12156997_branch_name=Jalview-JS/develop\nbamboo_planRepository_branch=Jalview-JS/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=54f6fe32b978af0932428981a56c9960b0df44a7\nbamboo_planRepository_branchDisplayName=Jalview-JS/develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=Jalview-JS/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_plan_storageTag=plan-11960457\nbamboo_repository_12156997_git_username=\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_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1\nbamboo_planKey=JB-GJB0\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_12156997_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_12156997_previous_revision_number=54f6fe32b978af0932428981a56c9960b0df44a7\nbamboo_repository_12156997_revision_number=650bca3ef095d09a5354240e7d2bafb6fc524122\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=Jalview-JS/develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 12-Jan-2021 00:55:59 Initialized native services in: /srv/bamboo/home/bamboo/.gradle/native build 12-Jan-2021 00:55:59 Removing 0 daemon stop events from registry build 12-Jan-2021 00:55:59 Starting a Gradle Daemon, 2 busy Daemons could not be reused, use --status for details build 12-Jan-2021 00:55:59 Starting process 'Gradle build daemon'. Working directory: /srv/bamboo/home/bamboo/.gradle/daemon/5.6.4 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.invoke=ALL-UNNAMED --add-opens java.prefs/java.util.prefs=ALL-UNNAMED -XX:MaxMetaspaceSize=256m -XX:+HeapDumpOnOutOfMemoryError -Xms256m -Xmx512m -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/home/bamboo/buildtools/gradle-5.6.4/lib/gradle-launcher-5.6.4.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 5.6.4 build 12-Jan-2021 00:55:59 Successfully started process 'Gradle build daemon' build 12-Jan-2021 00:56:01 An attempt to start the daemon took 1.975 secs. build 12-Jan-2021 00:56:01 The client will now receive all logging from the daemon (pid: 4767). The daemon log file: /srv/bamboo/home/bamboo/.gradle/daemon/5.6.4/daemon-4767.out.log build 12-Jan-2021 00:56:01 Starting build in new daemon [memory: 536.9 MB] build 12-Jan-2021 00:56:01 Using 4 worker leases. build 12-Jan-2021 00:56:02 Starting Build build 12-Jan-2021 00:56:03 Settings evaluated using settings file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/settings.gradle'. build 12-Jan-2021 00:56:03 Projects loaded. Root project using build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build.gradle'. build 12-Jan-2021 00:56:03 Included projects: [root project 'jalview'] build 12-Jan-2021 00:56:05 build 12-Jan-2021 00:56:05 > Configure project : build 12-Jan-2021 00:56:05 Evaluating root project 'jalview' using build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build.gradle'. build 12-Jan-2021 00:56:05 Compiling build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build.gradle' using SubsetScriptTransformer. build 12-Jan-2021 00:56:07 Compiling build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build.gradle' using BuildScriptTransformer. build 12-Jan-2021 00:56:08 HEADLESS BUILD build 12-Jan-2021 00:56:08 J2S ENABLED build 12-Jan-2021 00:56:08 Using a LOCAL profile. build 12-Jan-2021 00:56:09 file or directory '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/main/java', not found build 12-Jan-2021 00:56:09 file or directory '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/classes', not found build 12-Jan-2021 00:56:09 eclipseDir exists build 12-Jan-2021 00:56:09 All projects evaluated. build 12-Jan-2021 00:56:09 Selected primary task 'clean' from project : build 12-Jan-2021 00:56:09 Selected primary task 'eclipse' from project : build 12-Jan-2021 00:56:09 Selected primary task 'jalviewjsCreateJ2sSettings' from project : build 12-Jan-2021 00:56:09 Selected primary task 'jalviewjs' from project : build 12-Jan-2021 00:56:09 Selected primary task 'jalviewjsSiteTar' from project : build 12-Jan-2021 00:56:09 Tasks to be executed: [task ':clean', task ':eclipseClasspath', task ':eclipseJdt', task ':eclipseProject', task ':eclipse', task ':jalviewjsCreateJ2sSettings', task ':jalviewjsEclipsePaths', task ':jalviewjsEclipseCopyDropins', task ':jalviewjsSetEclipseWorkspace', task ':jalviewjsEclipseSetup', task ':jalviewjsEnableAltFileProperty', task ':eclipseSetup', task ':jalviewjsProjectImport', task ':jalviewjsTranspile', task ':jalviewjsCopyTransferSiteJs', task ':jalviewjsTransferUnzipLib', task ':jalviewjsTransferUnzipSwingJs', task ':jalviewjsTransferUnzipAllLibs', task ':jalviewjsSyncAllLibs', task ':setGitVals', task ':createBuildProperties', task ':jalviewjsSyncBuildProperties', task ':jalviewjsBuildAllCores', task ':jalviewjsPublishCoreTemplates', task ':jalviewjsSyncCore', task ':jalviewjsSyncResources', task ':jalviewjsSyncSiteResources', task ':jalviewjsPrepareSite', task ':jalviewjsBuildSite', task ':jalviewjs', task ':jalviewjsSiteTar'] build 12-Jan-2021 00:56:09 :clean (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:56:10 build 12-Jan-2021 00:56:10 > Task :clean build 12-Jan-2021 00:56:10 Caching disabled for task ':clean' because: build 12-Jan-2021 00:56:10 Build cache is disabled build 12-Jan-2021 00:56:10 Task ':clean' is not up-to-date because: build 12-Jan-2021 00:56:10 Task has not declared any outputs despite executing actions. build 12-Jan-2021 00:56:10 :clean (Thread[Execution worker for ':',5,main]) completed. Took 0.841 secs. build 12-Jan-2021 00:56:10 :eclipseClasspath (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:56:11 build 12-Jan-2021 00:56:11 > Task :eclipseClasspath build 12-Jan-2021 00:56:11 Caching disabled for task ':eclipseClasspath' because: build 12-Jan-2021 00:56:11 Build cache is disabled build 12-Jan-2021 00:56:11 Task ':eclipseClasspath' is not up-to-date because: build 12-Jan-2021 00:56:11 Task.upToDateWhen is false. build 12-Jan-2021 00:56:11 :eclipseClasspath (Thread[Execution worker for ':',5,main]) completed. Took 0.377 secs. build 12-Jan-2021 00:56:11 :eclipseJdt (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:56:11 build 12-Jan-2021 00:56:11 > Task :eclipseJdt build 12-Jan-2021 00:56:11 Caching disabled for task ':eclipseJdt' because: build 12-Jan-2021 00:56:11 Build cache is disabled build 12-Jan-2021 00:56:11 Task ':eclipseJdt' is not up-to-date because: build 12-Jan-2021 00:56:11 Task.upToDateWhen is false. build 12-Jan-2021 00:56:11 :eclipseJdt (Thread[Execution worker for ':',5,main]) completed. Took 0.047 secs. build 12-Jan-2021 00:56:11 :eclipseProject (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:56:11 build 12-Jan-2021 00:56:11 > Task :eclipseProject build 12-Jan-2021 00:56:11 Caching disabled for task ':eclipseProject' because: build 12-Jan-2021 00:56:11 Build cache is disabled build 12-Jan-2021 00:56:11 Task ':eclipseProject' is not up-to-date because: build 12-Jan-2021 00:56:11 Task.upToDateWhen is false. build 12-Jan-2021 00:56:11 :eclipseProject (Thread[Execution worker for ':',5,main]) completed. Took 0.011 secs. build 12-Jan-2021 00:56:11 :eclipse (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:56:11 build 12-Jan-2021 00:56:11 > Task :eclipse build 12-Jan-2021 00:56:11 Skipping task ':eclipse' as it has no actions. build 12-Jan-2021 00:56:11 :eclipse (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 12-Jan-2021 00:56:11 :jalviewjsCreateJ2sSettings (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:56:11 build 12-Jan-2021 00:56:11 > Task :jalviewjsCreateJ2sSettings build 12-Jan-2021 00:56:11 Caching disabled for task ':jalviewjsCreateJ2sSettings' because: build 12-Jan-2021 00:56:11 Build cache is disabled build 12-Jan-2021 00:56:11 Task ':jalviewjsCreateJ2sSettings' is not up-to-date because: build 12-Jan-2021 00:56:11 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/.j2s has been removed. build 12-Jan-2021 00:56:11 Output property 'outputFile' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/.j2s has been removed. build 12-Jan-2021 00:56:11 :jalviewjsCreateJ2sSettings (Thread[Execution worker for ':',5,main]) completed. Took 0.022 secs. build 12-Jan-2021 00:56:11 :jalviewjsEclipsePaths (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:56:11 build 12-Jan-2021 00:56:11 > Task :jalviewjsEclipsePaths build 12-Jan-2021 00:56:11 Caching disabled for task ':jalviewjsEclipsePaths' because: build 12-Jan-2021 00:56:11 Build cache is disabled build 12-Jan-2021 00:56:11 Task ':jalviewjsEclipsePaths' is not up-to-date because: build 12-Jan-2021 00:56:11 Task has not declared any outputs despite executing actions. build 12-Jan-2021 00:56:11 Running task jalviewjsEclipsePaths as IN_ECLIPSE=false build 12-Jan-2021 00:56:11 ECLIPSE VERSION=4.14.0 build 12-Jan-2021 00:56:11 :jalviewjsEclipsePaths (Thread[Execution worker for ':',5,main]) completed. Took 0.003 secs. build 12-Jan-2021 00:56:11 :jalviewjsEclipseCopyDropins (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:56:11 build 12-Jan-2021 00:56:11 > Task :jalviewjsEclipseCopyDropins build 12-Jan-2021 00:56:11 Caching disabled for task ':jalviewjsEclipseCopyDropins' because: build 12-Jan-2021 00:56:11 Build cache is disabled build 12-Jan-2021 00:56:11 Task ':jalviewjsEclipseCopyDropins' is not up-to-date because: build 12-Jan-2021 00:56:11 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/eclipse_dropins has been removed. build 12-Jan-2021 00:56:11 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/eclipse_dropins/com.seeq.eclipse.importprojects.jar has been removed. build 12-Jan-2021 00:56:11 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/eclipse_dropins/net.sf.j2s.core-j11.jar has been removed. build 12-Jan-2021 00:56:11 :jalviewjsEclipseCopyDropins (Thread[Execution worker for ':',5,main]) completed. Took 0.031 secs. build 12-Jan-2021 00:56:11 :jalviewjsSetEclipseWorkspace (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:56:11 build 12-Jan-2021 00:56:11 > Task :jalviewjsSetEclipseWorkspace build 12-Jan-2021 00:56:11 Caching disabled for task ':jalviewjsSetEclipseWorkspace' because: build 12-Jan-2021 00:56:11 Build cache is disabled build 12-Jan-2021 00:56:11 Task ':jalviewjsSetEclipseWorkspace' is not up-to-date because: build 12-Jan-2021 00:56:11 Task.upToDateWhen is false. build 12-Jan-2021 00:56:11 Running task jalviewjsSetEclipseWorkspace as IN_ECLIPSE=false build 12-Jan-2021 00:56:11 NEW ECLIPSE WORKSPACE: /tmp/groovy-generated-4131780424687256073-tmpdir build 12-Jan-2021 00:56:11 :jalviewjsSetEclipseWorkspace (Thread[Execution worker for ':',5,main]) completed. Took 0.009 secs. build 12-Jan-2021 00:56:11 :jalviewjsEclipseSetup (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:56:11 build 12-Jan-2021 00:56:11 > Task :jalviewjsEclipseSetup build 12-Jan-2021 00:56:11 Skipping task ':jalviewjsEclipseSetup' as it has no actions. build 12-Jan-2021 00:56:11 :jalviewjsEclipseSetup (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 12-Jan-2021 00:56:11 :jalviewjsEnableAltFileProperty (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:56:11 build 12-Jan-2021 00:56:11 > Task :jalviewjsEnableAltFileProperty build 12-Jan-2021 00:56:11 Caching disabled for task ':jalviewjsEnableAltFileProperty' because: build 12-Jan-2021 00:56:11 Build cache is disabled build 12-Jan-2021 00:56:11 Task ':jalviewjsEnableAltFileProperty' is not up-to-date because: build 12-Jan-2021 00:56:11 No history is available. build 12-Jan-2021 00:56:11 :jalviewjsEnableAltFileProperty (Thread[Execution worker for ':',5,main]) completed. Took 0.005 secs. build 12-Jan-2021 00:56:11 :eclipseSetup (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:56:11 build 12-Jan-2021 00:56:11 > Task :eclipseSetup build 12-Jan-2021 00:56:11 Skipping task ':eclipseSetup' as it has no actions. build 12-Jan-2021 00:56:11 :eclipseSetup (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 12-Jan-2021 00:56:11 :jalviewjsProjectImport (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:56:13 build 12-Jan-2021 00:56:13 > Task :jalviewjsProjectImport build 12-Jan-2021 00:56:13 Caching disabled for task ':jalviewjsProjectImport' because: build 12-Jan-2021 00:56:13 Build cache is disabled build 12-Jan-2021 00:56:13 Task ':jalviewjsProjectImport' is not up-to-date because: build 12-Jan-2021 00:56:13 Task.upToDateWhen is false. build 12-Jan-2021 00:56:13 Running task jalviewjsProjectImport as IN_ECLIPSE=false build 12-Jan-2021 00:56:13 Starting process 'command '/home/bamboo/buildtools/eclipse/jee-2019-12/eclipse/eclipse''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 Command: /home/bamboo/buildtools/eclipse/jee-2019-12/eclipse/eclipse -nosplash --launcher.suppressErrors -application com.seeq.eclipse.importprojects.headlessimport -data /tmp/groovy-generated-4131780424687256073-tmpdir -import /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 --launcher.appendVmargs -vmargs -Dorg.eclipse.equinox.p2.reconciler.dropins.directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/eclipse_dropins -Dnet.sf.j2s.core.headlessbuild=true -Dorg.jalview.jalviewjsj2sfilename=./build/jalviewjs/config/j2s build 12-Jan-2021 00:56:13 Successfully started process 'command '/home/bamboo/buildtools/eclipse/jee-2019-12/eclipse/eclipse'' build 12-Jan-2021 00:56:38 org.eclipse.m2e.logback.configuration: The org.eclipse.m2e.logback.configuration bundle was activated before the state location was initialized. Will retry after the state location is initialized. build 12-Jan-2021 00:56:39 org.eclipse.m2e.logback.configuration: Logback config file: /tmp/groovy-generated-4131780424687256073-tmpdir/.metadata/.plugins/org.eclipse.m2e.logback.configuration/logback.1.14.0.20191209-1925.xml build 12-Jan-2021 00:56:39 org.eclipse.m2e.logback.configuration: Initializing logback build 12-Jan-2021 00:57:19 :jalviewjsProjectImport (Thread[Execution worker for ':',5,main]) completed. Took 1 mins 8.611 secs. build 12-Jan-2021 00:57:19 :jalviewjsTranspile (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:57:21 build 12-Jan-2021 00:57:21 > Task :jalviewjsTranspile build 12-Jan-2021 00:57:21 Caching disabled for task ':jalviewjsTranspile' because: build 12-Jan-2021 00:57:21 Build cache is disabled build 12-Jan-2021 00:57:21 Task ':jalviewjsTranspile' is not up-to-date because: build 12-Jan-2021 00:57:21 Task.upToDateWhen is false. build 12-Jan-2021 00:57:21 Running task jalviewjsTranspile as IN_ECLIPSE=false build 12-Jan-2021 00:57:21 Starting process 'command '/home/bamboo/buildtools/eclipse/jee-2019-12/eclipse/eclipse''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 Command: /home/bamboo/buildtools/eclipse/jee-2019-12/eclipse/eclipse -nosplash --launcher.suppressErrors -application org.eclipse.jdt.apt.core.aptBuild -data /tmp/groovy-generated-4131780424687256073-tmpdir -cleanBuild jalview --launcher.appendVmargs -vmargs -Dorg.eclipse.equinox.p2.reconciler.dropins.directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/eclipse_dropins -Dnet.sf.j2s.core.headlessbuild=true -Dorg.jalview.jalviewjsj2sfilename=./build/jalviewjs/config/j2s build 12-Jan-2021 00:57:21 Successfully started process 'command '/home/bamboo/buildtools/eclipse/jee-2019-12/eclipse/eclipse'' build 12-Jan-2021 00:57:21 org.eclipse.m2e.logback.configuration: The org.eclipse.m2e.logback.configuration bundle was activated before the state location was initialized. Will retry after the state location is initialized. build 12-Jan-2021 00:57:21 org.eclipse.m2e.logback.configuration: Logback config file: /tmp/groovy-generated-4131780424687256073-tmpdir/.metadata/.plugins/org.eclipse.m2e.logback.configuration/logback.1.14.0.20191209-1925.xml build 12-Jan-2021 00:57:21 org.eclipse.m2e.logback.configuration: Initializing logback build 12-Jan-2021 00:57:52 Invoking 'Java Builder' on '/jalview'. build 12-Jan-2021 00:57:53 net.sf.j2s.core.3.2.10/3.2.10-v1 started build 12-Jan-2021 00:57:53 J2S CompilationParticipant started build 12-Jan-2021 00:57:53 J2S isActive true /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 build 12-Jan-2021 00:57:53 J2S aboutToBuild jalview /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 build 12-Jan-2021 00:57:53 J2S cleanStarting /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 build 12-Jan-2021 00:57:53 Cleaning output folder for jalview build 12-Jan-2021 00:57:53 Build done build 12-Jan-2021 00:57:53 Invoking 'Gradle Project Builder' on '/jalview'. build 12-Jan-2021 00:57:53 Invoking 'Java Builder' on '/jalview'. build 12-Jan-2021 00:57:53 J2S aboutToBuild jalview /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 build 12-Jan-2021 00:57:53 Preparing to build jalview build 12-Jan-2021 00:57:53 Cleaning output folder for jalview build 12-Jan-2021 00:57:53 J2S cleanStarting /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 build 12-Jan-2021 00:57:53 Copying resources to the output folder build 12-Jan-2021 00:57:53 Analyzing sources build 12-Jan-2021 00:57:53 J2S buildStarting 1032 files, contexts.size() = 1, isBatch=true build 12-Jan-2021 00:57:53 Compiling jalview/src/com/github/reinert/jjschema build 12-Jan-2021 00:57:56 Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 1 warning) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 2 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 3 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 4 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 5 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 9 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 12 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 13 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 14 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 15 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 37 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 38 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 46 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 47 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 48 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 49 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 50 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 51 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 52 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 59 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 63 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 67 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 69 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 89 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 90 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 91 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 98 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 108 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 113 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 114 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 115 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 119 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 120 warnings) Compiling jalview/src/com/stevesoft/pat build 12-Jan-2021 00:57:56 (Found 120 warnings) Compiling jalview/src/com/stevesoft/pat/wrap build 12-Jan-2021 00:57:56 (Found 120 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2 build 12-Jan-2021 00:57:57 (Found 122 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2 build 12-Jan-2021 00:57:57 (Found 129 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2 build 12-Jan-2021 00:57:57 (Found 132 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2/port build 12-Jan-2021 00:57:57 (Found 132 warnings) Compiling jalview/src/ext/vamsas build 12-Jan-2021 00:57:57 (Found 139 warnings) Compiling jalview/src/ext/vamsas build 12-Jan-2021 00:57:57 (Found 146 warnings) Compiling jalview/src/ext/vamsas build 12-Jan-2021 00:57:57 (Found 184 warnings) Compiling jalview/src/ext/vamsas build 12-Jan-2021 00:57:57 (Found 191 warnings) Compiling jalview/src/ext/vamsas build 12-Jan-2021 00:57:57 (Found 247 warnings) Compiling jalview/src/ext/vamsas build 12-Jan-2021 00:57:57 (Found 279 warnings) Compiling jalview/src/ext/vamsas build 12-Jan-2021 00:57:57 (Found 286 warnings) Compiling jalview/src/ext/vamsas build 12-Jan-2021 00:57:57 (Found 354 warnings) Compiling jalview/src/ext/vamsas build 12-Jan-2021 00:57:57 (Found 357 warnings) Compiling jalview/src/ext/vamsas build 12-Jan-2021 00:57:57 (Found 360 warnings) Compiling jalview/src/ext/vamsas build 12-Jan-2021 00:57:57 (Found 360 warnings) Compiling jalview/src/jalview/analysis build 12-Jan-2021 00:57:57 (Found 361 warnings) Compiling jalview/src/jalview/analysis build 12-Jan-2021 00:57:57 (Found 362 warnings) Compiling jalview/src/jalview/analysis build 12-Jan-2021 00:57:57 (Found 363 warnings) Compiling jalview/src/jalview/analysis build 12-Jan-2021 00:57:57 (Found 364 warnings) Compiling jalview/src/jalview/analysis build 12-Jan-2021 00:57:57 (Found 365 warnings) Compiling jalview/src/jalview/analysis build 12-Jan-2021 00:57:57 (Found 391 warnings) Compiling jalview/src/jalview/analysis build 12-Jan-2021 00:57:57 (Found 395 warnings) Compiling jalview/src/jalview/analysis build 12-Jan-2021 00:57:57 (Found 396 warnings) Compiling jalview/src/jalview/analysis build 12-Jan-2021 00:57:57 (Found 396 warnings) Compiling jalview/src/jalview/analysis/scoremodels build 12-Jan-2021 00:57:57 (Found 396 warnings) Compiling jalview/src/jalview/api build 12-Jan-2021 00:57:57 (Found 396 warnings) Compiling jalview/src/jalview/api/analysis build 12-Jan-2021 00:57:57 (Found 396 warnings) Compiling jalview/src/jalview/api/structures build 12-Jan-2021 00:57:57 (Found 397 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 449 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 458 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 459 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 464 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 465 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 466 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 477 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 479 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 482 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 483 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 484 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 485 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 487 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 489 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 490 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 491 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 496 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 497 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 498 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 499 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 503 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 505 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 513 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 523 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 524 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 525 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 527 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 528 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 529 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 532 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 540 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 542 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 543 warnings) Compiling jalview/src/jalview/appletgui build 12-Jan-2021 00:57:58 (Found 553 warnings) Compiling jalview/src/jalview/appletgui/js build 12-Jan-2021 00:57:58 (Found 555 warnings) Compiling jalview/src/jalview/appletgui/js build 12-Jan-2021 00:57:58 (Found 555 warnings) Compiling jalview/src/jalview/bin build 12-Jan-2021 00:57:58 (Found 561 warnings) Compiling jalview/src/jalview/bin build 12-Jan-2021 00:57:58 (Found 563 warnings) Compiling jalview/src/jalview/bin build 12-Jan-2021 00:57:58 (Found 565 warnings) Compiling jalview/src/jalview/bin build 12-Jan-2021 00:57:58 (Found 626 warnings) Compiling jalview/src/jalview/bin build 12-Jan-2021 00:57:58 (Found 631 warnings) Compiling jalview/src/jalview/bin build 12-Jan-2021 00:57:58 (Found 631 warnings) Compiling jalview/src/jalview/commands build 12-Jan-2021 00:57:58 (Found 631 warnings) Compiling jalview/src/jalview/controller build 12-Jan-2021 00:57:58 (Found 631 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:58 (Found 644 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 645 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 646 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 649 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 650 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 651 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 657 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 661 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 663 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 664 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 672 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 673 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 676 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 682 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 684 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 685 warnings) Compiling jalview/src/jalview/datamodel build 12-Jan-2021 00:57:59 (Found 685 warnings) Compiling jalview/src/jalview/datamodel/features build 12-Jan-2021 00:57:59 (Found 685 warnings) Compiling jalview/src/jalview/exceptions build 12-Jan-2021 00:57:59 (Found 685 warnings) Compiling jalview/src/jalview/ext/android build 12-Jan-2021 00:57:59 (Found 685 warnings) Compiling jalview/src/jalview/ext/ensembl build 12-Jan-2021 00:57:59 (Found 686 warnings) Compiling jalview/src/jalview/ext/ensembl build 12-Jan-2021 00:57:59 (Found 689 warnings) Compiling jalview/src/jalview/ext/htsjdk build 12-Jan-2021 00:57:59 (Found 690 warnings) Compiling jalview/src/jalview/ext/htsjdk build 12-Jan-2021 00:57:59 (Found 692 warnings) Compiling jalview/src/jalview/ext/jmol build 12-Jan-2021 00:57:59 (Found 694 warnings) Compiling jalview/src/jalview/ext/jmol build 12-Jan-2021 00:57:59 (Found 698 warnings) Compiling jalview/src/jalview/ext/paradise build 12-Jan-2021 00:57:59 (Found 698 warnings) Compiling jalview/src/jalview/ext/rbvi/chimera build 12-Jan-2021 00:57:59 (Found 700 warnings) Compiling jalview/src/jalview/ext/rbvi/chimera build 12-Jan-2021 00:57:59 (Found 700 warnings) Compiling jalview/src/jalview/ext/so build 12-Jan-2021 00:57:59 (Found 700 warnings) Compiling jalview/src/jalview/ext/varna build 12-Jan-2021 00:57:59 (Found 700 warnings) Compiling jalview/src/jalview/fts/api build 12-Jan-2021 00:57:59 (Found 701 warnings) Compiling jalview/src/jalview/fts/api build 12-Jan-2021 00:57:59 (Found 702 warnings) Compiling jalview/src/jalview/fts/core build 12-Jan-2021 00:57:59 (Found 704 warnings) Compiling jalview/src/jalview/fts/core build 12-Jan-2021 00:57:59 (Found 705 warnings) Compiling jalview/src/jalview/fts/core build 12-Jan-2021 00:57:59 (Found 706 warnings) Compiling jalview/src/jalview/fts/core build 12-Jan-2021 00:57:59 (Found 725 warnings) Compiling jalview/src/jalview/fts/service/pdb build 12-Jan-2021 00:57:59 (Found 725 warnings) Compiling jalview/src/jalview/fts/service/uniprot build 12-Jan-2021 00:57:59 (Found 744 warnings) Compiling jalview/src/jalview/fts/service/uniprot build 12-Jan-2021 00:57:59 (Found 748 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:57:59 (Found 751 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:57:59 (Found 757 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:57:59 (Found 758 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 759 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 760 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 762 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 764 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 765 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 766 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 775 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 776 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 806 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 807 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 808 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 813 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 815 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 817 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 819 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 823 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 828 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 829 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 833 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 834 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 835 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 836 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 837 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 843 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 844 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 845 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 846 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 855 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 856 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 857 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 858 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 859 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 865 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 880 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 882 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 883 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 889 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 897 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 909 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 910 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 911 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 912 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 913 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 917 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 927 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 954 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 962 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 971 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 972 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:00 (Found 973 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:01 (Found 1000 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:01 (Found 1001 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:01 (Found 1008 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:01 (Found 1066 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:01 (Found 1083 warnings) Compiling jalview/src/jalview/gui build 12-Jan-2021 00:58:01 (Found 1083 warnings) Compiling jalview/src/jalview/httpserver build 12-Jan-2021 00:58:01 (Found 1083 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1088 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1090 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1110 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1111 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1113 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1114 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1118 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1119 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1120 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1121 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1159 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1161 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1163 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1182 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1184 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1185 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1186 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1199 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1260 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1261 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1343 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1348 warnings) Compiling jalview/src/jalview/io build 12-Jan-2021 00:58:01 (Found 1348 warnings) Compiling jalview/src/jalview/io/cache build 12-Jan-2021 00:58:01 (Found 1348 warnings) Compiling jalview/src/jalview/io/gff build 12-Jan-2021 00:58:01 (Found 1349 warnings) Compiling jalview/src/jalview/io/gff build 12-Jan-2021 00:58:01 (Found 1349 warnings) Compiling jalview/src/jalview/io/packed build 12-Jan-2021 00:58:01 (Found 1355 warnings) Compiling jalview/src/jalview/io/packed build 12-Jan-2021 00:58:01 (Found 1356 warnings) Compiling jalview/src/jalview/io/packed build 12-Jan-2021 00:58:01 (Found 1356 warnings) Compiling jalview/src/jalview/io/vamsas build 12-Jan-2021 00:58:01 (Found 1374 warnings) Compiling jalview/src/jalview/io/vamsas build 12-Jan-2021 00:58:01 (Found 1385 warnings) Compiling jalview/src/jalview/io/vamsas build 12-Jan-2021 00:58:01 (Found 1386 warnings) Compiling jalview/src/jalview/io/vamsas build 12-Jan-2021 00:58:01 (Found 1399 warnings) Compiling jalview/src/jalview/io/vamsas build 12-Jan-2021 00:58:01 (Found 1403 warnings) Compiling jalview/src/jalview/io/vamsas build 12-Jan-2021 00:58:01 (Found 1407 warnings) Compiling jalview/src/jalview/io/vamsas build 12-Jan-2021 00:58:01 (Found 1420 warnings) Compiling jalview/src/jalview/io/vamsas build 12-Jan-2021 00:58:01 (Found 1423 warnings) Compiling jalview/src/jalview/io/vcf build 12-Jan-2021 00:58:01 (Found 1424 warnings) Compiling jalview/src/jalview/javascript/json build 12-Jan-2021 00:58:01 (Found 1424 warnings) Compiling jalview/src/jalview/javascript/log4j build 12-Jan-2021 00:58:01 (Found 1426 warnings) Compiling jalview/src/jalview/javascript/log4j build 12-Jan-2021 00:58:01 (Found 1428 warnings) Compiling jalview/src/jalview/javascript/log4j build 12-Jan-2021 00:58:01 (Found 1429 warnings) Compiling jalview/src/jalview/javascript/log4j/spi build 12-Jan-2021 00:58:01 (Found 1429 warnings) Compiling jalview/src/jalview/javascript/web build 12-Jan-2021 00:58:01 (Found 1429 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1430 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1431 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1434 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1435 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1436 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1437 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1441 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1443 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1451 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1452 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1453 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1458 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1459 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1460 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1463 warnings) Compiling jalview/src/jalview/jbgui build 12-Jan-2021 00:58:01 (Found 1463 warnings) Compiling jalview/src/jalview/json/binding/biojs build 12-Jan-2021 00:58:01 (Found 1463 warnings) Compiling jalview/src/jalview/json/binding/biojson/v1 build 12-Jan-2021 00:58:01 (Found 1463 warnings) Compiling jalview/src/jalview/math build 12-Jan-2021 00:58:02 (Found 1494 warnings) Compiling jalview/src/jalview/project build 12-Jan-2021 00:58:02 (Found 1494 warnings) Compiling jalview/src/jalview/renderer build 12-Jan-2021 00:58:02 (Found 1494 warnings) Compiling jalview/src/jalview/renderer/seqfeatures build 12-Jan-2021 00:58:02 (Found 1494 warnings) Compiling jalview/src/jalview/rest build 12-Jan-2021 00:58:02 (Found 1494 warnings) Compiling jalview/src/jalview/schemes build 12-Jan-2021 00:58:02 (Found 1494 warnings) Compiling jalview/src/jalview/structure build 12-Jan-2021 00:58:02 (Found 1494 warnings) Compiling jalview/src/jalview/structures/models build 12-Jan-2021 00:58:02 (Found 1494 warnings) Compiling jalview/src/jalview/urls build 12-Jan-2021 00:58:02 (Found 1495 warnings) Compiling jalview/src/jalview/urls build 12-Jan-2021 00:58:02 (Found 1495 warnings) Compiling jalview/src/jalview/urls/api build 12-Jan-2021 00:58:02 (Found 1495 warnings) Compiling jalview/src/jalview/urls/applet build 12-Jan-2021 00:58:02 (Found 1495 warnings) Compiling jalview/src/jalview/urls/desktop build 12-Jan-2021 00:58:02 (Found 1495 warnings) Compiling jalview/src/jalview/util build 12-Jan-2021 00:58:02 (Found 1518 warnings) Compiling jalview/src/jalview/util build 12-Jan-2021 00:58:02 (Found 1519 warnings) Compiling jalview/src/jalview/util build 12-Jan-2021 00:58:02 (Found 1531 warnings) Compiling jalview/src/jalview/util build 12-Jan-2021 00:58:02 (Found 1533 warnings) Compiling jalview/src/jalview/util build 12-Jan-2021 00:58:02 (Found 1537 warnings) Compiling jalview/src/jalview/util build 12-Jan-2021 00:58:02 (Found 1541 warnings) Compiling jalview/src/jalview/util build 12-Jan-2021 00:58:02 (Found 1565 warnings) Compiling jalview/src/jalview/util build 12-Jan-2021 00:58:02 (Found 1566 warnings) Compiling jalview/src/jalview/util build 12-Jan-2021 00:58:02 (Found 1566 warnings) Compiling jalview/src/jalview/util/dialogrunner build 12-Jan-2021 00:58:02 (Found 1566 warnings) Compiling jalview/src/jalview/util build 12-Jan-2021 00:58:02 (Found 1566 warnings) Compiling jalview/src/jalview/util/matcher build 12-Jan-2021 00:58:02 (Found 1566 warnings) Compiling jalview/src/jalview/viewmodel build 12-Jan-2021 00:58:02 (Found 1566 warnings) Compiling jalview/src/jalview/viewmodel/annotationfilter build 12-Jan-2021 00:58:02 (Found 1566 warnings) Compiling jalview/src/jalview/viewmodel/seqfeatures build 12-Jan-2021 00:58:02 (Found 1566 warnings) Compiling jalview/src/jalview/viewmodel/styles build 12-Jan-2021 00:58:02 (Found 1566 warnings) Compiling jalview/src/jalview/workers build 12-Jan-2021 00:58:02 (Found 1570 warnings) Compiling jalview/src/jalview/workers build 12-Jan-2021 00:58:02 (Found 1570 warnings) Compiling jalview/src/jalview/ws build 12-Jan-2021 00:58:02 (Found 1574 warnings) Compiling jalview/src/jalview/ws build 12-Jan-2021 00:58:02 (Found 1574 warnings) Compiling jalview/src/jalview/ws/dbsources build 12-Jan-2021 00:58:02 (Found 1574 warnings) Compiling jalview/src/jalview/ws/ebi build 12-Jan-2021 00:58:02 (Found 1574 warnings) Compiling jalview/src/jalview/ws/io/mime build 12-Jan-2021 00:58:02 (Found 1574 warnings) Compiling jalview/src/jalview/ws/jws1 build 12-Jan-2021 00:58:02 (Found 1575 warnings) Compiling jalview/src/jalview/ws/jws1 build 12-Jan-2021 00:58:02 (Found 1579 warnings) Compiling jalview/src/jalview/ws/jws1 build 12-Jan-2021 00:58:02 (Found 1595 warnings) Compiling jalview/src/jalview/ws/jws1 build 12-Jan-2021 00:58:02 (Found 1608 warnings) Compiling jalview/src/jalview/ws/jws1 build 12-Jan-2021 00:58:02 (Found 1622 warnings) Compiling jalview/src/jalview/ws/jws1 build 12-Jan-2021 00:58:02 (Found 1628 warnings) Compiling jalview/src/jalview/ws/jws1 build 12-Jan-2021 00:58:02 (Found 1629 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:02 (Found 1630 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:02 (Found 1640 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:02 (Found 1647 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:02 (Found 1661 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:03 (Found 1664 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:03 (Found 1668 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:03 (Found 1674 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:03 (Found 1680 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:03 (Found 1691 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:03 (Found 1695 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:03 (Found 1721 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:03 (Found 1744 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:03 (Found 1745 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:03 (Found 1750 warnings) Compiling jalview/src/jalview/ws/jws2 build 12-Jan-2021 00:58:03 (Found 1756 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 12-Jan-2021 00:58:03 (Found 1760 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 12-Jan-2021 00:58:03 (Found 1763 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 12-Jan-2021 00:58:03 (Found 1774 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 12-Jan-2021 00:58:03 (Found 1781 warnings) Compiling jalview/src/jalview/ws/jws2/jabaws2 build 12-Jan-2021 00:58:03 (Found 1781 warnings) Compiling jalview/src/jalview/ws/params build 12-Jan-2021 00:58:03 (Found 1782 warnings) Compiling jalview/src/jalview/ws/params build 12-Jan-2021 00:58:03 (Found 1782 warnings) Compiling jalview/src/jalview/ws/params/simple build 12-Jan-2021 00:58:03 (Found 1783 warnings) Compiling jalview/src/jalview/ws/params/simple build 12-Jan-2021 00:58:03 (Found 1783 warnings) Compiling jalview/src/jalview/ws/rest build 12-Jan-2021 00:58:03 (Found 1784 warnings) Compiling jalview/src/jalview/ws/rest build 12-Jan-2021 00:58:03 (Found 1789 warnings) Compiling jalview/src/jalview/ws/rest build 12-Jan-2021 00:58:03 (Found 1790 warnings) Compiling jalview/src/jalview/ws/rest build 12-Jan-2021 00:58:03 (Found 1791 warnings) Compiling jalview/src/jalview/ws/rest build 12-Jan-2021 00:58:03 (Found 1797 warnings) Compiling jalview/src/jalview/ws/rest build 12-Jan-2021 00:58:03 (Found 1806 warnings) Compiling jalview/src/jalview/ws/rest build 12-Jan-2021 00:58:03 (Found 1812 warnings) Compiling jalview/src/jalview/ws/rest build 12-Jan-2021 00:58:03 (Found 1812 warnings) Compiling jalview/src/jalview/ws/rest/params build 12-Jan-2021 00:58:03 (Found 1815 warnings) Compiling jalview/src/jalview/ws/seqfetcher build 12-Jan-2021 00:58:03 (Found 1815 warnings) Compiling jalview/src/jalview/ws/sifts build 12-Jan-2021 00:58:03 (Found 1817 warnings) Compiling jalview/src/jalview/ws/sifts build 12-Jan-2021 00:58:03 (Found 1820 warnings) Compiling jalview/src/jalview/ws/uimodel build 12-Jan-2021 00:58:03 (Found 1820 warnings) Compiling jalview/src/jalview/ws/utils build 12-Jan-2021 00:58:03 (Found 1820 warnings) Compiling jalview/src/jalview/xml/binding/embl build 12-Jan-2021 00:58:03 (Found 1820 warnings) Compiling jalview/src/jalview/xml/binding/jalview build 12-Jan-2021 00:58:03 (Found 1820 warnings) Compiling jalview/src/jalview/xml/binding/sifts build 12-Jan-2021 00:58:03 (Found 1820 warnings) Compiling jalview/src/jalview/xml/binding/uniprot build 12-Jan-2021 00:58:03 (Found 1821 warnings) Compiling jalview/src/javajs/async build 12-Jan-2021 00:58:03 (Found 1822 warnings) Compiling jalview/src/javajs/async build 12-Jan-2021 00:58:03 (Found 1824 warnings) Compiling jalview/src/javajs/async build 12-Jan-2021 00:58:03 (Found 1831 warnings) Compiling jalview/src/mc_view build 12-Jan-2021 00:58:03 (Found 1832 warnings) Compiling jalview/src/mc_view build 12-Jan-2021 00:58:03 (Found 1837 warnings) Compiling jalview/src/mc_view build 12-Jan-2021 00:58:03 (Found 1844 warnings) Compiling jalview/src/mc_view build 12-Jan-2021 00:58:03 (Found 1845 warnings) Compiling jalview/src/mc_view build 12-Jan-2021 00:58:03 (Found 1846 warnings) Compiling jalview/src/mc_view build 12-Jan-2021 00:58:03 (Found 1846 warnings) Compiling jalview/src/org/jibble/epsgraphics build 12-Jan-2021 00:58:03 (Found 1847 warnings) Compiling jalview/src/org/jibble/epsgraphics build 12-Jan-2021 00:58:03 (Found 1853 warnings) Compiling jalview/src/org/jibble/epsgraphics build 12-Jan-2021 00:58:03 (Found 1853 warnings) Compiling jalview/src/org/json build 12-Jan-2021 00:58:03 (Found 1854 warnings) Compiling jalview/src/org/json build 12-Jan-2021 00:58:03 (Found 1855 warnings) Compiling jalview/src/org/json build 12-Jan-2021 00:58:03 (Found 1866 warnings) Compiling jalview/src/org/json/simple build 12-Jan-2021 00:58:03 (Found 1872 warnings) Compiling jalview/src/org/json/simple build 12-Jan-2021 00:58:03 (Found 1881 warnings) Compiling jalview/src/org/json/simple build 12-Jan-2021 00:58:03 (Found 1883 warnings) Compiling jalview/src/org/json/simple build 12-Jan-2021 00:58:03 (Found 1885 warnings) Compiling jalview/src/org/json/simple/parser build 12-Jan-2021 00:58:03 (Found 1960 warnings) Compiling jalview/src/org/json/simple/parser build 12-Jan-2021 00:58:03 (Found 1964 warnings) Compiling jalview/src/org/json/simple/parser build 12-Jan-2021 00:58:03 (Found 1964 warnings) Compiling jalview/src/org/stackoverflowusers/file build 12-Jan-2021 00:58:03 (Found 1965 warnings) Compiling jalview/src/swingjs/api build 12-Jan-2021 00:58:03 (Found 1965 warnings) Compiling jalview/src/swingjs/api/js build 12-Jan-2021 00:58:03 (Found 1966 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 12-Jan-2021 00:58:03 (Found 1968 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 12-Jan-2021 00:58:03 (Found 1969 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 12-Jan-2021 00:58:03 (Found 1971 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 12-Jan-2021 00:58:03 (Found 1974 warnings) Compiling jalview/src/uk/ac/ebi/www build 12-Jan-2021 00:58:03 (Found 1977 warnings) Compiling jalview/src/uk/ac/ebi/www build 12-Jan-2021 00:58:03 (Found 1980 warnings) Compiling jalview/src/uk/ac/ebi/www build 12-Jan-2021 00:58:03 (Found 1987 warnings) Compiling jalview/src/uk/ac/ebi/www build 12-Jan-2021 00:58:03 (Found 2035 warnings) Compiling jalview/src/uk/ac/ebi/www build 12-Jan-2021 00:58:03 (Found 2077 warnings) Compiling jalview/src/uk/ac/ebi/www/picr/AccessionMappingService build 12-Jan-2021 00:58:03 (Found 2084 warnings) Compiling jalview/src/uk/ac/ebi/www/picr/AccessionMappingService build 12-Jan-2021 00:58:03 (Found 2084 warnings) Compiling jalview/src/vamsas build 12-Jan-2021 00:58:03 (Found 2085 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2087 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2088 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2090 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2091 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2093 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2094 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2096 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2097 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2099 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2100 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2102 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2103 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2105 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2106 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2108 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2109 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2110 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2112 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2114 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2115 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2117 warnings) Compiling jalview/src/vamsas/objects/simple build 12-Jan-2021 00:58:03 (Found 2117 warnings) Cleaning output folder for jalview build 12-Jan-2021 00:58:03 (Found 2117 warnings) Copying resources to the output folder build 12-Jan-2021 00:58:04 (Found 2117 warnings) Analyzing sources build 12-Jan-2021 00:58:04 J2S buildStarting 257 files, contexts.size() = 2, isBatch=true build 12-Jan-2021 00:58:04 (Found 2117 warnings) Compiling jalview/test/jalview/analysis build 12-Jan-2021 00:58:04 (Found 2125 warnings) Compiling jalview/test/jalview/analysis build 12-Jan-2021 00:58:04 (Found 2131 warnings) Compiling jalview/test/jalview/analysis build 12-Jan-2021 00:58:04 (Found 2132 warnings) Compiling jalview/test/jalview/analysis build 12-Jan-2021 00:58:05 (Found 2134 warnings) Compiling jalview/test/jalview/analysis build 12-Jan-2021 00:58:05 (Found 2175 warnings) Compiling jalview/test/jalview/analysis build 12-Jan-2021 00:58:05 (Found 2175 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 12-Jan-2021 00:58:05 (Found 2180 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 12-Jan-2021 00:58:05 (Found 2181 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 12-Jan-2021 00:58:05 (Found 2181 warnings) Compiling jalview/test/jalview/bin build 12-Jan-2021 00:58:05 (Found 2182 warnings) Compiling jalview/test/jalview/commands build 12-Jan-2021 00:58:05 (Found 2183 warnings) Compiling jalview/test/jalview/controller build 12-Jan-2021 00:58:05 (Found 2183 warnings) Compiling jalview/test/jalview/datamodel build 12-Jan-2021 00:58:05 (Found 2184 warnings) Compiling jalview/test/jalview/datamodel build 12-Jan-2021 00:58:05 (Found 2196 warnings) Compiling jalview/test/jalview/datamodel build 12-Jan-2021 00:58:05 (Found 2198 warnings) Compiling jalview/test/jalview/datamodel build 12-Jan-2021 00:58:05 (Found 2207 warnings) Compiling jalview/test/jalview/datamodel build 12-Jan-2021 00:58:05 (Found 2208 warnings) Compiling jalview/test/jalview/datamodel build 12-Jan-2021 00:58:05 (Found 2209 warnings) Compiling jalview/test/jalview/datamodel build 12-Jan-2021 00:58:05 (Found 2210 warnings) Compiling jalview/test/jalview/datamodel build 12-Jan-2021 00:58:05 (Found 2211 warnings) Compiling jalview/test/jalview/datamodel build 12-Jan-2021 00:58:05 (Found 2212 warnings) Compiling jalview/test/jalview/datamodel build 12-Jan-2021 00:58:05 (Found 2213 warnings) Compiling jalview/test/jalview/datamodel build 12-Jan-2021 00:58:05 (Found 2214 warnings) Compiling jalview/test/jalview/datamodel/features build 12-Jan-2021 00:58:05 (Found 2215 warnings) Compiling jalview/test/jalview/datamodel/features build 12-Jan-2021 00:58:05 (Found 2215 warnings) Compiling jalview/test/jalview/ext/android build 12-Jan-2021 00:58:05 (Found 2215 warnings) Compiling jalview/test/jalview/ext/ensembl build 12-Jan-2021 00:58:05 (Found 2215 warnings) Compiling jalview/test/jalview/ext/htsjdk build 12-Jan-2021 00:58:05 (Found 2216 warnings) Compiling jalview/test/jalview/ext/jmol build 12-Jan-2021 00:58:05 (Found 2217 warnings) Compiling jalview/test/jalview/ext/jmol build 12-Jan-2021 00:58:05 (Found 2217 warnings) Compiling jalview/test/jalview/ext/paradise build 12-Jan-2021 00:58:05 (Found 2217 warnings) Compiling jalview/test/jalview/ext/rbvi/chimera build 12-Jan-2021 00:58:05 (Found 2217 warnings) Compiling jalview/test/jalview/ext/so build 12-Jan-2021 00:58:05 (Found 2217 warnings) Compiling jalview/test/jalview/fts/core build 12-Jan-2021 00:58:05 (Found 2217 warnings) Compiling jalview/test/jalview/fts/service/pdb build 12-Jan-2021 00:58:05 (Found 2218 warnings) Compiling jalview/test/jalview/fts/service/pdb build 12-Jan-2021 00:58:05 (Found 2218 warnings) Compiling jalview/test/jalview/gui build 12-Jan-2021 00:58:05 (Found 2220 warnings) Compiling jalview/test/jalview/gui build 12-Jan-2021 00:58:05 (Found 2221 warnings) Compiling jalview/test/jalview/gui build 12-Jan-2021 00:58:05 (Found 2222 warnings) Compiling jalview/test/jalview/gui build 12-Jan-2021 00:58:05 (Found 2224 warnings) Compiling jalview/test/jalview/gui build 12-Jan-2021 00:58:05 (Found 2227 warnings) Compiling jalview/test/jalview/gui build 12-Jan-2021 00:58:05 (Found 2229 warnings) Compiling jalview/test/jalview/gui build 12-Jan-2021 00:58:05 (Found 2230 warnings) Compiling jalview/test/jalview/io build 12-Jan-2021 00:58:05 (Found 2231 warnings) Compiling jalview/test/jalview/io build 12-Jan-2021 00:58:05 (Found 2235 warnings) Compiling jalview/test/jalview/io build 12-Jan-2021 00:58:05 (Found 2239 warnings) Compiling jalview/test/jalview/io build 12-Jan-2021 00:58:05 (Found 2241 warnings) Compiling jalview/test/jalview/io build 12-Jan-2021 00:58:05 (Found 2241 warnings) Compiling jalview/test/jalview/io/cache build 12-Jan-2021 00:58:05 (Found 2241 warnings) Compiling jalview/test/jalview/io/gff build 12-Jan-2021 00:58:05 (Found 2242 warnings) Compiling jalview/test/jalview/io/gff build 12-Jan-2021 00:58:06 (Found 2251 warnings) Compiling jalview/test/jalview/io/vcf build 12-Jan-2021 00:58:06 (Found 2251 warnings) Compiling jalview/test/jalview/math build 12-Jan-2021 00:58:06 (Found 2252 warnings) Compiling jalview/test/jalview/project build 12-Jan-2021 00:58:06 (Found 2253 warnings) Compiling jalview/test/jalview/renderer build 12-Jan-2021 00:58:06 (Found 2254 warnings) Compiling jalview/test/jalview/renderer build 12-Jan-2021 00:58:06 (Found 2254 warnings) Compiling jalview/test/jalview/renderer/seqfeatures build 12-Jan-2021 00:58:06 (Found 2254 warnings) Compiling jalview/test/jalview/schemes build 12-Jan-2021 00:58:06 (Found 2254 warnings) Compiling jalview/test/jalview/structure build 12-Jan-2021 00:58:06 (Found 2256 warnings) Compiling jalview/test/jalview/structure build 12-Jan-2021 00:58:06 (Found 2257 warnings) Compiling jalview/test/jalview/structure build 12-Jan-2021 00:58:06 (Found 2262 warnings) Compiling jalview/test/jalview/structure build 12-Jan-2021 00:58:06 (Found 2262 warnings) Compiling jalview/test/jalview/structures/models build 12-Jan-2021 00:58:06 (Found 2263 warnings) Compiling jalview/test/jalview/urls build 12-Jan-2021 00:58:06 (Found 2268 warnings) Compiling jalview/test/jalview/urls build 12-Jan-2021 00:58:06 (Found 2273 warnings) Compiling jalview/test/jalview/urls build 12-Jan-2021 00:58:06 (Found 2273 warnings) Compiling jalview/test/jalview/util build 12-Jan-2021 00:58:06 (Found 2280 warnings) Compiling jalview/test/jalview/util build 12-Jan-2021 00:58:06 (Found 2284 warnings) Compiling jalview/test/jalview/util build 12-Jan-2021 00:58:06 (Found 2289 warnings) Compiling jalview/test/jalview/util build 12-Jan-2021 00:58:06 (Found 2289 warnings) Compiling jalview/test/jalview/util/dialogrunner build 12-Jan-2021 00:58:06 (Found 2289 warnings) Compiling jalview/test/jalview/util/matcher build 12-Jan-2021 00:58:06 (Found 2292 warnings) Compiling jalview/test/jalview/util/matcher build 12-Jan-2021 00:58:06 (Found 2298 warnings) Compiling jalview/test/jalview/viewmodel build 12-Jan-2021 00:58:06 (Found 2304 warnings) Compiling jalview/test/jalview/viewmodel build 12-Jan-2021 00:58:06 (Found 2305 warnings) Compiling jalview/test/jalview/viewmodel/styles build 12-Jan-2021 00:58:06 (Found 2305 warnings) Compiling jalview/test/jalview/workers build 12-Jan-2021 00:58:06 (Found 2305 warnings) Compiling jalview/test/jalview/ws build 12-Jan-2021 00:58:06 (Found 2307 warnings) Compiling jalview/test/jalview/ws build 12-Jan-2021 00:58:06 (Found 2307 warnings) Compiling jalview/test/jalview/ws/dbsources build 12-Jan-2021 00:58:06 (Found 2307 warnings) Compiling jalview/test/jalview/ws/ebi build 12-Jan-2021 00:58:06 (Found 2314 warnings) Compiling jalview/test/jalview/ws/gui build 12-Jan-2021 00:58:06 (Found 2314 warnings) Compiling jalview/test/jalview/ws/jabaws build 12-Jan-2021 00:58:06 (Found 2315 warnings) Compiling jalview/test/jalview/ws/jabaws build 12-Jan-2021 00:58:06 (Found 2316 warnings) Compiling jalview/test/jalview/ws/jabaws build 12-Jan-2021 00:58:06 (Found 2320 warnings) Compiling jalview/test/jalview/ws/jabaws build 12-Jan-2021 00:58:06 (Found 2335 warnings) Compiling jalview/test/jalview/ws/jws2 build 12-Jan-2021 00:58:06 (Found 2335 warnings) Compiling jalview/test/jalview/ws/rest build 12-Jan-2021 00:58:06 (Found 2336 warnings) Compiling jalview/test/jalview/ws/rest build 12-Jan-2021 00:58:06 (Found 2336 warnings) Compiling jalview/test/jalview/ws/seqfetcher build 12-Jan-2021 00:58:06 (Found 2336 warnings) Compiling jalview/test/jalview/ws/sifts build 12-Jan-2021 00:58:06 (Found 2338 warnings) Compiling jalview/test/jalview/ws/utils build 12-Jan-2021 00:58:06 (Found 2354 warnings) Compiling jalview/test/junit/extensions build 12-Jan-2021 00:58:06 (Found 2356 warnings) Compiling jalview/test/junit/extensions build 12-Jan-2021 00:58:06 (Found 2356 warnings) Compiling jalview/test/mc_view build 12-Jan-2021 00:58:06 (Found 2357 warnings) Compiling jalview/test/mc_view build 12-Jan-2021 00:58:06 J2S using configuration file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/.j2s build 12-Jan-2021 00:58:06 j2s.config.altfileproperty = org.jalview.jalviewjsj2sfilename build 12-Jan-2021 00:58:06 J2S System.getProperty("org.jalview.jalviewjsj2sfilename") = ./build/jalviewjs/config/j2s build 12-Jan-2021 00:58:06 J2S using configuration file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/./build/jalviewjs/config/j2s build 12-Jan-2021 00:58:06 j2s.compiler.status = enable build 12-Jan-2021 00:58:06 j2s.compiler.java.version = 8 build 12-Jan-2021 00:58:06 J2S compiler version set to 8 build 12-Jan-2021 00:58:06 j2s.break.on.error = false build 12-Jan-2021 00:58:06 j2s.compiler.mode = nodebug build 12-Jan-2021 00:58:06 j2s.site.directory = ./build/jalviewjs/tmp/site_js build 12-Jan-2021 00:58:06 J2S writing to /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/./build/jalviewjs/tmp/site_js/swingjs/j2s build 12-Jan-2021 00:58:06 j2s.log.methods.declared = build 12-Jan-2021 00:58:06 j2s.log.methods.called = build 12-Jan-2021 00:58:06 j2s.excluded.paths = test;testng;util build 12-Jan-2021 00:58:06 j2s.compiler.read.annotations = true build 12-Jan-2021 00:58:06 j2s.compiler.ignored.annotations = CallerSensitive;ConstructorProperties;Deprecated;Override;SafeVarargs;SuppressWarnings;FunctionalInterface;Documented;Inherited;Native;Repeatable;Retention; build 12-Jan-2021 00:58:06 j2s.testing = false build 12-Jan-2021 00:58:06 j2s.compiler.nonqualified.packages = build 12-Jan-2021 00:58:06 j2s.compiler.nonqualified.classes = build 12-Jan-2021 00:58:06 j2s.class.replacements = org.apache.log4j.->jalview.javascript.log4j. build 12-Jan-2021 00:58:06 j2s.template.html = utils/jalviewjs/template.html build 12-Jan-2021 00:58:06 J2S using HTML template /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/utils/jalviewjs/template.html build 12-Jan-2021 00:58:06 class replacement org.apache.log4j. --> jalview.javascript.log4j. build 12-Jan-2021 00:58:06 J2S building JavaScript jalview /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 Tue Jan 12 00:58:06 GMT 2021 build 12-Jan-2021 00:58:06 J2S building JavaScript for 1032 files build 12-Jan-2021 00:58:06 J2S transpiling (1/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/github/reinert/jjschema/Attributes.java build 12-Jan-2021 00:58:07 j2s copying resources from /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com to /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/./build/jalviewjs/tmp/site_js/swingjs/j2s/com build 12-Jan-2021 00:58:07 J2S transpiling (2/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/AmpersandRule.java build 12-Jan-2021 00:58:07 J2S transpiling (3/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Any.java build 12-Jan-2021 00:58:07 J2S transpiling (4/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/BackG.java build 12-Jan-2021 00:58:07 J2S transpiling (5/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/BackMatch.java build 12-Jan-2021 00:58:07 J2S transpiling (6/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/BackRefRule.java build 12-Jan-2021 00:58:07 J2S transpiling (7/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Backup.java build 12-Jan-2021 00:58:07 J2S transpiling (8/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/BasicStringBufferLike.java build 12-Jan-2021 00:58:07 J2S transpiling (9/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Bits.java build 12-Jan-2021 00:58:07 J2S transpiling (10/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Boundary.java build 12-Jan-2021 00:58:07 J2S transpiling (11/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Bracket.java build 12-Jan-2021 00:58:07 J2S transpiling (12/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/CaseMgr.java build 12-Jan-2021 00:58:07 J2S transpiling (13/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/ChangeRule.java build 12-Jan-2021 00:58:07 J2S transpiling (14/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/CodeRule.java build 12-Jan-2021 00:58:07 J2S transpiling (15/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Ctrl.java build 12-Jan-2021 00:58:07 J2S transpiling (16/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Custom.java build 12-Jan-2021 00:58:07 J2S transpiling (17/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/CustomEndpoint.java build 12-Jan-2021 00:58:07 J2S transpiling (18/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/DirFileRegex.java build 12-Jan-2021 00:58:07 J2S transpiling (19/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/DotMulti.java build 12-Jan-2021 00:58:07 J2S transpiling (20/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/End.java build 12-Jan-2021 00:58:07 J2S transpiling (21/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/FastBracket.java build 12-Jan-2021 00:58:07 J2S transpiling (22/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/FastMulti.java build 12-Jan-2021 00:58:07 J2S transpiling (23/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/FileRegex.java build 12-Jan-2021 00:58:07 J2S transpiling (24/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Group.java build 12-Jan-2021 00:58:08 J2S transpiling (25/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/LeftRule.java build 12-Jan-2021 00:58:08 J2S transpiling (26/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Multi.java build 12-Jan-2021 00:58:08 J2S transpiling (27/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/MultiMin.java build 12-Jan-2021 00:58:08 J2S transpiling (28/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Multi_stage2.java build 12-Jan-2021 00:58:08 J2S transpiling (29/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/NoPattern.java build 12-Jan-2021 00:58:08 J2S transpiling (30/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/NonDirFileRegex.java build 12-Jan-2021 00:58:08 J2S transpiling (31/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/NotImplementedError.java build 12-Jan-2021 00:58:08 J2S transpiling (32/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/NullPattern.java build 12-Jan-2021 00:58:08 J2S transpiling (33/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/NullRule.java build 12-Jan-2021 00:58:08 J2S transpiling (34/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Or.java build 12-Jan-2021 00:58:08 J2S transpiling (35/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/OrMark.java build 12-Jan-2021 00:58:08 J2S transpiling (36/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/PartialBuffer.java build 12-Jan-2021 00:58:08 J2S transpiling (37/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Pattern.java build 12-Jan-2021 00:58:08 J2S transpiling (38/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/PatternSub.java build 12-Jan-2021 00:58:08 J2S transpiling (39/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/PopRule.java build 12-Jan-2021 00:58:08 J2S transpiling (40/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Prop.java build 12-Jan-2021 00:58:08 J2S transpiling (41/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Pthings.java build 12-Jan-2021 00:58:08 J2S transpiling (42/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/PushRule.java build 12-Jan-2021 00:58:08 J2S transpiling (43/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/RBuffer.java build 12-Jan-2021 00:58:08 J2S transpiling (44/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Range.java build 12-Jan-2021 00:58:08 J2S transpiling (45/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/RegOpt.java build 12-Jan-2021 00:58:08 J2S transpiling (46/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/RegRes.java build 12-Jan-2021 00:58:08 J2S transpiling (47/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/RegSyntax.java build 12-Jan-2021 00:58:08 J2S transpiling (48/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/RegSyntaxError.java build 12-Jan-2021 00:58:08 J2S transpiling (49/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Regex.java build 12-Jan-2021 00:58:08 J2S transpiling (50/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/RegexReader.java build 12-Jan-2021 00:58:08 J2S transpiling (51/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/RegexTokenizer.java build 12-Jan-2021 00:58:08 J2S transpiling (52/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/RegexWriter.java build 12-Jan-2021 00:58:08 >>>main found for com.stevesoft.pat.RegexWriter build 12-Jan-2021 00:58:08 J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/./build/jalviewjs/tmp/site_js/com_stevesoft_pat_RegexWriter.html build 12-Jan-2021 00:58:08 J2S transpiling (53/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/ReplaceRule.java build 12-Jan-2021 00:58:09 J2S transpiling (54/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Replacer.java build 12-Jan-2021 00:58:09 J2S transpiling (55/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/RightRule.java build 12-Jan-2021 00:58:09 J2S transpiling (56/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Rthings.java build 12-Jan-2021 00:58:09 J2S transpiling (57/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/RuleHolder.java build 12-Jan-2021 00:58:09 J2S transpiling (58/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Skip.java build 12-Jan-2021 00:58:09 J2S transpiling (59/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Skip2.java build 12-Jan-2021 00:58:09 J2S transpiling (60/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/SkipBMH.java build 12-Jan-2021 00:58:09 J2S transpiling (61/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Skipped.java build 12-Jan-2021 00:58:09 J2S transpiling (62/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/SpecialRule.java build 12-Jan-2021 00:58:09 J2S transpiling (63/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Start.java build 12-Jan-2021 00:58:09 J2S transpiling (64/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/StrPos.java build 12-Jan-2021 00:58:09 J2S transpiling (65/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/StringBufferLike.java build 12-Jan-2021 00:58:09 J2S transpiling (66/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/StringLike.java build 12-Jan-2021 00:58:09 J2S transpiling (67/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/StringRule.java build 12-Jan-2021 00:58:09 J2S transpiling (68/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/SubMark.java build 12-Jan-2021 00:58:09 J2S transpiling (69/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/TransPat.java build 12-Jan-2021 00:58:09 J2S transpiling (70/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Transformer.java build 12-Jan-2021 00:58:09 J2S transpiling (71/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/UniValidator.java build 12-Jan-2021 00:58:09 J2S transpiling (72/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/Validator.java build 12-Jan-2021 00:58:09 J2S transpiling (73/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/WantMoreTextReplaceRule.java build 12-Jan-2021 00:58:09 J2S transpiling (74/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/lookAhead.java build 12-Jan-2021 00:58:09 J2S transpiling (75/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/oneChar.java build 12-Jan-2021 00:58:09 J2S transpiling (76/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/parsePerl.java build 12-Jan-2021 00:58:09 J2S transpiling (77/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/patInf.java build 12-Jan-2021 00:58:09 J2S transpiling (78/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/patInt.java build 12-Jan-2021 00:58:09 J2S transpiling (79/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/wrap/CharArrayBufferWrap.java build 12-Jan-2021 00:58:09 J2S transpiling (80/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/wrap/CharArrayWrap.java build 12-Jan-2021 00:58:09 J2S transpiling (81/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java build 12-Jan-2021 00:58:09 J2S transpiling (82/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/wrap/StringBufferWrap.java build 12-Jan-2021 00:58:09 J2S transpiling (83/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/wrap/StringWrap.java build 12-Jan-2021 00:58:09 J2S transpiling (84/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/com/stevesoft/pat/wrap/WriterWrap.java build 12-Jan-2021 00:58:09 J2S transpiling (85/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java build 12-Jan-2021 00:58:09 j2s copying resources from /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext to /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/./build/jalviewjs/tmp/site_js/swingjs/j2s/ext build 12-Jan-2021 00:58:09 J2S transpiling (86/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java build 12-Jan-2021 00:58:09 J2S transpiling (87/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java build 12-Jan-2021 00:58:10 J2S transpiling (88/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java build 12-Jan-2021 00:58:10 J2S transpiling (89/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraResidue.java build 12-Jan-2021 00:58:10 J2S transpiling (90/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraStructuralObject.java build 12-Jan-2021 00:58:10 J2S transpiling (91/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java build 12-Jan-2021 00:58:10 J2S transpiling (92/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java build 12-Jan-2021 00:58:10 J2S transpiling (93/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/edu/ucsf/rbvi/strucviz2/StructureSettings.java build 12-Jan-2021 00:58:10 J2S transpiling (94/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.java build 12-Jan-2021 00:58:10 J2S transpiling (95/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/IRegistry.java build 12-Jan-2021 00:58:10 J2S transpiling (96/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/IRegistryService.java build 12-Jan-2021 00:58:10 J2S transpiling (97/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/IRegistryServiceLocator.java build 12-Jan-2021 00:58:10 J2S transpiling (98/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/Jpred.java build 12-Jan-2021 00:58:10 J2S transpiling (99/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/JpredService.java build 12-Jan-2021 00:58:10 J2S transpiling (100/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/JpredServiceLocator.java build 12-Jan-2021 00:58:10 J2S transpiling (101/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/JpredSoapBindingStub.java build 12-Jan-2021 00:58:10 J2S transpiling (102/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/MuscleWS.java build 12-Jan-2021 00:58:10 J2S transpiling (103/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/MuscleWSService.java build 12-Jan-2021 00:58:10 J2S transpiling (104/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/MuscleWSServiceLocator.java build 12-Jan-2021 00:58:10 J2S transpiling (105/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/MuscleWSSoapBindingStub.java build 12-Jan-2021 00:58:10 J2S transpiling (106/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/RegistryServiceSoapBindingStub.java build 12-Jan-2021 00:58:10 J2S transpiling (107/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/SeqSearchI.java build 12-Jan-2021 00:58:10 J2S transpiling (108/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/SeqSearchServiceLocator.java build 12-Jan-2021 00:58:10 J2S transpiling (109/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/SeqSearchServiceService.java build 12-Jan-2021 00:58:10 J2S transpiling (110/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java build 12-Jan-2021 00:58:10 J2S transpiling (111/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/ServiceHandle.java build 12-Jan-2021 00:58:10 J2S transpiling (112/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/ext/vamsas/ServiceHandles.java build 12-Jan-2021 00:58:10 J2S transpiling (113/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/analysis/AAFrequency.java build 12-Jan-2021 00:58:11 j2s copying resources from /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview to /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/./build/jalviewjs/tmp/site_js/swingjs/j2s/jalview build 12-Jan-2021 00:58:11 J2S transpiling (114/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/analysis/AlignSeq.java build 12-Jan-2021 00:58:11 J2S 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/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/appletgui/SliderPanel.java build 12-Jan-2021 00:58:15 J2S transpiling (217/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/appletgui/SplitFrame.java build 12-Jan-2021 00:58:15 J2S transpiling (218/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/appletgui/TitledPanel.java build 12-Jan-2021 00:58:15 J2S transpiling (219/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/appletgui/Tooltip.java build 12-Jan-2021 00:58:15 J2S transpiling (220/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/appletgui/TreeCanvas.java build 12-Jan-2021 00:58:15 J2S transpiling (221/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/appletgui/TreePanel.java build 12-Jan-2021 00:58:15 J2S transpiling (222/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/appletgui/UserDefinedColours.java build 12-Jan-2021 00:58:15 J2S transpiling (223/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/appletgui/js/JSFunctionExec.java build 12-Jan-2021 00:58:15 J2S transpiling (224/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/appletgui/js/JalviewLiteJsApi.java build 12-Jan-2021 00:58:15 J2S transpiling (225/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/appletgui/js/JsCallBack.java build 12-Jan-2021 00:58:15 J2S transpiling (226/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/appletgui/js/JsSelectionSender.java build 12-Jan-2021 00:58:15 J2S transpiling (227/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/appletgui/js/MouseOverListener.java build 12-Jan-2021 00:58:15 J2S transpiling (228/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/appletgui/js/MouseOverStructureListener.java build 12-Jan-2021 00:58:15 J2S transpiling (229/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/AppletParams.java build 12-Jan-2021 00:58:15 >>>main found for jalview.bin.AppletParams build 12-Jan-2021 00:58:15 J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/./build/jalviewjs/tmp/site_js/jalview_bin_AppletParams.html build 12-Jan-2021 00:58:15 J2S transpiling (230/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/ApplicationSingletonProvider.java build 12-Jan-2021 00:58:15 J2S transpiling (231/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/ArgsParser.java build 12-Jan-2021 00:58:15 J2S transpiling (232/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/BuildDetails.java build 12-Jan-2021 00:58:15 J2S transpiling (233/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/Cache.java build 12-Jan-2021 00:58:15 org.apache.log4j.Logger -> jalview.javascript.log4j.Logger build 12-Jan-2021 00:58:15 org.apache.log4j.ConsoleAppender -> jalview.javascript.log4j.ConsoleAppender build 12-Jan-2021 00:58:15 org.apache.log4j.ConsoleAppender -> jalview.javascript.log4j.ConsoleAppender build 12-Jan-2021 00:58:15 org.apache.log4j.ConsoleAppender -> jalview.javascript.log4j.ConsoleAppender build 12-Jan-2021 00:58:15 org.apache.log4j.Layout -> jalview.javascript.log4j.Layout build 12-Jan-2021 00:58:15 org.apache.log4j.SimpleLayout -> jalview.javascript.log4j.SimpleLayout build 12-Jan-2021 00:58:15 org.apache.log4j.SimpleLayout -> jalview.javascript.log4j.SimpleLayout build 12-Jan-2021 00:58:15 org.apache.log4j.SimpleLayout -> jalview.javascript.log4j.SimpleLayout build 12-Jan-2021 00:58:15 org.apache.log4j.Logger -> jalview.javascript.log4j.Logger build 12-Jan-2021 00:58:15 org.apache.log4j.Appender -> jalview.javascript.log4j.Appender build 12-Jan-2021 00:58:15 org.apache.log4j.Logger -> jalview.javascript.log4j.Logger build 12-Jan-2021 00:58:15 org.apache.log4j.Logger -> jalview.javascript.log4j.Logger build 12-Jan-2021 00:58:15 org.apache.log4j.Logger -> jalview.javascript.log4j.Logger build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Logger -> jalview.javascript.log4j.Logger build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Logger -> jalview.javascript.log4j.Logger build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Appender -> jalview.javascript.log4j.Appender build 12-Jan-2021 00:58:15 org.apache.log4j.Logger -> jalview.javascript.log4j.Logger build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Level -> jalview.javascript.log4j.Level build 12-Jan-2021 00:58:15 org.apache.log4j.Appender -> jalview.javascript.log4j.Appender build 12-Jan-2021 00:58:15 J2S transpiling (234/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/GetMemory.java build 12-Jan-2021 00:58:15 J2S transpiling (235/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/Jalview.java build 12-Jan-2021 00:58:15 >>>main found for jalview.bin.Jalview build 12-Jan-2021 00:58:15 J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/./build/jalviewjs/tmp/site_js/jalview_bin_Jalview.html build 12-Jan-2021 00:58:15 J2S transpiling (236/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/JalviewJS2.java build 12-Jan-2021 00:58:15 >>>main found for jalview.bin.JalviewJS2 build 12-Jan-2021 00:58:15 J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/./build/jalviewjs/tmp/site_js/jalview_bin_JalviewJS2.html build 12-Jan-2021 00:58:15 J2S transpiling (237/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/JalviewJSApp.java build 12-Jan-2021 00:58:15 J2S transpiling (238/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/JalviewLite.java build 12-Jan-2021 00:58:16 J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/./build/jalviewjs/tmp/site_js/jalview_bin_JalviewLite_applet.html build 12-Jan-2021 00:58:16 J2S transpiling (239/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/JalviewLiteURLRetrieve.java build 12-Jan-2021 00:58:16 J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/./build/jalviewjs/tmp/site_js/jalview_bin_JalviewLiteURLRetrieve_applet.html build 12-Jan-2021 00:58:16 J2S transpiling (240/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/JalviewTaskbar.java build 12-Jan-2021 00:58:16 J2S transpiling (241/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/Launcher.java build 12-Jan-2021 00:58:16 >>>main found for jalview.bin.Launcher build 12-Jan-2021 00:58:16 J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/./build/jalviewjs/tmp/site_js/jalview_bin_Launcher.html build 12-Jan-2021 00:58:16 J2S transpiling (242/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/bin/MemorySetting.java build 12-Jan-2021 00:58:16 J2S transpiling (243/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/commands/ChangeCaseCommand.java build 12-Jan-2021 00:58:16 J2S transpiling (244/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/commands/CommandI.java build 12-Jan-2021 00:58:16 J2S transpiling (245/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/commands/EditCommand.java build 12-Jan-2021 00:58:16 J2S transpiling (246/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/commands/OrderCommand.java build 12-Jan-2021 00:58:16 J2S transpiling (247/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/commands/RemoveGapColCommand.java build 12-Jan-2021 00:58:16 J2S transpiling (248/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/commands/RemoveGapsCommand.java build 12-Jan-2021 00:58:16 J2S transpiling (249/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/commands/SlideSequencesCommand.java build 12-Jan-2021 00:58:16 J2S transpiling (250/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/commands/TrimRegionCommand.java build 12-Jan-2021 00:58:16 J2S transpiling (251/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/controller/AlignViewController.java build 12-Jan-2021 00:58:16 J2S transpiling (252/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/controller/FeatureSettingsController.java build 12-Jan-2021 00:58:16 J2S transpiling (253/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/controller/FeatureSettingsControllerGuiI.java build 12-Jan-2021 00:58:16 J2S transpiling (254/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/ASequence.java build 12-Jan-2021 00:58:16 J2S transpiling (255/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/ASequenceI.java build 12-Jan-2021 00:58:16 J2S transpiling (256/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/AlignExportSettingsAdapter.java build 12-Jan-2021 00:58:16 J2S transpiling (257/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/AlignedCodon.java build 12-Jan-2021 00:58:16 J2S transpiling (258/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/AlignedCodonFrame.java build 12-Jan-2021 00:58:16 J2S transpiling (259/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/Alignment.java build 12-Jan-2021 00:58:16 J2S transpiling (260/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/AlignmentAnnotation.java build 12-Jan-2021 00:58:16 J2S transpiling (261/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/AlignmentExportData.java build 12-Jan-2021 00:58:16 J2S transpiling (262/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/AlignmentI.java build 12-Jan-2021 00:58:16 J2S transpiling (263/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/AlignmentOrder.java build 12-Jan-2021 00:58:16 J2S transpiling (264/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/AlignmentView.java build 12-Jan-2021 00:58:16 J2S transpiling (265/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/AllColsCollection.java build 12-Jan-2021 00:58:16 J2S transpiling (266/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/AllColsIterator.java build 12-Jan-2021 00:58:16 J2S transpiling (267/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/AllRowsCollection.java build 12-Jan-2021 00:58:16 J2S transpiling (268/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/AllRowsIterator.java build 12-Jan-2021 00:58:16 J2S transpiling (269/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/AnnotatedCollectionI.java build 12-Jan-2021 00:58:16 J2S transpiling (270/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/Annotation.java build 12-Jan-2021 00:58:16 J2S transpiling (271/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/BinaryNode.java build 12-Jan-2021 00:58:16 J2S transpiling (272/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/BinarySequence.java build 12-Jan-2021 00:58:16 J2S transpiling (273/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/CigarArray.java build 12-Jan-2021 00:58:16 J2S transpiling (274/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/CigarBase.java build 12-Jan-2021 00:58:16 J2S transpiling (275/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/CigarCigar.java build 12-Jan-2021 00:58:16 J2S transpiling (276/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/CigarSimple.java build 12-Jan-2021 00:58:16 J2S transpiling (277/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/ColumnSelection.java build 12-Jan-2021 00:58:16 J2S transpiling (278/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/ContiguousI.java build 12-Jan-2021 00:58:16 J2S transpiling (279/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/DBRefEntry.java build 12-Jan-2021 00:58:16 J2S transpiling (280/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/DBRefSource.java build 12-Jan-2021 00:58:16 J2S transpiling (281/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/FeatureProperties.java build 12-Jan-2021 00:58:16 J2S transpiling (282/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/GeneLociI.java build 12-Jan-2021 00:58:16 J2S transpiling (283/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/GeneLocus.java build 12-Jan-2021 00:58:16 J2S transpiling (284/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/GraphLine.java build 12-Jan-2021 00:58:16 J2S transpiling (285/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/HiddenColumns.java build 12-Jan-2021 00:58:16 J2S transpiling (286/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/HiddenColumnsCursor.java build 12-Jan-2021 00:58:16 J2S transpiling (287/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/HiddenCursorPosition.java build 12-Jan-2021 00:58:16 J2S transpiling (288/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/datamodel/HiddenSequences.java build 12-Jan-2021 00:58:16 J2S transpiling (289/1032) 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/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/CalculationChooser.java build 12-Jan-2021 00:58:20 J2S transpiling (410/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/ChimeraViewFrame.java build 12-Jan-2021 00:58:20 J2S transpiling (411/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/ColourMenuHelper.java build 12-Jan-2021 00:58:20 J2S transpiling (412/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/ComboBoxTooltipRenderer.java build 12-Jan-2021 00:58:20 J2S transpiling (413/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/Console.java build 12-Jan-2021 00:58:20 org.apache.log4j.Layout -> jalview.javascript.log4j.Layout build 12-Jan-2021 00:58:20 org.apache.log4j.SimpleLayout -> jalview.javascript.log4j.SimpleLayout build 12-Jan-2021 00:58:20 org.apache.log4j.SimpleLayout -> jalview.javascript.log4j.SimpleLayout build 12-Jan-2021 00:58:20 org.apache.log4j.SimpleLayout -> jalview.javascript.log4j.SimpleLayout build 12-Jan-2021 00:58:20 org.apache.log4j.Logger -> jalview.javascript.log4j.Logger build 12-Jan-2021 00:58:20 org.apache.log4j.Appender -> jalview.javascript.log4j.Appender build 12-Jan-2021 00:58:20 J2S transpiling (414/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/CrossRefAction.java build 12-Jan-2021 00:58:21 J2S transpiling (415/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/CutAndPasteHtmlTransfer.java build 12-Jan-2021 00:58:21 J2S transpiling (416/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/CutAndPasteTransfer.java build 12-Jan-2021 00:58:21 J2S transpiling (417/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/Desktop.java build 12-Jan-2021 00:58:21 J2S transpiling (418/1032) 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/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/FontChooser.java build 12-Jan-2021 00:58:21 J2S transpiling (425/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/Help.java build 12-Jan-2021 00:58:21 J2S transpiling (426/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/IProgressIndicator.java build 12-Jan-2021 00:58:21 J2S transpiling (427/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/IProgressIndicatorHandler.java build 12-Jan-2021 00:58:21 J2S transpiling (428/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/IdCanvas.java build 12-Jan-2021 00:58:22 J2S transpiling (429/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/gui/IdPanel.java build 12-Jan-2021 00:58:22 J2S transpiling (430/1032) 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build 12-Jan-2021 00:58:25 J2S transpiling (507/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/FileLoader.java build 12-Jan-2021 00:58:25 J2S transpiling (508/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/FileParse.java build 12-Jan-2021 00:58:25 J2S transpiling (509/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/FormatAdapter.java build 12-Jan-2021 00:58:25 J2S transpiling (510/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/HTMLOutput.java build 12-Jan-2021 00:58:25 J2S transpiling (511/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/HtmlFile.java build 12-Jan-2021 00:58:25 J2S transpiling (512/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/HtmlSvgOutput.java build 12-Jan-2021 00:58:25 J2S transpiling (513/1032) 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/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/gff/SequenceOntologyI.java build 12-Jan-2021 00:58:26 J2S transpiling (551/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/gff/SequenceOntologyLite.java build 12-Jan-2021 00:58:26 J2S transpiling (552/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/packed/DataProvider.java build 12-Jan-2021 00:58:26 J2S transpiling (553/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/packed/JalviewDataset.java build 12-Jan-2021 00:58:26 J2S transpiling (554/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/packed/ParsePackedSet.java build 12-Jan-2021 00:58:26 J2S transpiling (555/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/packed/SimpleDataProvider.java build 12-Jan-2021 00:58:26 J2S transpiling (556/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/vamsas/Datasetsequence.java build 12-Jan-2021 00:58:26 J2S transpiling (557/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/vamsas/DatastoreItem.java build 12-Jan-2021 00:58:26 org.apache.log4j.Logger -> jalview.javascript.log4j.Logger build 12-Jan-2021 00:58:26 org.apache.log4j.Logger -> jalview.javascript.log4j.Logger build 12-Jan-2021 00:58:26 J2S transpiling (558/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/vamsas/DatastoreRegistry.java build 12-Jan-2021 00:58:26 org.apache.log4j.Logger -> jalview.javascript.log4j.Logger build 12-Jan-2021 00:58:26 org.apache.log4j.Logger -> jalview.javascript.log4j.Logger build 12-Jan-2021 00:58:26 J2S transpiling (559/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/io/vamsas/Dbref.java build 12-Jan-2021 00:58:26 J2S transpiling (560/1032) 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12-Jan-2021 00:58:29 native: ICLaunchURL build 12-Jan-2021 00:58:29 J2S transpiling (691/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/util/CaseInsensitiveString.java build 12-Jan-2021 00:58:29 J2S transpiling (692/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/util/ColorUtils.java build 12-Jan-2021 00:58:29 J2S transpiling (693/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/util/Comparison.java build 12-Jan-2021 00:58:29 J2S transpiling (694/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/util/DBRefUtils.java build 12-Jan-2021 00:58:29 J2S transpiling (695/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/util/DnaUtils.java build 12-Jan-2021 00:58:29 J2S transpiling (696/1032) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/src/jalview/util/Format.java build 12-Jan-2021 00:58:29 J2S transpiling (697/1032) 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/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/jalview/ws/jabaws/RNAStructExportImport.java build 12-Jan-2021 00:58:34 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/jalview/ws/jws2/ParameterUtilsTest.java build 12-Jan-2021 00:58:34 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/jalview/ws/rest/RestClientTest.java build 12-Jan-2021 00:58:34 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/jalview/ws/rest/ShmmrRSBSService.java build 12-Jan-2021 00:58:34 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/jalview/ws/seqfetcher/DbRefFetcherTest.java build 12-Jan-2021 00:58:34 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/jalview/ws/sifts/SiftsClientTest.java build 12-Jan-2021 00:58:34 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/jalview/ws/utils/UrlDownloadClientTest.java build 12-Jan-2021 00:58:34 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/junit/extensions/PA.java build 12-Jan-2021 00:58:34 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/junit/extensions/PrivilegedAccessor.java build 12-Jan-2021 00:58:34 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/mc_view/AtomTest.java build 12-Jan-2021 00:58:34 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/mc_view/BondTest.java build 12-Jan-2021 00:58:34 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/mc_view/PDBChainTest.java build 12-Jan-2021 00:58:34 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/mc_view/PDBfileTest.java build 12-Jan-2021 00:58:34 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/test/mc_view/ResidueTest.java build 12-Jan-2021 00:58:34 J2S processed 1032 .java files, created 1060 .js files and 7 .html files, copied 5 resources build 12-Jan-2021 00:58:34 J2S buildFinished 1032 files transpiled for /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 build 12-Jan-2021 00:58:34 J2S buildFinished nerror = 0 Tue Jan 12 00:58:34 GMT 2021 build 12-Jan-2021 00:58:34 (Found 2357 warnings) Build done build 12-Jan-2021 00:58:34 Invoking 'Gradle Project Builder' on '/jalview'. build 12-Jan-2021 00:58:36 :jalviewjsTranspile (Thread[Execution worker for ':',5,main]) completed. Took 1 mins 16.093 secs. build 12-Jan-2021 00:58:36 :jalviewjsCopyTransferSiteJs (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:36 build 12-Jan-2021 00:58:36 > Task :jalviewjsCopyTransferSiteJs build 12-Jan-2021 00:58:36 Caching disabled for task ':jalviewjsCopyTransferSiteJs' because: build 12-Jan-2021 00:58:36 Build cache is disabled build 12-Jan-2021 00:58:36 Task ':jalviewjsCopyTransferSiteJs' is not up-to-date because: build 12-Jan-2021 00:58:36 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site has been removed. build 12-Jan-2021 00:58:36 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/com_stevesoft_pat_RegexWriter.html has been removed. build 12-Jan-2021 00:58:36 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/jalview_bin_AppletParams.html has been removed. build 12-Jan-2021 00:58:36 :jalviewjsCopyTransferSiteJs (Thread[Execution worker for ':',5,main]) completed. Took 0.349 secs. build 12-Jan-2021 00:58:36 :jalviewjsTransferUnzipLib (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:37 build 12-Jan-2021 00:58:37 > Task :jalviewjsTransferUnzipLib build 12-Jan-2021 00:58:37 Caching disabled for task ':jalviewjsTransferUnzipLib' because: build 12-Jan-2021 00:58:37 Build cache is disabled build 12-Jan-2021 00:58:37 Task ':jalviewjsTransferUnzipLib' is not up-to-date because: build 12-Jan-2021 00:58:37 One or more additional actions for task ':jalviewjsTransferUnzipLib' have changed. build 12-Jan-2021 00:58:37 :jalviewjsTransferUnzipLib (Thread[Execution worker for ':',5,main]) completed. Took 0.874 secs. build 12-Jan-2021 00:58:37 :jalviewjsTransferUnzipSwingJs (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:38 build 12-Jan-2021 00:58:38 > Task :jalviewjsTransferUnzipSwingJs build 12-Jan-2021 00:58:38 Caching disabled for task ':jalviewjsTransferUnzipSwingJs' because: build 12-Jan-2021 00:58:38 Build cache is disabled build 12-Jan-2021 00:58:38 Task ':jalviewjsTransferUnzipSwingJs' is not up-to-date because: build 12-Jan-2021 00:58:38 One or more additional actions for task ':jalviewjsTransferUnzipSwingJs' have changed. build 12-Jan-2021 00:58:38 :jalviewjsTransferUnzipSwingJs (Thread[Execution worker for ':',5,main]) completed. Took 1.343 secs. build 12-Jan-2021 00:58:38 :jalviewjsTransferUnzipAllLibs (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:38 build 12-Jan-2021 00:58:38 > Task :jalviewjsTransferUnzipAllLibs build 12-Jan-2021 00:58:38 Skipping task ':jalviewjsTransferUnzipAllLibs' as it has no actions. build 12-Jan-2021 00:58:38 :jalviewjsTransferUnzipAllLibs (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 12-Jan-2021 00:58:38 :jalviewjsSyncAllLibs (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:40 build 12-Jan-2021 00:58:40 > Task :jalviewjsSyncAllLibs build 12-Jan-2021 00:58:40 Caching disabled for task ':jalviewjsSyncAllLibs' because: build 12-Jan-2021 00:58:40 Build cache is disabled build 12-Jan-2021 00:58:40 Task ':jalviewjsSyncAllLibs' is not up-to-date because: build 12-Jan-2021 00:58:40 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/swingjs/j2s/javajs/async/Assets.js has changed. build 12-Jan-2021 00:58:40 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/swingjs/j2s/javajs/async/Async.js has changed. build 12-Jan-2021 00:58:40 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/swingjs/j2s/javajs/async/AsyncColorChooser.js has changed. build 12-Jan-2021 00:58:40 :jalviewjsSyncAllLibs (Thread[Execution worker for ':',5,main]) completed. Took 1.596 secs. build 12-Jan-2021 00:58:40 :setGitVals (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:40 build 12-Jan-2021 00:58:40 > Task :setGitVals build 12-Jan-2021 00:58:40 Caching disabled for task ':setGitVals' because: build 12-Jan-2021 00:58:40 Build cache is disabled build 12-Jan-2021 00:58:40 Task ':setGitVals' is not up-to-date because: build 12-Jan-2021 00:58:40 Task.upToDateWhen is false. build 12-Jan-2021 00:58:40 Starting process 'command 'git''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 Command: git rev-parse --short HEAD build 12-Jan-2021 00:58:40 Successfully started process 'command 'git'' build 12-Jan-2021 00:58:40 Starting process 'command 'git''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 Command: git rev-parse --abbrev-ref HEAD build 12-Jan-2021 00:58:40 Successfully started process 'command 'git'' build 12-Jan-2021 00:58:40 :setGitVals (Thread[Execution worker for ':',5,main]) completed. Took 0.051 secs. build 12-Jan-2021 00:58:40 :createBuildProperties (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:40 build 12-Jan-2021 00:58:40 > Task :createBuildProperties build 12-Jan-2021 00:58:40 Caching disabled for task ':createBuildProperties' because: build 12-Jan-2021 00:58:40 Build cache is disabled build 12-Jan-2021 00:58:40 Task ':createBuildProperties' is not up-to-date because: build 12-Jan-2021 00:58:40 Value of input property 'comment' has changed for task ':createBuildProperties' build 12-Jan-2021 00:58:40 Value of input property 'properties' has changed for task ':createBuildProperties' build 12-Jan-2021 00:58:40 :createBuildProperties (Thread[Execution worker for ':',5,main]) completed. Took 0.016 secs. build 12-Jan-2021 00:58:40 :jalviewjsSyncBuildProperties (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:40 build 12-Jan-2021 00:58:40 > Task :jalviewjsSyncBuildProperties build 12-Jan-2021 00:58:40 Caching disabled for task ':jalviewjsSyncBuildProperties' because: build 12-Jan-2021 00:58:40 Build cache is disabled build 12-Jan-2021 00:58:40 Task ':jalviewjsSyncBuildProperties' is not up-to-date because: build 12-Jan-2021 00:58:40 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/swingjs/j2s/.build_properties has been removed. build 12-Jan-2021 00:58:40 :jalviewjsSyncBuildProperties (Thread[Execution worker for ':',5,main]) completed. Took 0.172 secs. build 12-Jan-2021 00:58:40 :jalviewjsBuildAllCores (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:42 build 12-Jan-2021 00:58:42 > Task :jalviewjsBuildAllCores build 12-Jan-2021 00:58:42 Caching disabled for task ':jalviewjsBuildAllCores' because: build 12-Jan-2021 00:58:42 Build cache is disabled build 12-Jan-2021 00:58:42 Task ':jalviewjsBuildAllCores' is not up-to-date because: build 12-Jan-2021 00:58:42 One or more additional actions for task ':jalviewjsBuildAllCores' have changed. build 12-Jan-2021 00:58:42 Creating core for stevesoft... build 12-Jan-2021 00:58:42 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.js build 12-Jan-2021 00:58:42 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.z.js build 12-Jan-2021 00:58:42 build 12-Jan-2021 00:58:42 Running '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.z.js' build 12-Jan-2021 00:58:42 build 12-Jan-2021 00:58:42 Starting process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.z.js build 12-Jan-2021 00:58:42 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' build 12-Jan-2021 00:58:44 -- build 12-Jan-2021 00:58:44 Creating core for jvjmol... build 12-Jan-2021 00:58:44 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jvjmol.js build 12-Jan-2021 00:58:44 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jvjmol.z.js build 12-Jan-2021 00:58:44 build 12-Jan-2021 00:58:44 Running '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jvjmol.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jvjmol.z.js' build 12-Jan-2021 00:58:44 build 12-Jan-2021 00:58:44 Starting process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jvjmol.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jvjmol.z.js build 12-Jan-2021 00:58:44 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' build 12-Jan-2021 00:58:46 -- build 12-Jan-2021 00:58:46 Creating core for jalview... build 12-Jan-2021 00:58:46 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.js build 12-Jan-2021 00:58:46 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.z.js build 12-Jan-2021 00:58:46 build 12-Jan-2021 00:58:46 Running '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.z.js' build 12-Jan-2021 00:58:46 build 12-Jan-2021 00:58:46 Starting process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.z.js build 12-Jan-2021 00:58:46 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' build 12-Jan-2021 00:58:47 -- build 12-Jan-2021 00:58:47 :jalviewjsBuildAllCores (Thread[Execution worker for ':',5,main]) completed. Took 7.119 secs. build 12-Jan-2021 00:58:47 :jalviewjsPublishCoreTemplates (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:47 build 12-Jan-2021 00:58:47 > Task :jalviewjsPublishCoreTemplates build 12-Jan-2021 00:58:47 Caching disabled for task ':jalviewjsPublishCoreTemplates' because: build 12-Jan-2021 00:58:47 Build cache is disabled build 12-Jan-2021 00:58:47 Task ':jalviewjsPublishCoreTemplates' is not up-to-date because: build 12-Jan-2021 00:58:47 One or more additional actions for task ':jalviewjsPublishCoreTemplates' have changed. build 12-Jan-2021 00:58:47 :jalviewjsPublishCoreTemplates (Thread[Execution worker for ':',5,main]) completed. Took 0.038 secs. build 12-Jan-2021 00:58:47 :jalviewjsSyncCore (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:47 build 12-Jan-2021 00:58:47 > Task :jalviewjsSyncCore build 12-Jan-2021 00:58:47 Caching disabled for task ':jalviewjsSyncCore' because: build 12-Jan-2021 00:58:47 Build cache is disabled build 12-Jan-2021 00:58:47 Task ':jalviewjsSyncCore' is not up-to-date because: build 12-Jan-2021 00:58:47 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/JalviewJS_jalview.html has been removed. build 12-Jan-2021 00:58:47 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/JalviewJS_jvjmol.html has been removed. build 12-Jan-2021 00:58:47 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/JalviewJS_stevesoft.html has been removed. build 12-Jan-2021 00:58:47 :jalviewjsSyncCore (Thread[Execution worker for ':',5,main]) completed. Took 0.165 secs. build 12-Jan-2021 00:58:47 :jalviewjsSyncResources (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:48 build 12-Jan-2021 00:58:48 > Task :jalviewjsSyncResources build 12-Jan-2021 00:58:48 Caching disabled for task ':jalviewjsSyncResources' because: build 12-Jan-2021 00:58:48 Build cache is disabled build 12-Jan-2021 00:58:48 Task ':jalviewjsSyncResources' is not up-to-date because: build 12-Jan-2021 00:58:48 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/swingjs/j2s/.build_properties has changed. build 12-Jan-2021 00:58:48 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/swingjs/j2s/AmbiguityCodes.dat has been removed. build 12-Jan-2021 00:58:48 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/swingjs/j2s/GeneticCodes.dat has been removed. build 12-Jan-2021 00:58:48 :jalviewjsSyncResources (Thread[Execution worker for ':',5,main]) completed. Took 0.394 secs. build 12-Jan-2021 00:58:48 :jalviewjsSyncSiteResources (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:48 build 12-Jan-2021 00:58:48 > Task :jalviewjsSyncSiteResources build 12-Jan-2021 00:58:48 Caching disabled for task ':jalviewjsSyncSiteResources' because: build 12-Jan-2021 00:58:48 Build cache is disabled build 12-Jan-2021 00:58:48 Task ':jalviewjsSyncSiteResources' is not up-to-date because: build 12-Jan-2021 00:58:48 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/___j2sflags.htm has changed. build 12-Jan-2021 00:58:48 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/jalview_bin_JalviewJS2.html has changed. build 12-Jan-2021 00:58:48 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/jalviewjs/site/_jalview_bin_JalviewJS_core.html has been removed. build 12-Jan-2021 00:58:48 :jalviewjsSyncSiteResources (Thread[Execution worker for ':',5,main]) completed. Took 0.753 secs. build 12-Jan-2021 00:58:48 :jalviewjsPrepareSite (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:48 build 12-Jan-2021 00:58:48 > Task :jalviewjsPrepareSite build 12-Jan-2021 00:58:48 Skipping task ':jalviewjsPrepareSite' as it has no actions. build 12-Jan-2021 00:58:48 :jalviewjsPrepareSite (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 12-Jan-2021 00:58:48 :jalviewjsBuildSite (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:48 build 12-Jan-2021 00:58:48 > Task :jalviewjsBuildSite build 12-Jan-2021 00:58:48 Skipping task ':jalviewjsBuildSite' as it has no actions. build 12-Jan-2021 00:58:48 :jalviewjsBuildSite (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 12-Jan-2021 00:58:48 :jalviewjs (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:48 build 12-Jan-2021 00:58:48 > Task :jalviewjs build 12-Jan-2021 00:58:48 Skipping task ':jalviewjs' as it has no actions. build 12-Jan-2021 00:58:48 :jalviewjs (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 12-Jan-2021 00:58:48 :jalviewjsSiteTar (Thread[Execution worker for ':',5,main]) started. build 12-Jan-2021 00:58:50 build 12-Jan-2021 00:58:50 > Task :jalviewjsSiteTar build 12-Jan-2021 00:58:50 Caching disabled for task ':jalviewjsSiteTar' because: build 12-Jan-2021 00:58:50 Build cache is disabled build 12-Jan-2021 00:58:50 Task ':jalviewjsSiteTar' is not up-to-date because: build 12-Jan-2021 00:58:50 Output property 'archiveFile' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/build/distributions/jalviewjs-site-TEST.tar.gz has been removed. build 12-Jan-2021 00:58:51 :jalviewjsSiteTar (Thread[Execution worker for ':',5,main]) completed. Took 2.577 secs. build 12-Jan-2021 00:58:51 build 12-Jan-2021 00:58:51 BUILD SUCCESSFUL in 2m 53s build 12-Jan-2021 00:58:51 24 actionable tasks: 24 executed build 12-Jan-2021 00:58:51 VCS Checkout Cache (/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/.gradle/vcs-1) removing files not accessed on or after Tue Jan 05 00:56:04 GMT 2021. build 12-Jan-2021 00:58:51 VCS Checkout Cache (/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJB0-JOB1/.gradle/vcs-1) cleaned up in 0.002 secs. simple 12-Jan-2021 00:58:51 Finished task 'JalviewJS build site and distributable tar' with result: Success simple 12-Jan-2021 00:58:51 Running post build plugin 'NCover Results Collector' simple 12-Jan-2021 00:58:51 Running post build plugin 'Artifact Copier' simple 12-Jan-2021 00:58:51 Publishing an artifact: JalviewJS site tar file simple 12-Jan-2021 00:58:51 Finished publishing of artifact Shared artifact: [JalviewJS site tar file], pattern: [jalviewjs-site-*.tar.gz] anchored at: [build/distributions/] in 35.15 ms simple 12-Jan-2021 00:58:51 Publishing an artifact: JalviewJS site simple 12-Jan-2021 00:58:53 Finished publishing of artifact Shared artifact: [JalviewJS site], pattern: [**/*] anchored at: [build/jalviewjs/site] in 1.272 s simple 12-Jan-2021 00:58:53 Running post build plugin 'Artifactory Release Management Staging' simple 12-Jan-2021 00:58:53 Running post build plugin 'Artifactory Build Info Copier' simple 12-Jan-2021 00:58:53 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 12-Jan-2021 00:58:53 Running post build plugin 'npm Cache Cleanup' simple 12-Jan-2021 00:58:53 Running post build plugin 'Clover Results Collector' simple 12-Jan-2021 00:58:53 Running post build plugin 'Docker Container Cleanup' simple 12-Jan-2021 00:58:53 Finalising the build... simple 12-Jan-2021 00:58:53 Stopping timer. simple 12-Jan-2021 00:58:53 Build JB-GJB0-JOB1-182 completed. simple 12-Jan-2021 00:58:53 Running on server: post build plugin 'NCover Results Collector' simple 12-Jan-2021 00:58:53 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 12-Jan-2021 00:58:53 Running on server: post build plugin 'Clover Delta Calculator' simple 12-Jan-2021 00:58:53 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 12-Jan-2021 00:58:53 All post build plugins have finished simple 12-Jan-2021 00:58:53 Generating build results summary... simple 12-Jan-2021 00:58:53 Saving build results to disk... simple 12-Jan-2021 00:58:53 Logging substituted variables... simple 12-Jan-2021 00:58:53 Indexing build results... simple 12-Jan-2021 00:58:53 Finished building JB-GJB0-JOB1-182.