simple 09-Jun-2022 11:03:49 Build Jalview Builds - Gradle JalviewJS 2022-03 Build - Default Job #5 (JB-GJ2B-JOB1-5) started building on agent Default Agent simple 09-Jun-2022 11:03:49 simple 09-Jun-2022 11:03:49 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1 simple 09-Jun-2022 11:03:49 Executing build Jalview Builds - Gradle JalviewJS 2022-03 Build - Default Job #5 (JB-GJ2B-JOB1-5) simple 09-Jun-2022 11:03:49 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 09-Jun-2022 11:03:49 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1 simple 09-Jun-2022 11:03:49 Updating source code to revision: 986834f1db7bd344d067bb450970578acb32c10f simple 09-Jun-2022 11:03:49 Fetching 'refs/heads/develop' from 'http://source.jalview.org/git/jalview.git'. simple 09-Jun-2022 11:03:49 Checking out revision 986834f1db7bd344d067bb450970578acb32c10f. simple 09-Jun-2022 11:03:49 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 09-Jun-2022 11:03:49 99bfb1a..986834f develop -> origin/develop simple 09-Jun-2022 11:03:49 * [new branch] flakytests/JAL-4026_AlignViewportWaitforcalculations -> origin/flakytests/JAL-4026_AlignViewportWaitforcalculations simple 09-Jun-2022 11:03:49 Already on 'develop' simple 09-Jun-2022 11:03:49 Your branch is behind 'origin/develop' by 1 commit, and can be fast-forwarded. simple 09-Jun-2022 11:03:49 (use "git pull" to update your local branch) simple 09-Jun-2022 11:03:49 HEAD is now at 986834f JAL-4026 always wait 50ms before checking if the calculation worker is still running so it has time to start. simple 09-Jun-2022 11:03:49 Updated source code to revision: 986834f1db7bd344d067bb450970578acb32c10f simple 09-Jun-2022 11:03:49 Finished task 'Checkout Default Repository' with result: Success simple 09-Jun-2022 11:03:49 Running pre-build action: VCS Version Collector simple 09-Jun-2022 11:03:49 Running pre-build action: Artifactory Release Staging simple 09-Jun-2022 11:03:49 Starting task 'JalviewJS build site and distributable tar' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 09-Jun-2022 11:03:49 Bamboo Artifactory Plugin version: 2.6.2 command 09-Jun-2022 11:03:49 Beginning to execute external process for build 'Jalview Builds - Gradle JalviewJS 2022-03 Build - Default Job #5 (JB-GJ2B-JOB1-5)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PJAVA_VERSION=11 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/jee-2022-03 --info clean eclipse jalviewjsCreateJ2sSettings jalviewjs jalviewjsSiteTar\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=develop\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_27918935_git_username=\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=develop\nbamboo_repository_revision_number=986834f1db7bd344d067bb450970578acb32c10f\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GJ2B-JOB1-5\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-GJ2B-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GJ2B-JOB1\nbamboo_shortPlanName=Gradle JalviewJS 2022-03 Build\nbamboo_repository_27918935_revision_number=986834f1db7bd344d067bb450970578acb32c10f\nbamboo_repository_27918935_git_branch=develop\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=5\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-GJ2B-JOB1-5\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle JalviewJS 2022-03 Build\nbamboo_shortPlanKey=GJ2B\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=986834f1db7bd344d067bb450970578acb32c10f\nbamboo_buildTimeStamp=2022-06-09T11:03:49.401+01:00\nbamboo_repository_previous_revision_number=99bfb1a08e5ceb3a3c990bb49dcd7433a0880558\nbamboo_planRepository_previousRevision=99bfb1a08e5ceb3a3c990bb49dcd7433a0880558\nbamboo_repository_git_branch=develop\nbamboo_buildResultKey=JB-GJ2B-JOB1-5\nbamboo_repository_branch_name=develop\nbamboo_buildPlanName=Jalview Builds - Gradle JalviewJS 2022-03 Build - Default Job\nbamboo_repository_27918935_name=Jalview Git\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=986834f1db7bd344d067bb450970578acb32c10f\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_planRepository_branch=develop\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=99bfb1a08e5ceb3a3c990bb49dcd7433a0880558\nbamboo_planRepository_branchDisplayName=develop\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=develop\nbamboo_repository_27918935_git_repositoryUrl=http://source.jalview.org/git/jalview.git\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_27918935_branch_name=develop\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-27624621\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-GJ2B-JOB1\nbamboo_planKey=JB-GJ2B\nbamboo_repository_27918935_previous_revision_number=99bfb1a08e5ceb3a3c990bb49dcd7433a0880558\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=develop\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 09-Jun-2022 11:03:50 Initialized native services in: /srv/bamboo/home/bamboo/.gradle/native build 09-Jun-2022 11:03:50 Initialized jansi services in: /srv/bamboo/home/bamboo/.gradle/native build 09-Jun-2022 11:03:50 The client will now receive all logging from the daemon (pid: 17015). The daemon log file: /srv/bamboo/home/bamboo/.gradle/daemon/7.4.2/daemon-17015.out.log build 09-Jun-2022 11:03:50 Starting 12th build in daemon [uptime: 2 hrs 42 mins 22.84 secs, performance: 99%, non-heap usage: 37% of 256 MiB] build 09-Jun-2022 11:03:50 Using 4 worker leases. build 09-Jun-2022 11:03:50 Watching the file system is configured to be enabled if available build 09-Jun-2022 11:03:50 File system watching is inactive build 09-Jun-2022 11:03:50 Starting Build build 09-Jun-2022 11:03:50 Settings evaluated using settings file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/settings.gradle'. build 09-Jun-2022 11:03:50 Projects loaded. Root project using build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build.gradle'. build 09-Jun-2022 11:03:50 Included projects: [root project 'jalview'] build 09-Jun-2022 11:03:51 build 09-Jun-2022 11:03:51 > Configure project : build 09-Jun-2022 11:03:51 Evaluating root project 'jalview' using build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build.gradle'. build 09-Jun-2022 11:03:51 Using properties from file './utils/channels/default/channel_gradle.properties' build 09-Jun-2022 11:03:51 JALVIEW_VERSION is set to '2.11.2.3' build 09-Jun-2022 11:03:51 HEADLESS BUILD build 09-Jun-2022 11:03:51 J2S ENABLED build 09-Jun-2022 11:03:51 Using a LOCAL profile. build 09-Jun-2022 11:03:51 file or directory '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/src/main/java', not found build 09-Jun-2022 11:03:51 file or directory '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/resources/doc_build', not found build 09-Jun-2022 11:03:51 file or directory '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/classes', not found build 09-Jun-2022 11:03:51 eclipseDir exists build 09-Jun-2022 11:03:51 All projects evaluated. build 09-Jun-2022 11:03:51 Selected primary task 'clean' from project : build 09-Jun-2022 11:03:51 Selected primary task 'eclipse' from project : build 09-Jun-2022 11:03:51 Selected primary task 'jalviewjsCreateJ2sSettings' from project : build 09-Jun-2022 11:03:51 Selected primary task 'jalviewjs' from project : build 09-Jun-2022 11:03:51 Selected primary task 'jalviewjsSiteTar' from project : build 09-Jun-2022 11:03:51 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 ':copyResources', task ':createBuildProperties', task ':jalviewjsSyncBuildProperties', task ':jalviewjsBuildAllCores', task ':jalviewjsPublishCoreTemplates', task ':jalviewjsSyncCore', task ':copyChannelResources', task ':buildResources', task ':jalviewjsSyncResources', task ':jalviewjsSyncSiteResources', task ':jalviewjsPrepareSite', task ':jalviewjsBuildSite', task ':jalviewjs', task ':jalviewjsSiteTar'] build 09-Jun-2022 11:03:51 Tasks that were excluded: [] build 09-Jun-2022 11:03:51 :clean (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:51 build 09-Jun-2022 11:03:51 > Task :clean build 09-Jun-2022 11:03:51 Caching disabled for task ':clean' because: build 09-Jun-2022 11:03:51 Build cache is disabled build 09-Jun-2022 11:03:51 Task ':clean' is not up-to-date because: build 09-Jun-2022 11:03:51 Task has not declared any outputs despite executing actions. build 09-Jun-2022 11:03:51 :clean (Thread[Execution worker for ':',5,main]) completed. Took 0.683 secs. build 09-Jun-2022 11:03:51 :jalviewjsEclipsePaths (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:51 build 09-Jun-2022 11:03:51 > Task :jalviewjsEclipsePaths build 09-Jun-2022 11:03:51 Caching disabled for task ':jalviewjsEclipsePaths' because: build 09-Jun-2022 11:03:51 Build cache is disabled build 09-Jun-2022 11:03:51 Task ':jalviewjsEclipsePaths' is not up-to-date because: build 09-Jun-2022 11:03:51 Task has not declared any outputs despite executing actions. build 09-Jun-2022 11:03:51 Running task jalviewjsEclipsePaths as IN_ECLIPSE=false build 09-Jun-2022 11:03:51 ECLIPSE VERSION=4.23.0 build 09-Jun-2022 11:03:51 :jalviewjsEclipsePaths (Thread[Execution worker for ':',5,main]) completed. Took 0.001 secs. build 09-Jun-2022 11:03:51 destroyer locations for task group 0 (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:51 destroyer locations for task group 0 (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:03:51 :eclipseClasspath (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:51 build 09-Jun-2022 11:03:51 > Task :eclipseClasspath build 09-Jun-2022 11:03:51 Caching disabled for task ':eclipseClasspath' because: build 09-Jun-2022 11:03:51 Build cache is disabled build 09-Jun-2022 11:03:51 Task ':eclipseClasspath' is not up-to-date because: build 09-Jun-2022 11:03:51 Task.upToDateWhen is false. build 09-Jun-2022 11:03:51 :eclipseClasspath (Thread[Execution worker for ':',5,main]) completed. Took 0.044 secs. build 09-Jun-2022 11:03:51 :eclipseJdt (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:51 build 09-Jun-2022 11:03:51 > Task :eclipseJdt build 09-Jun-2022 11:03:51 Caching disabled for task ':eclipseJdt' because: build 09-Jun-2022 11:03:51 Build cache is disabled build 09-Jun-2022 11:03:51 Task ':eclipseJdt' is not up-to-date because: build 09-Jun-2022 11:03:51 Task.upToDateWhen is false. build 09-Jun-2022 11:03:51 :eclipseJdt (Thread[Execution worker for ':',5,main]) completed. Took 0.014 secs. build 09-Jun-2022 11:03:51 :eclipseProject (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:51 build 09-Jun-2022 11:03:51 > Task :eclipseProject build 09-Jun-2022 11:03:51 Caching disabled for task ':eclipseProject' because: build 09-Jun-2022 11:03:51 Build cache is disabled build 09-Jun-2022 11:03:51 Task ':eclipseProject' is not up-to-date because: build 09-Jun-2022 11:03:51 Task.upToDateWhen is false. build 09-Jun-2022 11:03:51 :eclipseProject (Thread[Execution worker for ':',5,main]) completed. Took 0.004 secs. build 09-Jun-2022 11:03:51 :eclipse (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:51 build 09-Jun-2022 11:03:51 > Task :eclipse build 09-Jun-2022 11:03:51 Skipping task ':eclipse' as it has no actions. build 09-Jun-2022 11:03:51 :eclipse (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:03:51 :jalviewjsCreateJ2sSettings (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:51 build 09-Jun-2022 11:03:51 > Task :jalviewjsCreateJ2sSettings build 09-Jun-2022 11:03:51 Caching disabled for task ':jalviewjsCreateJ2sSettings' because: build 09-Jun-2022 11:03:51 Build cache is disabled build 09-Jun-2022 11:03:51 Task ':jalviewjsCreateJ2sSettings' is not up-to-date because: build 09-Jun-2022 11:03:51 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/config/j2s has been removed. build 09-Jun-2022 11:03:51 Output property 'outputFile' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/config/j2s has been removed. build 09-Jun-2022 11:03:51 :jalviewjsCreateJ2sSettings (Thread[Execution worker for ':',5,main]) completed. Took 0.003 secs. build 09-Jun-2022 11:03:51 :jalviewjsEclipseCopyDropins (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:51 build 09-Jun-2022 11:03:51 > Task :jalviewjsEclipseCopyDropins build 09-Jun-2022 11:03:51 Caching disabled for task ':jalviewjsEclipseCopyDropins' because: build 09-Jun-2022 11:03:51 Build cache is disabled build 09-Jun-2022 11:03:51 Task ':jalviewjsEclipseCopyDropins' is not up-to-date because: build 09-Jun-2022 11:03:51 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/eclipse_dropins has been removed. build 09-Jun-2022 11:03:51 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/eclipse_dropins/com.seeq.eclipse.importprojects.jar has been removed. build 09-Jun-2022 11:03:51 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/eclipse_dropins/net.sf.j2s.core-j11.jar has been removed. build 09-Jun-2022 11:03:51 :jalviewjsEclipseCopyDropins (Thread[Execution worker for ':',5,main]) completed. Took 0.004 secs. build 09-Jun-2022 11:03:51 :jalviewjsSetEclipseWorkspace (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:51 build 09-Jun-2022 11:03:51 > Task :jalviewjsSetEclipseWorkspace build 09-Jun-2022 11:03:51 Caching disabled for task ':jalviewjsSetEclipseWorkspace' because: build 09-Jun-2022 11:03:51 Build cache is disabled build 09-Jun-2022 11:03:51 Task ':jalviewjsSetEclipseWorkspace' is not up-to-date because: build 09-Jun-2022 11:03:51 Task.upToDateWhen is false. build 09-Jun-2022 11:03:51 Running task jalviewjsSetEclipseWorkspace as IN_ECLIPSE=false build 09-Jun-2022 11:03:51 NEW ECLIPSE WORKSPACE: /tmp/groovy-generated-tmpdir-10345690696238764144 build 09-Jun-2022 11:03:51 :jalviewjsSetEclipseWorkspace (Thread[Execution worker for ':',5,main]) completed. Took 0.004 secs. build 09-Jun-2022 11:03:51 :jalviewjsEclipseSetup (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:51 build 09-Jun-2022 11:03:51 > Task :jalviewjsEclipseSetup build 09-Jun-2022 11:03:51 Skipping task ':jalviewjsEclipseSetup' as it has no actions. build 09-Jun-2022 11:03:51 :jalviewjsEclipseSetup (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:03:51 :jalviewjsEnableAltFileProperty (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:51 build 09-Jun-2022 11:03:51 > Task :jalviewjsEnableAltFileProperty UP-TO-DATE build 09-Jun-2022 11:03:51 Caching disabled for task ':jalviewjsEnableAltFileProperty' because: build 09-Jun-2022 11:03:51 Build cache is disabled build 09-Jun-2022 11:03:51 Skipping task ':jalviewjsEnableAltFileProperty' as it is up-to-date. build 09-Jun-2022 11:03:51 :jalviewjsEnableAltFileProperty (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:03:51 :eclipseSetup (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:51 build 09-Jun-2022 11:03:51 > Task :eclipseSetup build 09-Jun-2022 11:03:51 Skipping task ':eclipseSetup' as it has no actions. build 09-Jun-2022 11:03:51 :eclipseSetup (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:03:51 :jalviewjsProjectImport (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:03:53 build 09-Jun-2022 11:03:53 > Task :jalviewjsProjectImport build 09-Jun-2022 11:03:53 Caching disabled for task ':jalviewjsProjectImport' because: build 09-Jun-2022 11:03:53 Build cache is disabled build 09-Jun-2022 11:03:53 Task ':jalviewjsProjectImport' is not up-to-date because: build 09-Jun-2022 11:03:53 Task.upToDateWhen is false. build 09-Jun-2022 11:03:53 Running task jalviewjsProjectImport as IN_ECLIPSE=false build 09-Jun-2022 11:03:53 Starting process 'command '/home/bamboo/buildtools/eclipse/jee-2022-03/eclipse/eclipse''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1 Command: /home/bamboo/buildtools/eclipse/jee-2022-03/eclipse/eclipse -nosplash --launcher.suppressErrors -application com.seeq.eclipse.importprojects.headlessimport -data /tmp/groovy-generated-tmpdir-10345690696238764144 -import /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1 --launcher.appendVmargs -vmargs -Dorg.eclipse.equinox.p2.reconciler.dropins.directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/eclipse_dropins -Dnet.sf.j2s.core.headlessbuild=true -Dorg.jalview.jalviewjsj2sfilename=./build/jalviewjs/config/j2s build 09-Jun-2022 11:03:53 Successfully started process 'command '/home/bamboo/buildtools/eclipse/jee-2022-03/eclipse/eclipse'' build 09-Jun-2022 11:03:54 org.eclipse.m2e.logback.configuration: Activated before the state location was initialized. Retry after the state location is initialized. build 09-Jun-2022 11:03:55 org.eclipse.m2e.logback.configuration: Logback config file: /tmp/groovy-generated-tmpdir-10345690696238764144/.metadata/.plugins/org.eclipse.m2e.logback.configuration/logback.1.16.3.20211002-1029.xml build 09-Jun-2022 11:03:55 org.eclipse.m2e.logback.configuration: Initializing logback build 09-Jun-2022 11:04:32 :jalviewjsProjectImport (Thread[Execution worker for ':',5,main]) completed. Took 40.732 secs. build 09-Jun-2022 11:04:32 :jalviewjsTranspile (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:04:34 build 09-Jun-2022 11:04:34 > Task :jalviewjsTranspile build 09-Jun-2022 11:04:34 Caching disabled for task ':jalviewjsTranspile' because: build 09-Jun-2022 11:04:34 Build cache is disabled build 09-Jun-2022 11:04:34 Task ':jalviewjsTranspile' is not up-to-date because: build 09-Jun-2022 11:04:34 Task.upToDateWhen is false. build 09-Jun-2022 11:04:34 Running task jalviewjsTranspile as IN_ECLIPSE=false build 09-Jun-2022 11:04:34 Starting process 'command '/home/bamboo/buildtools/eclipse/jee-2022-03/eclipse/eclipse''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1 Command: /home/bamboo/buildtools/eclipse/jee-2022-03/eclipse/eclipse -nosplash --launcher.suppressErrors -application org.eclipse.jdt.apt.core.aptBuild -data /tmp/groovy-generated-tmpdir-10345690696238764144 -cleanBuild jalview --launcher.appendVmargs -vmargs -Dorg.eclipse.equinox.p2.reconciler.dropins.directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/eclipse_dropins -Dnet.sf.j2s.core.headlessbuild=true -Dorg.jalview.jalviewjsj2sfilename=./build/jalviewjs/config/j2s build 09-Jun-2022 11:04:34 Successfully started process 'command '/home/bamboo/buildtools/eclipse/jee-2022-03/eclipse/eclipse'' build 09-Jun-2022 11:04:34 org.eclipse.m2e.logback.configuration: Activated before the state location was initialized. Retry after the state location is initialized. build 09-Jun-2022 11:04:34 org.eclipse.m2e.logback.configuration: Logback config file: /tmp/groovy-generated-tmpdir-10345690696238764144/.metadata/.plugins/org.eclipse.m2e.logback.configuration/logback.1.16.3.20211002-1029.xml build 09-Jun-2022 11:04:34 org.eclipse.m2e.logback.configuration: Initializing logback build 09-Jun-2022 11:05:05 Invoking 'Java Builder' on '/jalview'. build 09-Jun-2022 11:05:06 net.sf.j2s.core.3.3.1/3.3.1-v1 started build 09-Jun-2022 11:05:06 J2S CompilationParticipant started build 09-Jun-2022 11:05:06 J2S isActive true /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1 build 09-Jun-2022 11:05:06 J2S aboutToBuild jalview /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1 build 09-Jun-2022 11:05:06 J2S cleanStarting /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1 build 09-Jun-2022 11:05:06 Cleaning output folder for jalview build 09-Jun-2022 11:05:06 Build done build 09-Jun-2022 11:05:06 Invoking 'Gradle Project Builder' on '/jalview'. build 09-Jun-2022 11:05:06 Invoking 'Java Builder' on '/jalview'. build 09-Jun-2022 11:05:06 J2S aboutToBuild jalview /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1 build 09-Jun-2022 11:05:06 Preparing to build jalview build 09-Jun-2022 11:05:06 Cleaning output folder for jalview build 09-Jun-2022 11:05:06 J2S cleanStarting /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1 build 09-Jun-2022 11:05:06 Copying resources to the output folder build 09-Jun-2022 11:05:06 Analyzing sources build 09-Jun-2022 11:05:06 J2S buildStarting 1036 files, contexts.size() = 1, isBatch=true build 09-Jun-2022 11:05:06 Compiling jalview/src/com/github/reinert/jjschema build 09-Jun-2022 11:05:07 Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:07 (Found 1 warning) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:07 (Found 2 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:07 (Found 3 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:07 (Found 4 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:07 (Found 5 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:07 (Found 9 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 12 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 13 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 14 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 15 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 37 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 38 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 46 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 47 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 48 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 49 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 50 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 51 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 52 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 59 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 63 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 67 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 69 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 89 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 90 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 91 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 98 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 108 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 113 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 114 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 115 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 119 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 120 warnings) Compiling jalview/src/com/stevesoft/pat build 09-Jun-2022 11:05:08 (Found 120 warnings) Compiling jalview/src/com/stevesoft/pat/wrap build 09-Jun-2022 11:05:08 (Found 120 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2 build 09-Jun-2022 11:05:08 (Found 122 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2 build 09-Jun-2022 11:05:08 (Found 129 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2 build 09-Jun-2022 11:05:08 (Found 132 warnings) Compiling jalview/src/ext/edu/ucsf/rbvi/strucviz2/port build 09-Jun-2022 11:05:08 (Found 132 warnings) Compiling jalview/src/ext/vamsas build 09-Jun-2022 11:05:08 (Found 139 warnings) Compiling jalview/src/ext/vamsas build 09-Jun-2022 11:05:08 (Found 146 warnings) Compiling jalview/src/ext/vamsas build 09-Jun-2022 11:05:08 (Found 184 warnings) Compiling jalview/src/ext/vamsas build 09-Jun-2022 11:05:08 (Found 191 warnings) Compiling jalview/src/ext/vamsas build 09-Jun-2022 11:05:08 (Found 247 warnings) Compiling jalview/src/ext/vamsas build 09-Jun-2022 11:05:08 (Found 279 warnings) Compiling jalview/src/ext/vamsas build 09-Jun-2022 11:05:08 (Found 286 warnings) Compiling jalview/src/ext/vamsas build 09-Jun-2022 11:05:08 (Found 354 warnings) Compiling jalview/src/ext/vamsas build 09-Jun-2022 11:05:08 (Found 357 warnings) Compiling jalview/src/ext/vamsas build 09-Jun-2022 11:05:08 (Found 360 warnings) Compiling jalview/src/ext/vamsas build 09-Jun-2022 11:05:08 (Found 360 warnings) Compiling jalview/src/jalview/analysis build 09-Jun-2022 11:05:08 (Found 361 warnings) Compiling jalview/src/jalview/analysis build 09-Jun-2022 11:05:08 (Found 362 warnings) Compiling jalview/src/jalview/analysis build 09-Jun-2022 11:05:08 (Found 363 warnings) Compiling jalview/src/jalview/analysis build 09-Jun-2022 11:05:08 (Found 365 warnings) Compiling jalview/src/jalview/analysis build 09-Jun-2022 11:05:08 (Found 366 warnings) Compiling jalview/src/jalview/analysis build 09-Jun-2022 11:05:08 (Found 392 warnings) Compiling jalview/src/jalview/analysis build 09-Jun-2022 11:05:08 (Found 396 warnings) Compiling jalview/src/jalview/analysis build 09-Jun-2022 11:05:08 (Found 397 warnings) Compiling jalview/src/jalview/analysis build 09-Jun-2022 11:05:08 (Found 398 warnings) Compiling jalview/src/jalview/analysis build 09-Jun-2022 11:05:08 (Found 398 warnings) Compiling jalview/src/jalview/analysis/scoremodels build 09-Jun-2022 11:05:08 (Found 398 warnings) Compiling jalview/src/jalview/api build 09-Jun-2022 11:05:08 (Found 398 warnings) Compiling jalview/src/jalview/api/analysis build 09-Jun-2022 11:05:08 (Found 398 warnings) Compiling jalview/src/jalview/api/structures build 09-Jun-2022 11:05:08 (Found 401 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:08 (Found 456 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 465 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 466 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 471 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 472 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 474 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 485 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 487 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 492 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 493 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 494 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 495 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 497 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 499 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 500 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 502 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 503 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 508 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 509 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 510 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 511 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 512 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 514 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 522 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 532 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 533 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 534 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 536 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 537 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 542 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 545 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 553 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 555 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 556 warnings) Compiling jalview/src/jalview/appletgui build 09-Jun-2022 11:05:09 (Found 556 warnings) Compiling jalview/src/jalview/bin build 09-Jun-2022 11:05:09 (Found 565 warnings) Compiling jalview/src/jalview/bin build 09-Jun-2022 11:05:09 (Found 566 warnings) Compiling jalview/src/jalview/bin build 09-Jun-2022 11:05:09 (Found 567 warnings) Compiling jalview/src/jalview/bin build 09-Jun-2022 11:05:09 (Found 573 warnings) Compiling jalview/src/jalview/bin build 09-Jun-2022 11:05:09 (Found 575 warnings) Compiling jalview/src/jalview/bin build 09-Jun-2022 11:05:09 (Found 3 errors + 633 warnings) Compiling jalview/src/jalview/bin build 09-Jun-2022 11:05:09 (Found 3 errors + 638 warnings) Compiling jalview/src/jalview/bin build 09-Jun-2022 11:05:09 (Found 3 errors + 638 warnings) Compiling jalview/src/jalview/commands build 09-Jun-2022 11:05:09 (Found 3 errors + 638 warnings) Compiling jalview/src/jalview/controller build 09-Jun-2022 11:05:09 (Found 3 errors + 638 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 651 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 652 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 653 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 656 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 657 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 658 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 664 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 668 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 670 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 671 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 679 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 680 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 683 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 689 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 691 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 692 warnings) Compiling jalview/src/jalview/datamodel build 09-Jun-2022 11:05:09 (Found 3 errors + 692 warnings) Compiling jalview/src/jalview/datamodel/features build 09-Jun-2022 11:05:09 (Found 3 errors + 692 warnings) Compiling jalview/src/jalview/exceptions build 09-Jun-2022 11:05:09 (Found 3 errors + 692 warnings) Compiling jalview/src/jalview/ext/android build 09-Jun-2022 11:05:09 (Found 3 errors + 692 warnings) Compiling jalview/src/jalview/ext/ensembl build 09-Jun-2022 11:05:09 (Found 3 errors + 694 warnings) Compiling jalview/src/jalview/ext/ensembl build 09-Jun-2022 11:05:09 (Found 3 errors + 696 warnings) Compiling jalview/src/jalview/ext/ensembl build 09-Jun-2022 11:05:09 (Found 3 errors + 697 warnings) Compiling jalview/src/jalview/ext/ensembl build 09-Jun-2022 11:05:09 (Found 3 errors + 699 warnings) Compiling jalview/src/jalview/ext/ensembl build 09-Jun-2022 11:05:09 (Found 3 errors + 702 warnings) Compiling jalview/src/jalview/ext/htsjdk build 09-Jun-2022 11:05:09 (Found 3 errors + 703 warnings) Compiling jalview/src/jalview/ext/htsjdk build 09-Jun-2022 11:05:09 (Found 3 errors + 705 warnings) Compiling jalview/src/jalview/ext/jmol build 09-Jun-2022 11:05:09 (Found 3 errors + 706 warnings) Compiling jalview/src/jalview/ext/jmol build 09-Jun-2022 11:05:09 (Found 3 errors + 710 warnings) Compiling jalview/src/jalview/ext/paradise build 09-Jun-2022 11:05:09 (Found 3 errors + 710 warnings) Compiling jalview/src/jalview/ext/pymol build 09-Jun-2022 11:05:09 (Found 3 errors + 713 warnings) Compiling jalview/src/jalview/ext/pymol build 09-Jun-2022 11:05:09 (Found 3 errors + 714 warnings) Compiling jalview/src/jalview/ext/rbvi/chimera build 09-Jun-2022 11:05:09 (Found 3 errors + 715 warnings) Compiling jalview/src/jalview/ext/rbvi/chimera build 09-Jun-2022 11:05:09 (Found 3 errors + 716 warnings) Compiling jalview/src/jalview/ext/rbvi/chimera build 09-Jun-2022 11:05:09 (Found 3 errors + 716 warnings) Compiling jalview/src/jalview/ext/so build 09-Jun-2022 11:05:09 (Found 3 errors + 716 warnings) Compiling jalview/src/jalview/ext/varna build 09-Jun-2022 11:05:09 (Found 3 errors + 716 warnings) Compiling jalview/src/jalview/fts/api build 09-Jun-2022 11:05:09 (Found 3 errors + 717 warnings) Compiling jalview/src/jalview/fts/api build 09-Jun-2022 11:05:09 (Found 3 errors + 718 warnings) Compiling jalview/src/jalview/fts/core build 09-Jun-2022 11:05:09 (Found 3 errors + 721 warnings) Compiling jalview/src/jalview/fts/core build 09-Jun-2022 11:05:10 (Found 3 errors + 723 warnings) Compiling jalview/src/jalview/fts/core build 09-Jun-2022 11:05:10 (Found 3 errors + 724 warnings) Compiling jalview/src/jalview/fts/core build 09-Jun-2022 11:05:10 (Found 3 errors + 726 warnings) Compiling jalview/src/jalview/fts/service/alphafold build 09-Jun-2022 11:05:10 (Found 3 errors + 726 warnings) Compiling jalview/src/jalview/fts/service/pdb build 09-Jun-2022 11:05:10 (Found 3 errors + 733 warnings) Compiling jalview/src/jalview/fts/service/pdb build 09-Jun-2022 11:05:10 (Found 3 errors + 733 warnings) Compiling jalview/src/jalview/fts/service/threedbeacons build 09-Jun-2022 11:05:10 (Found 3 errors + 745 warnings) Compiling jalview/src/jalview/fts/service/threedbeacons build 09-Jun-2022 11:05:10 (Found 3 errors + 750 warnings) Compiling jalview/src/jalview/fts/service/threedbeacons build 09-Jun-2022 11:05:10 (Found 3 errors + 750 warnings) Compiling jalview/src/jalview/fts/service/uniprot build 09-Jun-2022 11:05:10 (Found 3 errors + 754 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 756 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 757 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 758 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 759 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 762 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 765 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 770 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 771 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 780 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 781 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 782 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 812 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 813 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 814 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 815 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 816 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 821 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 822 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 823 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 827 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 831 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 837 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 838 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 840 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 841 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 842 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 843 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 844 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 850 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 851 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 852 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 853 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 855 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 856 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 857 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 858 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:10 (Found 3 errors + 864 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 866 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 868 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 869 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 870 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 872 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 876 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 885 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 894 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 895 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 896 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 897 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 899 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 901 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 903 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 909 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 911 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 912 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 913 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 915 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 916 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 917 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 944 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 947 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 954 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 1012 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 1025 warnings) Compiling jalview/src/jalview/gui build 09-Jun-2022 11:05:11 (Found 3 errors + 1027 warnings) Compiling jalview/src/jalview/gui/structurechooser build 09-Jun-2022 11:05:11 (Found 3 errors + 1029 warnings) Compiling jalview/src/jalview/gui/structurechooser build 09-Jun-2022 11:05:11 (Found 3 errors + 1034 warnings) Compiling jalview/src/jalview/gui/structurechooser build 09-Jun-2022 11:05:11 (Found 3 errors + 1034 warnings) Compiling jalview/src/jalview/httpserver build 09-Jun-2022 11:05:11 (Found 3 errors + 1034 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1039 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1041 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1043 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1045 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1065 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1067 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1069 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1073 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1075 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1076 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1077 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1115 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1117 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1137 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1140 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1142 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1143 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1144 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1157 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1219 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1220 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1302 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1307 warnings) Compiling jalview/src/jalview/io build 09-Jun-2022 11:05:11 (Found 3 errors + 1307 warnings) Compiling jalview/src/jalview/io/cache build 09-Jun-2022 11:05:11 (Found 3 errors + 1307 warnings) Compiling jalview/src/jalview/io/gff build 09-Jun-2022 11:05:11 (Found 3 errors + 1308 warnings) Compiling jalview/src/jalview/io/gff build 09-Jun-2022 11:05:11 (Found 3 errors + 1308 warnings) Compiling jalview/src/jalview/io/packed build 09-Jun-2022 11:05:11 (Found 3 errors + 1314 warnings) Compiling jalview/src/jalview/io/packed build 09-Jun-2022 11:05:11 (Found 3 errors + 1316 warnings) Compiling jalview/src/jalview/io/packed build 09-Jun-2022 11:05:11 (Found 3 errors + 1316 warnings) Compiling jalview/src/jalview/io/vamsas build 09-Jun-2022 11:05:11 (Found 3 errors + 1334 warnings) Compiling jalview/src/jalview/io/vamsas build 09-Jun-2022 11:05:11 (Found 3 errors + 1345 warnings) Compiling jalview/src/jalview/io/vamsas build 09-Jun-2022 11:05:11 (Found 3 errors + 1346 warnings) Compiling jalview/src/jalview/io/vamsas build 09-Jun-2022 11:05:11 (Found 3 errors + 1359 warnings) Compiling jalview/src/jalview/io/vamsas build 09-Jun-2022 11:05:11 (Found 3 errors + 1363 warnings) Compiling jalview/src/jalview/io/vamsas build 09-Jun-2022 11:05:11 (Found 3 errors + 1367 warnings) Compiling jalview/src/jalview/io/vamsas build 09-Jun-2022 11:05:11 (Found 3 errors + 1380 warnings) Compiling jalview/src/jalview/io/vamsas build 09-Jun-2022 11:05:11 (Found 3 errors + 1383 warnings) Compiling jalview/src/jalview/io/vcf build 09-Jun-2022 11:05:11 (Found 4 errors + 1392 warnings) Compiling jalview/src/jalview/javascript build 09-Jun-2022 11:05:11 (Found 4 errors + 1396 warnings) Compiling jalview/src/jalview/javascript build 09-Jun-2022 11:05:11 (Found 4 errors + 1397 warnings) Compiling jalview/src/jalview/javascript/json build 09-Jun-2022 11:05:11 (Found 4 errors + 1397 warnings) Compiling jalview/src/jalview/javascript/web build 09-Jun-2022 11:05:11 (Found 4 errors + 1398 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1399 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1401 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1404 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1405 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1406 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1407 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1410 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1412 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1420 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1421 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1422 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1430 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1432 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:11 (Found 4 errors + 1433 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:12 (Found 4 errors + 1436 warnings) Compiling jalview/src/jalview/jbgui build 09-Jun-2022 11:05:12 (Found 4 errors + 1436 warnings) Compiling jalview/src/jalview/json/binding/biojs build 09-Jun-2022 11:05:12 (Found 4 errors + 1436 warnings) Compiling jalview/src/jalview/json/binding/biojson/v1 build 09-Jun-2022 11:05:12 (Found 4 errors + 1439 warnings) Compiling jalview/src/jalview/log build 09-Jun-2022 11:05:12 (Found 4 errors + 1441 warnings) Compiling jalview/src/jalview/log build 09-Jun-2022 11:05:12 (Found 4 errors + 1442 warnings) Compiling jalview/src/jalview/log build 09-Jun-2022 11:05:12 (Found 4 errors + 1442 warnings) Compiling jalview/src/jalview/math build 09-Jun-2022 11:05:12 (Found 4 errors + 1468 warnings) Compiling jalview/src/jalview/project build 09-Jun-2022 11:05:12 (Found 4 errors + 1468 warnings) Compiling jalview/src/jalview/renderer build 09-Jun-2022 11:05:12 (Found 4 errors + 1468 warnings) Compiling jalview/src/jalview/renderer/seqfeatures build 09-Jun-2022 11:05:12 (Found 4 errors + 1468 warnings) Compiling jalview/src/jalview/rest build 09-Jun-2022 11:05:12 (Found 4 errors + 1468 warnings) Compiling jalview/src/jalview/schemes build 09-Jun-2022 11:05:12 (Found 4 errors + 1468 warnings) Compiling jalview/src/jalview/structure build 09-Jun-2022 11:05:12 (Found 4 errors + 1471 warnings) Compiling jalview/src/jalview/structure build 09-Jun-2022 11:05:12 (Found 4 errors + 1471 warnings) Compiling jalview/src/jalview/structures/models build 09-Jun-2022 11:05:12 (Found 4 errors + 1471 warnings) Compiling jalview/src/jalview/urls build 09-Jun-2022 11:05:12 (Found 4 errors + 1472 warnings) Compiling jalview/src/jalview/urls build 09-Jun-2022 11:05:12 (Found 4 errors + 1472 warnings) Compiling jalview/src/jalview/urls/api build 09-Jun-2022 11:05:12 (Found 4 errors + 1472 warnings) Compiling jalview/src/jalview/urls/applet build 09-Jun-2022 11:05:12 (Found 4 errors + 1472 warnings) Compiling jalview/src/jalview/urls/desktop build 09-Jun-2022 11:05:12 (Found 4 errors + 1472 warnings) Compiling jalview/src/jalview/util build 09-Jun-2022 11:05:12 (Found 4 errors + 1473 warnings) Compiling jalview/src/jalview/util build 09-Jun-2022 11:05:12 (Found 4 errors + 1474 warnings) Compiling jalview/src/jalview/util build 09-Jun-2022 11:05:12 (Found 4 errors + 1486 warnings) Compiling jalview/src/jalview/util build 09-Jun-2022 11:05:12 (Found 4 errors + 1487 warnings) Compiling jalview/src/jalview/util build 09-Jun-2022 11:05:12 (Found 4 errors + 1491 warnings) Compiling jalview/src/jalview/util build 09-Jun-2022 11:05:12 (Found 4 errors + 1492 warnings) Compiling jalview/src/jalview/util build 09-Jun-2022 11:05:12 (Found 4 errors + 1495 warnings) Compiling jalview/src/jalview/util build 09-Jun-2022 11:05:12 (Found 4 errors + 1499 warnings) Compiling jalview/src/jalview/util build 09-Jun-2022 11:05:12 (Found 4 errors + 1503 warnings) Compiling jalview/src/jalview/util build 09-Jun-2022 11:05:12 (Found 4 errors + 1527 warnings) Compiling jalview/src/jalview/util build 09-Jun-2022 11:05:12 (Found 4 errors + 1528 warnings) Compiling jalview/src/jalview/util build 09-Jun-2022 11:05:12 (Found 4 errors + 1528 warnings) Compiling jalview/src/jalview/util/dialogrunner build 09-Jun-2022 11:05:12 (Found 4 errors + 1528 warnings) Compiling jalview/src/jalview/util build 09-Jun-2022 11:05:12 (Found 4 errors + 1528 warnings) Compiling jalview/src/jalview/util/matcher build 09-Jun-2022 11:05:12 (Found 4 errors + 1528 warnings) Compiling jalview/src/jalview/viewmodel build 09-Jun-2022 11:05:12 (Found 4 errors + 1528 warnings) Compiling jalview/src/jalview/viewmodel/annotationfilter build 09-Jun-2022 11:05:12 (Found 4 errors + 1529 warnings) Compiling jalview/src/jalview/viewmodel/seqfeatures build 09-Jun-2022 11:05:12 (Found 4 errors + 1529 warnings) Compiling jalview/src/jalview/viewmodel/styles build 09-Jun-2022 11:05:12 (Found 4 errors + 1529 warnings) Compiling jalview/src/jalview/workers build 09-Jun-2022 11:05:12 (Found 4 errors + 1533 warnings) Compiling jalview/src/jalview/workers build 09-Jun-2022 11:05:12 (Found 4 errors + 1533 warnings) Compiling jalview/src/jalview/ws build 09-Jun-2022 11:05:12 (Found 4 errors + 1534 warnings) Compiling jalview/src/jalview/ws build 09-Jun-2022 11:05:12 (Found 4 errors + 1535 warnings) Compiling jalview/src/jalview/ws build 09-Jun-2022 11:05:12 (Found 4 errors + 1539 warnings) Compiling jalview/src/jalview/ws build 09-Jun-2022 11:05:12 (Found 4 errors + 1546 warnings) Compiling jalview/src/jalview/ws/dbsources build 09-Jun-2022 11:05:12 (Found 4 errors + 1548 warnings) Compiling jalview/src/jalview/ws/dbsources build 09-Jun-2022 11:05:12 (Found 4 errors + 1548 warnings) Compiling jalview/src/jalview/ws/ebi build 09-Jun-2022 11:05:12 (Found 4 errors + 1548 warnings) Compiling jalview/src/jalview/ws/io/mime build 09-Jun-2022 11:05:12 (Found 4 errors + 1548 warnings) Compiling jalview/src/jalview/ws/jws1 build 09-Jun-2022 11:05:12 (Found 4 errors + 1552 warnings) Compiling jalview/src/jalview/ws/jws1 build 09-Jun-2022 11:05:12 (Found 4 errors + 1560 warnings) Compiling jalview/src/jalview/ws/jws1 build 09-Jun-2022 11:05:12 (Found 4 errors + 1573 warnings) Compiling jalview/src/jalview/ws/jws1 build 09-Jun-2022 11:05:12 (Found 4 errors + 1587 warnings) Compiling jalview/src/jalview/ws/jws1 build 09-Jun-2022 11:05:12 (Found 4 errors + 1593 warnings) Compiling jalview/src/jalview/ws/jws1 build 09-Jun-2022 11:05:12 (Found 4 errors + 1594 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1595 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1605 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1612 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1626 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1629 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1633 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1639 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1645 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1657 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1659 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1663 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1689 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1712 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1713 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1718 warnings) Compiling jalview/src/jalview/ws/jws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1724 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 09-Jun-2022 11:05:12 (Found 4 errors + 1728 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 09-Jun-2022 11:05:12 (Found 4 errors + 1731 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 09-Jun-2022 11:05:12 (Found 4 errors + 1742 warnings) Compiling jalview/src/jalview/ws/jws2/dm build 09-Jun-2022 11:05:12 (Found 4 errors + 1749 warnings) Compiling jalview/src/jalview/ws/jws2/jabaws2 build 09-Jun-2022 11:05:12 (Found 4 errors + 1749 warnings) Compiling jalview/src/jalview/ws/params build 09-Jun-2022 11:05:12 (Found 4 errors + 1750 warnings) Compiling jalview/src/jalview/ws/params build 09-Jun-2022 11:05:12 (Found 4 errors + 1750 warnings) Compiling jalview/src/jalview/ws/params/simple build 09-Jun-2022 11:05:12 (Found 4 errors + 1751 warnings) Compiling jalview/src/jalview/ws/params/simple build 09-Jun-2022 11:05:12 (Found 4 errors + 1751 warnings) Compiling jalview/src/jalview/ws/rest build 09-Jun-2022 11:05:12 (Found 4 errors + 1752 warnings) Compiling jalview/src/jalview/ws/rest build 09-Jun-2022 11:05:12 (Found 4 errors + 1757 warnings) Compiling jalview/src/jalview/ws/rest build 09-Jun-2022 11:05:12 (Found 4 errors + 1758 warnings) Compiling jalview/src/jalview/ws/rest build 09-Jun-2022 11:05:12 (Found 4 errors + 1759 warnings) Compiling jalview/src/jalview/ws/rest build 09-Jun-2022 11:05:12 (Found 4 errors + 1765 warnings) Compiling jalview/src/jalview/ws/rest build 09-Jun-2022 11:05:12 (Found 4 errors + 1774 warnings) Compiling jalview/src/jalview/ws/rest build 09-Jun-2022 11:05:12 (Found 4 errors + 1780 warnings) Compiling jalview/src/jalview/ws/rest build 09-Jun-2022 11:05:12 (Found 4 errors + 1780 warnings) Compiling jalview/src/jalview/ws/rest/params build 09-Jun-2022 11:05:12 (Found 4 errors + 1783 warnings) Compiling jalview/src/jalview/ws/seqfetcher build 09-Jun-2022 11:05:12 (Found 4 errors + 1783 warnings) Compiling jalview/src/jalview/ws/sifts build 09-Jun-2022 11:05:12 (Found 4 errors + 1785 warnings) Compiling jalview/src/jalview/ws/sifts build 09-Jun-2022 11:05:12 (Found 4 errors + 1788 warnings) Compiling jalview/src/jalview/ws/uimodel build 09-Jun-2022 11:05:12 (Found 4 errors + 1788 warnings) Compiling jalview/src/jalview/ws/utils build 09-Jun-2022 11:05:12 (Found 4 errors + 1788 warnings) Compiling jalview/src/jalview/xml/binding/embl build 09-Jun-2022 11:05:12 (Found 4 errors + 1788 warnings) Compiling jalview/src/jalview/xml/binding/jalview build 09-Jun-2022 11:05:12 (Found 4 errors + 1788 warnings) Compiling jalview/src/jalview/xml/binding/sifts build 09-Jun-2022 11:05:12 (Found 4 errors + 1788 warnings) Compiling jalview/src/jalview/xml/binding/uniprot build 09-Jun-2022 11:05:12 (Found 4 errors + 1795 warnings) Compiling jalview/src/mc_view build 09-Jun-2022 11:05:12 (Found 4 errors + 1796 warnings) Compiling jalview/src/mc_view build 09-Jun-2022 11:05:12 (Found 4 errors + 1801 warnings) Compiling jalview/src/mc_view build 09-Jun-2022 11:05:13 (Found 4 errors + 1808 warnings) Compiling jalview/src/mc_view build 09-Jun-2022 11:05:13 (Found 4 errors + 1809 warnings) Compiling jalview/src/mc_view build 09-Jun-2022 11:05:13 (Found 4 errors + 1810 warnings) Compiling jalview/src/mc_view build 09-Jun-2022 11:05:13 (Found 4 errors + 1810 warnings) Compiling jalview/src/org/jibble/epsgraphics build 09-Jun-2022 11:05:13 (Found 4 errors + 1811 warnings) Compiling jalview/src/org/jibble/epsgraphics build 09-Jun-2022 11:05:13 (Found 4 errors + 1817 warnings) Compiling jalview/src/org/jibble/epsgraphics build 09-Jun-2022 11:05:13 (Found 4 errors + 1817 warnings) Compiling jalview/src/org/json build 09-Jun-2022 11:05:13 (Found 4 errors + 1819 warnings) Compiling jalview/src/org/json build 09-Jun-2022 11:05:13 (Found 4 errors + 1820 warnings) Compiling jalview/src/org/json build 09-Jun-2022 11:05:13 (Found 4 errors + 1831 warnings) Compiling jalview/src/org/json/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 1837 warnings) Compiling jalview/src/org/json/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 1846 warnings) Compiling jalview/src/org/json/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 1848 warnings) Compiling jalview/src/org/json/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 1850 warnings) Compiling jalview/src/org/json/simple/parser build 09-Jun-2022 11:05:13 (Found 4 errors + 1925 warnings) Compiling jalview/src/org/json/simple/parser build 09-Jun-2022 11:05:13 (Found 4 errors + 1929 warnings) Compiling jalview/src/org/json/simple/parser build 09-Jun-2022 11:05:13 (Found 4 errors + 1929 warnings) Compiling jalview/src/org/stackoverflowusers/file build 09-Jun-2022 11:05:13 (Found 4 errors + 1929 warnings) Compiling jalview/src/swingjs/api build 09-Jun-2022 11:05:13 (Found 4 errors + 1929 warnings) Compiling jalview/src/swingjs/api/js build 09-Jun-2022 11:05:13 (Found 4 errors + 1930 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 09-Jun-2022 11:05:13 (Found 4 errors + 1932 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 09-Jun-2022 11:05:13 (Found 4 errors + 1933 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 09-Jun-2022 11:05:13 (Found 4 errors + 1935 warnings) Compiling jalview/src/uk/ac/ebi/picr/model build 09-Jun-2022 11:05:13 (Found 4 errors + 1938 warnings) Compiling jalview/src/uk/ac/ebi/www build 09-Jun-2022 11:05:13 (Found 4 errors + 1941 warnings) Compiling jalview/src/uk/ac/ebi/www build 09-Jun-2022 11:05:13 (Found 4 errors + 1944 warnings) Compiling jalview/src/uk/ac/ebi/www build 09-Jun-2022 11:05:13 (Found 4 errors + 1951 warnings) Compiling jalview/src/uk/ac/ebi/www build 09-Jun-2022 11:05:13 (Found 4 errors + 1999 warnings) Compiling jalview/src/uk/ac/ebi/www build 09-Jun-2022 11:05:13 (Found 4 errors + 2041 warnings) Compiling jalview/src/uk/ac/ebi/www/picr/AccessionMappingService build 09-Jun-2022 11:05:13 (Found 4 errors + 2048 warnings) Compiling jalview/src/uk/ac/ebi/www/picr/AccessionMappingService build 09-Jun-2022 11:05:13 (Found 4 errors + 2048 warnings) Compiling jalview/src/vamsas build 09-Jun-2022 11:05:13 (Found 4 errors + 2049 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2051 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2052 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2054 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2055 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2057 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2058 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2060 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2061 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2063 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2064 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2066 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2067 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2069 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2070 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2072 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2073 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2074 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2076 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2078 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2079 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2081 warnings) Compiling jalview/src/vamsas/objects/simple build 09-Jun-2022 11:05:13 (Found 4 errors + 2081 warnings) Cleaning output folder for jalview build 09-Jun-2022 11:05:13 (Found 4 errors + 2081 warnings) Copying resources to the output folder build 09-Jun-2022 11:05:13 (Found 4 errors + 2081 warnings) Analyzing sources build 09-Jun-2022 11:05:13 J2S buildStarting 269 files, contexts.size() = 2, isBatch=true build 09-Jun-2022 11:05:13 (Found 4 errors + 2081 warnings) Compiling jalview/test/jalview/analysis build 09-Jun-2022 11:05:13 (Found 4 errors + 2089 warnings) Compiling jalview/test/jalview/analysis build 09-Jun-2022 11:05:13 (Found 4 errors + 2091 warnings) Compiling jalview/test/jalview/analysis build 09-Jun-2022 11:05:13 (Found 4 errors + 2101 warnings) Compiling jalview/test/jalview/analysis build 09-Jun-2022 11:05:13 (Found 4 errors + 2103 warnings) Compiling jalview/test/jalview/analysis build 09-Jun-2022 11:05:13 (Found 4 errors + 2105 warnings) Compiling jalview/test/jalview/analysis build 09-Jun-2022 11:05:13 (Found 4 errors + 2146 warnings) Compiling jalview/test/jalview/analysis build 09-Jun-2022 11:05:13 (Found 4 errors + 2146 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 09-Jun-2022 11:05:13 (Found 4 errors + 2151 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 09-Jun-2022 11:05:13 (Found 4 errors + 2152 warnings) Compiling jalview/test/jalview/analysis/scoremodels build 09-Jun-2022 11:05:13 (Found 4 errors + 2152 warnings) Compiling jalview/test/jalview/bin build 09-Jun-2022 11:05:13 (Found 4 errors + 2153 warnings) Compiling jalview/test/jalview/bin build 09-Jun-2022 11:05:13 (Found 4 errors + 2154 warnings) Compiling jalview/test/jalview/commands build 09-Jun-2022 11:05:13 (Found 4 errors + 2155 warnings) Compiling jalview/test/jalview/controller build 09-Jun-2022 11:05:13 (Found 4 errors + 2155 warnings) Compiling jalview/test/jalview/datamodel build 09-Jun-2022 11:05:13 (Found 4 errors + 2156 warnings) Compiling jalview/test/jalview/datamodel build 09-Jun-2022 11:05:13 (Found 4 errors + 2168 warnings) Compiling jalview/test/jalview/datamodel build 09-Jun-2022 11:05:13 (Found 4 errors + 2170 warnings) Compiling jalview/test/jalview/datamodel build 09-Jun-2022 11:05:13 (Found 4 errors + 2179 warnings) Compiling jalview/test/jalview/datamodel build 09-Jun-2022 11:05:13 (Found 4 errors + 2180 warnings) Compiling jalview/test/jalview/datamodel build 09-Jun-2022 11:05:13 (Found 4 errors + 2181 warnings) Compiling jalview/test/jalview/datamodel build 09-Jun-2022 11:05:13 (Found 4 errors + 2182 warnings) Compiling jalview/test/jalview/datamodel build 09-Jun-2022 11:05:13 (Found 4 errors + 2183 warnings) Compiling jalview/test/jalview/datamodel build 09-Jun-2022 11:05:13 (Found 4 errors + 2184 warnings) Compiling jalview/test/jalview/datamodel build 09-Jun-2022 11:05:13 (Found 4 errors + 2188 warnings) Compiling jalview/test/jalview/datamodel build 09-Jun-2022 11:05:13 (Found 4 errors + 2189 warnings) Compiling jalview/test/jalview/datamodel/features build 09-Jun-2022 11:05:13 (Found 4 errors + 2190 warnings) Compiling jalview/test/jalview/datamodel/features build 09-Jun-2022 11:05:13 (Found 4 errors + 2190 warnings) Compiling jalview/test/jalview/ext/android build 09-Jun-2022 11:05:13 (Found 4 errors + 2190 warnings) Compiling jalview/test/jalview/ext/ensembl build 09-Jun-2022 11:05:13 (Found 4 errors + 2190 warnings) Compiling jalview/test/jalview/ext/htsjdk build 09-Jun-2022 11:05:13 (Found 4 errors + 2191 warnings) Compiling jalview/test/jalview/ext/jmol build 09-Jun-2022 11:05:13 (Found 4 errors + 2192 warnings) Compiling jalview/test/jalview/ext/jmol build 09-Jun-2022 11:05:13 (Found 4 errors + 2192 warnings) Compiling jalview/test/jalview/ext/paradise build 09-Jun-2022 11:05:13 (Found 4 errors + 2192 warnings) Compiling jalview/test/jalview/ext/pymol build 09-Jun-2022 11:05:13 (Found 4 errors + 2192 warnings) Compiling jalview/test/jalview/ext/rbvi/chimera build 09-Jun-2022 11:05:13 (Found 4 errors + 2192 warnings) Compiling jalview/test/jalview/ext/so build 09-Jun-2022 11:05:13 (Found 4 errors + 2192 warnings) Compiling jalview/test/jalview/fts/core build 09-Jun-2022 11:05:13 (Found 4 errors + 2193 warnings) Compiling jalview/test/jalview/fts/service/pdb build 09-Jun-2022 11:05:13 (Found 4 errors + 2194 warnings) Compiling jalview/test/jalview/fts/service/pdb build 09-Jun-2022 11:05:13 (Found 4 errors + 2195 warnings) Compiling jalview/test/jalview/fts/threedbeacons build 09-Jun-2022 11:05:13 (Found 4 errors + 2200 warnings) Compiling jalview/test/jalview/fts/threedbeacons build 09-Jun-2022 11:05:13 (Found 4 errors + 2200 warnings) Compiling jalview/test/jalview/gui build 09-Jun-2022 11:05:13 (Found 4 errors + 2202 warnings) Compiling jalview/test/jalview/gui build 09-Jun-2022 11:05:13 (Found 4 errors + 2203 warnings) Compiling jalview/test/jalview/gui build 09-Jun-2022 11:05:13 (Found 4 errors + 2204 warnings) Compiling jalview/test/jalview/gui build 09-Jun-2022 11:05:13 (Found 4 errors + 2207 warnings) Compiling jalview/test/jalview/gui build 09-Jun-2022 11:05:14 (Found 4 errors + 2208 warnings) Compiling jalview/test/jalview/gui build 09-Jun-2022 11:05:14 (Found 4 errors + 2210 warnings) Compiling jalview/test/jalview/gui build 09-Jun-2022 11:05:14 (Found 4 errors + 2211 warnings) Compiling jalview/test/jalview/gui/structurechooser build 09-Jun-2022 11:05:14 (Found 4 errors + 2212 warnings) Compiling jalview/test/jalview/io build 09-Jun-2022 11:05:14 (Found 4 errors + 2213 warnings) Compiling jalview/test/jalview/io build 09-Jun-2022 11:05:14 (Found 4 errors + 2217 warnings) Compiling jalview/test/jalview/io build 09-Jun-2022 11:05:14 (Found 4 errors + 2221 warnings) Compiling jalview/test/jalview/io build 09-Jun-2022 11:05:14 (Found 4 errors + 2223 warnings) Compiling jalview/test/jalview/io build 09-Jun-2022 11:05:14 (Found 4 errors + 2225 warnings) Compiling jalview/test/jalview/io build 09-Jun-2022 11:05:14 (Found 4 errors + 2225 warnings) Compiling jalview/test/jalview/io/cache build 09-Jun-2022 11:05:14 (Found 4 errors + 2225 warnings) Compiling jalview/test/jalview/io/gff build 09-Jun-2022 11:05:14 (Found 4 errors + 2226 warnings) Compiling jalview/test/jalview/io/gff build 09-Jun-2022 11:05:14 (Found 4 errors + 2235 warnings) Compiling jalview/test/jalview/io/vcf build 09-Jun-2022 11:05:14 (Found 4 errors + 2235 warnings) Compiling jalview/test/jalview/math build 09-Jun-2022 11:05:14 (Found 4 errors + 2236 warnings) Compiling jalview/test/jalview/project build 09-Jun-2022 11:05:14 (Found 4 errors + 2236 warnings) Compiling jalview/test/jalview/renderer build 09-Jun-2022 11:05:14 (Found 4 errors + 2237 warnings) Compiling jalview/test/jalview/renderer build 09-Jun-2022 11:05:14 (Found 4 errors + 2237 warnings) Compiling jalview/test/jalview/renderer/seqfeatures build 09-Jun-2022 11:05:14 (Found 4 errors + 2237 warnings) Compiling jalview/test/jalview/schemes build 09-Jun-2022 11:05:14 (Found 4 errors + 2237 warnings) Compiling jalview/test/jalview/structure build 09-Jun-2022 11:05:14 (Found 4 errors + 2239 warnings) Compiling jalview/test/jalview/structure build 09-Jun-2022 11:05:14 (Found 4 errors + 2240 warnings) Compiling jalview/test/jalview/structure build 09-Jun-2022 11:05:14 (Found 4 errors + 2241 warnings) Compiling jalview/test/jalview/structure build 09-Jun-2022 11:05:14 (Found 4 errors + 2244 warnings) Compiling jalview/test/jalview/structure build 09-Jun-2022 11:05:14 (Found 4 errors + 2244 warnings) Compiling jalview/test/jalview/structures/models build 09-Jun-2022 11:05:14 (Found 4 errors + 2245 warnings) Compiling jalview/test/jalview/urls build 09-Jun-2022 11:05:14 (Found 4 errors + 2250 warnings) Compiling jalview/test/jalview/urls build 09-Jun-2022 11:05:14 (Found 4 errors + 2255 warnings) Compiling jalview/test/jalview/urls build 09-Jun-2022 11:05:14 (Found 4 errors + 2255 warnings) Compiling jalview/test/jalview/util build 09-Jun-2022 11:05:14 (Found 4 errors + 2262 warnings) Compiling jalview/test/jalview/util build 09-Jun-2022 11:05:14 (Found 4 errors + 2266 warnings) Compiling jalview/test/jalview/util build 09-Jun-2022 11:05:14 (Found 4 errors + 2267 warnings) Compiling jalview/test/jalview/util build 09-Jun-2022 11:05:14 (Found 4 errors + 2272 warnings) Compiling jalview/test/jalview/util build 09-Jun-2022 11:05:14 (Found 4 errors + 2272 warnings) Compiling jalview/test/jalview/util/dialogrunner build 09-Jun-2022 11:05:14 (Found 4 errors + 2272 warnings) Compiling jalview/test/jalview/util/matcher build 09-Jun-2022 11:05:14 (Found 4 errors + 2275 warnings) Compiling jalview/test/jalview/util/matcher build 09-Jun-2022 11:05:14 (Found 4 errors + 2275 warnings) Compiling jalview/test/jalview/viewmodel build 09-Jun-2022 11:05:14 (Found 4 errors + 2276 warnings) Compiling jalview/test/jalview/viewmodel/styles build 09-Jun-2022 11:05:14 (Found 4 errors + 2276 warnings) Compiling jalview/test/jalview/workers build 09-Jun-2022 11:05:14 (Found 4 errors + 2276 warnings) Compiling jalview/test/jalview/ws build 09-Jun-2022 11:05:14 (Found 4 errors + 2278 warnings) Compiling jalview/test/jalview/ws build 09-Jun-2022 11:05:14 (Found 4 errors + 2278 warnings) Compiling jalview/test/jalview/ws/dbsources build 09-Jun-2022 11:05:14 (Found 4 errors + 2278 warnings) Compiling jalview/test/jalview/ws/ebi build 09-Jun-2022 11:05:14 (Found 4 errors + 2285 warnings) Compiling jalview/test/jalview/ws/gui build 09-Jun-2022 11:05:14 (Found 4 errors + 2285 warnings) Compiling jalview/test/jalview/ws/jabaws build 09-Jun-2022 11:05:14 (Found 4 errors + 2286 warnings) Compiling jalview/test/jalview/ws/jabaws build 09-Jun-2022 11:05:14 (Found 4 errors + 2287 warnings) Compiling jalview/test/jalview/ws/jabaws build 09-Jun-2022 11:05:14 (Found 4 errors + 2291 warnings) Compiling jalview/test/jalview/ws/jabaws build 09-Jun-2022 11:05:14 (Found 4 errors + 2306 warnings) Compiling jalview/test/jalview/ws/jws2 build 09-Jun-2022 11:05:14 (Found 4 errors + 2306 warnings) Compiling jalview/test/jalview/ws/rest build 09-Jun-2022 11:05:14 (Found 4 errors + 2307 warnings) Compiling jalview/test/jalview/ws/rest build 09-Jun-2022 11:05:14 (Found 4 errors + 2307 warnings) Compiling jalview/test/jalview/ws/seqfetcher build 09-Jun-2022 11:05:14 (Found 4 errors + 2308 warnings) Compiling jalview/test/jalview/ws/sifts build 09-Jun-2022 11:05:14 (Found 4 errors + 2310 warnings) Compiling jalview/test/jalview/ws/utils build 09-Jun-2022 11:05:14 (Found 4 errors + 2326 warnings) Compiling jalview/test/junit/extensions build 09-Jun-2022 11:05:14 (Found 4 errors + 2328 warnings) Compiling jalview/test/junit/extensions build 09-Jun-2022 11:05:14 (Found 4 errors + 2328 warnings) Compiling jalview/test/mc_view build 09-Jun-2022 11:05:14 (Found 4 errors + 2329 warnings) Compiling jalview/test/mc_view build 09-Jun-2022 11:05:14 J2S using configuration file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/.j2s build 09-Jun-2022 11:05:14 j2s.config.altfileproperty = org.jalview.jalviewjsj2sfilename build 09-Jun-2022 11:05:14 J2S System.getProperty("org.jalview.jalviewjsj2sfilename") = ./build/jalviewjs/config/j2s build 09-Jun-2022 11:05:14 J2S using configuration file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/./build/jalviewjs/config/j2s build 09-Jun-2022 11:05:14 j2s.compiler.status = enable build 09-Jun-2022 11:05:14 j2s.compiler.java.version = 8 build 09-Jun-2022 11:05:14 J2S compiler version set to 8 build 09-Jun-2022 11:05:14 j2s.break.on.error = false build 09-Jun-2022 11:05:14 j2s.exact.long = true build 09-Jun-2022 11:05:14 j2s.async.thread = false build 09-Jun-2022 11:05:14 j2s.compiler.mode = nodebug build 09-Jun-2022 11:05:14 j2s.site.directory = ./build/jalviewjs/tmp/site_js build 09-Jun-2022 11:05:14 J2S writing to /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/./build/jalviewjs/tmp/site_js/swingjs/j2s build 09-Jun-2022 11:05:14 j2s.log.methods.declared = build 09-Jun-2022 11:05:14 j2s.log.methods.called = build 09-Jun-2022 11:05:14 j2s.excluded.paths = test;testng;util build 09-Jun-2022 11:05:14 j2s.compiler.read.annotations = true build 09-Jun-2022 11:05:14 j2s.compiler.ignored.annotations = CallerSensitive;ConstructorProperties;Deprecated;Override;SafeVarargs;SuppressWarnings;FunctionalInterface;Documented;Inherited;Native;Repeatable;Retention; build 09-Jun-2022 11:05:14 j2s.testing = false build 09-Jun-2022 11:05:14 j2s.compiler.nonqualified.packages = build 09-Jun-2022 11:05:14 j2s.compiler.nonqualified.classes = build 09-Jun-2022 11:05:14 j2s.class.replacements = build 09-Jun-2022 11:05:14 j2s.template.html = utils/jalviewjs/template.html build 09-Jun-2022 11:05:14 J2S using HTML template /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/utils/jalviewjs/template.html build 09-Jun-2022 11:05:14 J2S building JavaScript jalview /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1 Thu Jun 09 11:05:14 BST 2022 build 09-Jun-2022 11:05:14 J2S building JavaScript for 1036 files build 09-Jun-2022 11:05:14 J2S transpiling (1/1036) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/src/com/github/reinert/jjschema/Attributes.java build 09-Jun-2022 11:05:15 j2s copying resources from /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/src/com to /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/./build/jalviewjs/tmp/site_js/swingjs/j2s/com build 09-Jun-2022 11:05:15 J2S transpiling (2/1036) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/src/com/stevesoft/pat/AmpersandRule.java build 09-Jun-2022 11:05:15 J2S transpiling (3/1036) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/src/com/stevesoft/pat/Any.java build 09-Jun-2022 11:05:15 J2S transpiling (4/1036) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/src/com/stevesoft/pat/BackG.java build 09-Jun-2022 11:05:15 J2S transpiling (5/1036) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/src/com/stevesoft/pat/BackMatch.java build 09-Jun-2022 11:05:15 J2S transpiling (6/1036) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/src/com/stevesoft/pat/BackRefRule.java build 09-Jun-2022 11:05:15 J2S transpiling (7/1036) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/src/com/stevesoft/pat/Backup.java build 09-Jun-2022 11:05:15 J2S transpiling (8/1036) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/src/com/stevesoft/pat/BasicStringBufferLike.java build 09-Jun-2022 11:05:15 J2S transpiling (9/1036) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/src/com/stevesoft/pat/Bits.java build 09-Jun-2022 11:05:15 J2S transpiling (10/1036) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/src/com/stevesoft/pat/Boundary.java build 09-Jun-2022 11:05:15 J2S transpiling (11/1036) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/src/com/stevesoft/pat/Bracket.java build 09-Jun-2022 11:05:15 J2S transpiling (12/1036) 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/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/util/SparseCountTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/util/StringUtilsTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/util/UrlLinkTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/util/dialogrunner/DialogRunnerTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/util/matcher/ConditionTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/util/matcher/MatcherTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/viewmodel/OverviewDimensionsHideHiddenTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/viewmodel/ViewportRangesTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/viewmodel/styles/ViewStyleTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/workers/AlignCalcManagerTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/PDBSequenceFetcherTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/SequenceFetcherTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/dbsources/EmblXmlSourceTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/dbsources/PfamFullTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/dbsources/PfamSeedTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/dbsources/RemoteFormatTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/dbsources/RfamFullTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/dbsources/RfamSeedTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/dbsources/UniprotTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/dbsources/XfamFetcherTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/ebi/EBIFetchClientTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/gui/Jws2ParamView.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/jabaws/DisorderAnnotExportImport.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/jabaws/MinJabawsClientTests.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/jabaws/RNAStructExportImport.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/jws2/ParameterUtilsTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/rest/RestClientTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/rest/ShmmrRSBSService.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/seqfetcher/DbRefFetcherTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/sifts/SiftsClientTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/jalview/ws/utils/UrlDownloadClientTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/junit/extensions/PA.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/junit/extensions/PrivilegedAccessor.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/mc_view/AtomTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/mc_view/BondTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/mc_view/PDBChainTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/mc_view/PDBfileTest.java build 09-Jun-2022 11:05:35 J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/test/mc_view/ResidueTest.java build 09-Jun-2022 11:05:35 J2S processed 1036 .java files, created 1066 .js files and 6 .html files, copied 5 resources build 09-Jun-2022 11:05:35 J2S buildFinished 1036 files transpiled for /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1 build 09-Jun-2022 11:05:35 J2S buildFinished nerror = 0 Thu Jun 09 11:05:35 BST 2022 build 09-Jun-2022 11:05:35 (Found 4 errors + 2329 warnings) Build done build 09-Jun-2022 11:05:35 Invoking 'Gradle Project Builder' on '/jalview'. build 09-Jun-2022 11:05:36 :jalviewjsTranspile (Thread[Execution worker for ':',5,main]) completed. Took 1 mins 4.235 secs. build 09-Jun-2022 11:05:36 :jalviewjsCopyTransferSiteJs (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:37 build 09-Jun-2022 11:05:37 > Task :jalviewjsCopyTransferSiteJs build 09-Jun-2022 11:05:37 Caching disabled for task ':jalviewjsCopyTransferSiteJs' because: build 09-Jun-2022 11:05:37 Build cache is disabled build 09-Jun-2022 11:05:37 Task ':jalviewjsCopyTransferSiteJs' is not up-to-date because: build 09-Jun-2022 11:05:37 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site has been removed. build 09-Jun-2022 11:05:37 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/com_stevesoft_pat_RegexWriter.html has been removed. build 09-Jun-2022 11:05:37 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/jalview_bin_Jalview.html has been removed. build 09-Jun-2022 11:05:37 :jalviewjsCopyTransferSiteJs (Thread[Execution worker for ':',5,main]) completed. Took 0.226 secs. build 09-Jun-2022 11:05:37 :jalviewjsTransferUnzipLib (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:37 build 09-Jun-2022 11:05:37 > Task :jalviewjsTransferUnzipLib build 09-Jun-2022 11:05:37 Caching disabled for task ':jalviewjsTransferUnzipLib' because: build 09-Jun-2022 11:05:37 Build cache is disabled build 09-Jun-2022 11:05:37 Task ':jalviewjsTransferUnzipLib' is not up-to-date because: build 09-Jun-2022 11:05:37 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/tmp/site_lib has been removed. build 09-Jun-2022 11:05:37 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/tmp/site_lib/fr_orsay_lri_varna_applications_AlignmentDemo.html has been removed. build 09-Jun-2022 11:05:37 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/tmp/site_lib/fr_orsay_lri_varna_applications_fragseq_FragSeqGUI.html has been removed. build 09-Jun-2022 11:05:37 :jalviewjsTransferUnzipLib (Thread[Execution worker for ':',5,main]) completed. Took 0.514 secs. build 09-Jun-2022 11:05:37 :jalviewjsTransferUnzipSwingJs (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:38 build 09-Jun-2022 11:05:38 > Task :jalviewjsTransferUnzipSwingJs build 09-Jun-2022 11:05:38 Caching disabled for task ':jalviewjsTransferUnzipSwingJs' because: build 09-Jun-2022 11:05:38 Build cache is disabled build 09-Jun-2022 11:05:38 Task ':jalviewjsTransferUnzipSwingJs' is not up-to-date because: build 09-Jun-2022 11:05:38 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/tmp/site_swingjs has been removed. build 09-Jun-2022 11:05:38 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/tmp/site_swingjs/___j2sflags.htm has been removed. build 09-Jun-2022 11:05:38 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/tmp/site_swingjs/debug.log has been removed. build 09-Jun-2022 11:05:38 :jalviewjsTransferUnzipSwingJs (Thread[Execution worker for ':',5,main]) completed. Took 0.949 secs. build 09-Jun-2022 11:05:38 :jalviewjsTransferUnzipAllLibs (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:38 build 09-Jun-2022 11:05:38 > Task :jalviewjsTransferUnzipAllLibs build 09-Jun-2022 11:05:38 Skipping task ':jalviewjsTransferUnzipAllLibs' as it has no actions. build 09-Jun-2022 11:05:38 :jalviewjsTransferUnzipAllLibs (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:05:38 :jalviewjsSyncAllLibs (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:39 build 09-Jun-2022 11:05:39 > Task :jalviewjsSyncAllLibs build 09-Jun-2022 11:05:39 Caching disabled for task ':jalviewjsSyncAllLibs' because: build 09-Jun-2022 11:05:39 Build cache is disabled build 09-Jun-2022 11:05:39 Task ':jalviewjsSyncAllLibs' is not up-to-date because: build 09-Jun-2022 11:05:39 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/swingjs/j2s/org/json/CDL.js has changed. build 09-Jun-2022 11:05:39 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/swingjs/j2s/org/json/Cookie.js has changed. build 09-Jun-2022 11:05:39 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/swingjs/j2s/org/json/CookieList.js has changed. build 09-Jun-2022 11:05:39 :jalviewjsSyncAllLibs (Thread[Execution worker for ':',5,main]) completed. Took 1.358 secs. build 09-Jun-2022 11:05:39 :copyResources (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:39 build 09-Jun-2022 11:05:39 > Task :copyResources build 09-Jun-2022 11:05:39 Caching disabled for task ':copyResources' because: build 09-Jun-2022 11:05:39 Build cache is disabled build 09-Jun-2022 11:05:39 Task ':copyResources' is not up-to-date because: build 09-Jun-2022 11:05:39 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/resources/resources_build has been removed. build 09-Jun-2022 11:05:39 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/resources/resources_build/AmbiguityCodes.dat has been removed. build 09-Jun-2022 11:05:39 Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/resources/resources_build/authors.props has been removed. build 09-Jun-2022 11:05:39 :copyResources (Thread[Execution worker for ':',5,main]) completed. Took 0.055 secs. build 09-Jun-2022 11:05:39 :createBuildProperties (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:39 build 09-Jun-2022 11:05:39 > Task :createBuildProperties build 09-Jun-2022 11:05:39 Caching disabled for task ':createBuildProperties' because: build 09-Jun-2022 11:05:39 Build cache is disabled build 09-Jun-2022 11:05:39 Task ':createBuildProperties' is not up-to-date because: build 09-Jun-2022 11:05:39 Value of input property 'comment' has changed for task ':createBuildProperties' build 09-Jun-2022 11:05:39 Value of input property 'properties' has changed for task ':createBuildProperties' build 09-Jun-2022 11:05:39 :createBuildProperties (Thread[Execution worker for ':',5,main]) completed. Took 0.004 secs. build 09-Jun-2022 11:05:39 :jalviewjsSyncBuildProperties (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:40 build 09-Jun-2022 11:05:40 > Task :jalviewjsSyncBuildProperties build 09-Jun-2022 11:05:40 Caching disabled for task ':jalviewjsSyncBuildProperties' because: build 09-Jun-2022 11:05:40 Build cache is disabled build 09-Jun-2022 11:05:40 Task ':jalviewjsSyncBuildProperties' is not up-to-date because: build 09-Jun-2022 11:05:40 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/swingjs/j2s/.build_properties has been removed. build 09-Jun-2022 11:05:40 :jalviewjsSyncBuildProperties (Thread[Execution worker for ':',5,main]) completed. Took 0.118 secs. build 09-Jun-2022 11:05:40 :jalviewjsBuildAllCores (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:42 build 09-Jun-2022 11:05:42 > Task :jalviewjsBuildAllCores build 09-Jun-2022 11:05:42 Execution optimizations have been disabled for task ':jalviewjsBuildAllCores' to ensure correctness due to the following reasons: build 09-Jun-2022 11:05:42 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/tmp/site_lib/swingjs/j2s'. Reason: Task ':jalviewjsBuildAllCores' uses this output of task ':jalviewjsTransferUnzipLib' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 09-Jun-2022 11:05:42 Invalidating VFS because task ':jalviewjsBuildAllCores' failed validation build 09-Jun-2022 11:05:42 Caching disabled for task ':jalviewjsBuildAllCores' because: build 09-Jun-2022 11:05:42 Build cache is disabled build 09-Jun-2022 11:05:42 Task ':jalviewjsBuildAllCores' is not up-to-date because: build 09-Jun-2022 11:05:42 Incremental execution has been disabled to ensure correctness. Please consult deprecation warnings for more details. build 09-Jun-2022 11:05:42 Creating core for jalview... build 09-Jun-2022 11:05:42 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.js build 09-Jun-2022 11:05:42 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.z.js build 09-Jun-2022 11:05:42 build 09-Jun-2022 11:05:42 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-GJ2B-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/corejalview.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.z.js' build 09-Jun-2022 11:05:42 build 09-Jun-2022 11:05:42 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-GJ2B-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-GJ2B-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/corejalview.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.z.js build 09-Jun-2022 11:05:42 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' build 09-Jun-2022 11:05:49 -- build 09-Jun-2022 11:05:49 Creating core for jvexamplefile... build 09-Jun-2022 11:05:49 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvexamplefile.js build 09-Jun-2022 11:05:49 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvexamplefile.z.js build 09-Jun-2022 11:05:49 build 09-Jun-2022 11:05:49 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-GJ2B-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/corejvexamplefile.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvexamplefile.z.js' build 09-Jun-2022 11:05:49 build 09-Jun-2022 11:05:49 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-GJ2B-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-GJ2B-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/corejvexamplefile.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvexamplefile.z.js build 09-Jun-2022 11:05:49 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' build 09-Jun-2022 11:05:51 -- build 09-Jun-2022 11:05:51 Creating core for _jalview... build 09-Jun-2022 11:05:51 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.js build 09-Jun-2022 11:05:51 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_jalview.z.js build 09-Jun-2022 11:05:51 build 09-Jun-2022 11:05:51 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-GJ2B-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 09-Jun-2022 11:05:51 build 09-Jun-2022 11:05:51 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-GJ2B-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-GJ2B-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 09-Jun-2022 11:05:51 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' build 09-Jun-2022 11:05:52 -- build 09-Jun-2022 11:05:52 Creating core for _stevesoft... build 09-Jun-2022 11:05:52 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.js build 09-Jun-2022 11:05:52 Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/core_stevesoft.z.js build 09-Jun-2022 11:05:52 build 09-Jun-2022 11:05:52 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-GJ2B-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 09-Jun-2022 11:05:52 build 09-Jun-2022 11:05:52 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-GJ2B-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-GJ2B-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 09-Jun-2022 11:05:52 Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' build 09-Jun-2022 11:05:55 -- build 09-Jun-2022 11:05:55 :jalviewjsBuildAllCores (Thread[Execution worker for ':',5,main]) completed. Took 15.687 secs. build 09-Jun-2022 11:05:55 :jalviewjsPublishCoreTemplates (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:55 build 09-Jun-2022 11:05:55 > Task :jalviewjsPublishCoreTemplates build 09-Jun-2022 11:05:55 Caching disabled for task ':jalviewjsPublishCoreTemplates' because: build 09-Jun-2022 11:05:55 Build cache is disabled build 09-Jun-2022 11:05:55 Task ':jalviewjsPublishCoreTemplates' is not up-to-date because: build 09-Jun-2022 11:05:55 Output property '$1$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/tmp/site_core/JalviewJS_jalview.html has been removed. build 09-Jun-2022 11:05:55 Output property '$1$2' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/tmp/site_core/JalviewJS_jvexamplefile.html has been removed. build 09-Jun-2022 11:05:55 Output property '$1$3' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/tmp/site_core/JalviewJS__jalview.html has been removed. build 09-Jun-2022 11:05:55 :jalviewjsPublishCoreTemplates (Thread[Execution worker for ':',5,main]) completed. Took 0.014 secs. build 09-Jun-2022 11:05:55 :jalviewjsSyncCore (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:55 build 09-Jun-2022 11:05:55 > Task :jalviewjsSyncCore build 09-Jun-2022 11:05:55 Caching disabled for task ':jalviewjsSyncCore' because: build 09-Jun-2022 11:05:55 Build cache is disabled build 09-Jun-2022 11:05:55 Task ':jalviewjsSyncCore' is not up-to-date because: build 09-Jun-2022 11:05:55 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/JalviewJS__jalview.html has been removed. build 09-Jun-2022 11:05:55 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/JalviewJS__stevesoft.html has been removed. build 09-Jun-2022 11:05:55 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/JalviewJS_jalview.html has been removed. build 09-Jun-2022 11:05:55 :jalviewjsSyncCore (Thread[Execution worker for ':',5,main]) completed. Took 0.177 secs. build 09-Jun-2022 11:05:55 :copyChannelResources (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:55 build 09-Jun-2022 11:05:55 > Task :copyChannelResources build 09-Jun-2022 11:05:55 Execution optimizations have been disabled for task ':copyChannelResources' to ensure correctness due to the following reasons: build 09-Jun-2022 11:05:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 09-Jun-2022 11:05:55 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/resources/resources_build'. Reason: Task ':jalviewjsSyncBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 09-Jun-2022 11:05:55 Invalidating VFS because task ':copyChannelResources' failed validation build 09-Jun-2022 11:05:55 Caching disabled for task ':copyChannelResources' because: build 09-Jun-2022 11:05:55 Build cache is disabled build 09-Jun-2022 11:05:55 Task ':copyChannelResources' is not up-to-date because: build 09-Jun-2022 11:05:55 Incremental execution has been disabled to ensure correctness. Please consult deprecation warnings for more details. build 09-Jun-2022 11:05:55 :copyChannelResources (Thread[Execution worker for ':',5,main]) completed. Took 0.015 secs. build 09-Jun-2022 11:05:55 :buildResources (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:55 build 09-Jun-2022 11:05:55 > Task :buildResources build 09-Jun-2022 11:05:55 Skipping task ':buildResources' as it has no actions. build 09-Jun-2022 11:05:55 :buildResources (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:05:55 :jalviewjsSyncResources (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:56 build 09-Jun-2022 11:05:56 > Task :jalviewjsSyncResources build 09-Jun-2022 11:05:56 Caching disabled for task ':jalviewjsSyncResources' because: build 09-Jun-2022 11:05:56 Build cache is disabled build 09-Jun-2022 11:05:56 Task ':jalviewjsSyncResources' is not up-to-date because: build 09-Jun-2022 11:05:56 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/swingjs/j2s/.build_properties has changed. build 09-Jun-2022 11:05:56 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/swingjs/j2s/AmbiguityCodes.dat has been removed. build 09-Jun-2022 11:05:56 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/swingjs/j2s/authors.props has been removed. build 09-Jun-2022 11:05:56 :jalviewjsSyncResources (Thread[Execution worker for ':',5,main]) completed. Took 0.163 secs. build 09-Jun-2022 11:05:56 :jalviewjsSyncSiteResources (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:56 build 09-Jun-2022 11:05:56 > Task :jalviewjsSyncSiteResources build 09-Jun-2022 11:05:56 Caching disabled for task ':jalviewjsSyncSiteResources' because: build 09-Jun-2022 11:05:56 Build cache is disabled build 09-Jun-2022 11:05:56 Task ':jalviewjsSyncSiteResources' is not up-to-date because: build 09-Jun-2022 11:05:56 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/jalview_bin_JalviewJS2.html has changed. build 09-Jun-2022 11:05:56 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/applets-nocore.html has been removed. build 09-Jun-2022 11:05:56 Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/jalviewjs/site/applets.html has been removed. build 09-Jun-2022 11:05:56 :jalviewjsSyncSiteResources (Thread[Execution worker for ':',5,main]) completed. Took 0.214 secs. build 09-Jun-2022 11:05:56 :jalviewjsPrepareSite (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:56 build 09-Jun-2022 11:05:56 > Task :jalviewjsPrepareSite build 09-Jun-2022 11:05:56 Skipping task ':jalviewjsPrepareSite' as it has no actions. build 09-Jun-2022 11:05:56 :jalviewjsPrepareSite (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:05:56 :jalviewjsBuildSite (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:56 build 09-Jun-2022 11:05:56 > Task :jalviewjsBuildSite build 09-Jun-2022 11:05:56 Skipping task ':jalviewjsBuildSite' as it has no actions. build 09-Jun-2022 11:05:56 :jalviewjsBuildSite (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:05:56 :jalviewjs (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:56 build 09-Jun-2022 11:05:56 > Task :jalviewjs build 09-Jun-2022 11:05:56 Skipping task ':jalviewjs' as it has no actions. build 09-Jun-2022 11:05:56 :jalviewjs (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:05:56 :jalviewjsSiteTar (Thread[included builds,5,main]) started. build 09-Jun-2022 11:05:58 build 09-Jun-2022 11:05:58 > Task :jalviewjsSiteTar build 09-Jun-2022 11:05:58 Caching disabled for task ':jalviewjsSiteTar' because: build 09-Jun-2022 11:05:58 Build cache is disabled build 09-Jun-2022 11:05:58 Task ':jalviewjsSiteTar' is not up-to-date because: build 09-Jun-2022 11:05:58 Output property 'archiveFile' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GJ2B-JOB1/build/distributions/jalviewjs-site-TEST.tar.gz has been removed. build 09-Jun-2022 11:05:58 :jalviewjsSiteTar (Thread[included builds,5,main]) completed. Took 2.679 secs. build 09-Jun-2022 11:05:58 producer locations for task group 1 (Thread[Execution worker for ':',5,main]) started. build 09-Jun-2022 11:05:58 producer locations for task group 2 (Thread[Execution worker for ':' Thread 3,5,main]) started. build 09-Jun-2022 11:05:58 producer locations for task group 2 (Thread[Execution worker for ':' Thread 3,5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:05:58 producer locations for task group 3 (Thread[Execution worker for ':' Thread 2,5,main]) started. build 09-Jun-2022 11:05:58 producer locations for task group 3 (Thread[Execution worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:05:58 producer locations for task group 4 (Thread[included builds,5,main]) started. build 09-Jun-2022 11:05:58 producer locations for task group 4 (Thread[included builds,5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:05:58 producer locations for task group 1 (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. build 09-Jun-2022 11:05:58 build 09-Jun-2022 11:05:58 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 09-Jun-2022 11:05:58 build 09-Jun-2022 11:05:58 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 09-Jun-2022 11:05:58 build 09-Jun-2022 11:05:58 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 09-Jun-2022 11:05:58 build 09-Jun-2022 11:05:58 Execution optimizations have been disabled for 2 invalid unit(s) of work during this build to ensure correctness. build 09-Jun-2022 11:05:58 Please consult deprecation warnings for more details. build 09-Jun-2022 11:05:58 build 09-Jun-2022 11:05:58 BUILD SUCCESSFUL in 2m 9s build 09-Jun-2022 11:05:58 25 actionable tasks: 24 executed, 1 up-to-date simple 09-Jun-2022 11:05:59 Finished task 'JalviewJS build site and distributable tar' with result: Success simple 09-Jun-2022 11:05:59 Running post build plugin 'NCover Results Collector' simple 09-Jun-2022 11:05:59 Running post build plugin 'Artifact Copier' simple 09-Jun-2022 11:05:59 Publishing an artifact: JalviewJS site tar file simple 09-Jun-2022 11:05:59 Finished publishing of artifact Shared artifact: [JalviewJS site tar file], pattern: [jalviewjs-site-*.tar.gz] anchored at: [build/distributions/] in 24.25 ms simple 09-Jun-2022 11:05:59 Publishing an artifact: JalviewJS site simple 09-Jun-2022 11:06:00 Finished publishing of artifact Shared artifact: [JalviewJS site], pattern: [**/*] anchored at: [build/jalviewjs/site] in 1.050 s simple 09-Jun-2022 11:06:00 Running post build plugin 'Artifactory Release Management Staging' simple 09-Jun-2022 11:06:00 Running post build plugin 'Artifactory Build Info Copier' simple 09-Jun-2022 11:06:00 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 09-Jun-2022 11:06:00 Running post build plugin 'npm Cache Cleanup' simple 09-Jun-2022 11:06:00 Running post build plugin 'Clover Results Collector' simple 09-Jun-2022 11:06:00 Running post build plugin 'Docker Container Cleanup' simple 09-Jun-2022 11:06:00 Finalising the build... simple 09-Jun-2022 11:06:00 Stopping timer. simple 09-Jun-2022 11:06:00 Build JB-GJ2B-JOB1-5 completed. simple 09-Jun-2022 11:06:00 Running on server: post build plugin 'NCover Results Collector' simple 09-Jun-2022 11:06:00 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 09-Jun-2022 11:06:00 Running on server: post build plugin 'Clover Delta Calculator' simple 09-Jun-2022 11:06:00 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 09-Jun-2022 11:06:00 All post build plugins have finished simple 09-Jun-2022 11:06:00 Generating build results summary... simple 09-Jun-2022 11:06:00 Saving build results to disk... simple 09-Jun-2022 11:06:00 Logging substituted variables... simple 09-Jun-2022 11:06:00 Indexing build results... simple 09-Jun-2022 11:06:00 Finished building JB-GJ2B-JOB1-5.