simple	07-Nov-2024 17:01:00	Build Jalview Builds - Gradle Develop Build - features-JAL-4489_clustering_and_pca_pasimap_views - Clover and Tests #1 (JB-GDB641-JOB1-1) started building on agent Default Agent
simple	07-Nov-2024 17:01:00	
simple	07-Nov-2024 17:01:00	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1
simple	07-Nov-2024 17:01:00	Executing build Jalview Builds - Gradle Develop Build - features-JAL-4489_clustering_and_pca_pasimap_views - Clover and Tests #1 (JB-GDB641-JOB1-1)
simple	07-Nov-2024 17:01:00	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	07-Nov-2024 17:01:00	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1
simple	07-Nov-2024 17:01:00	Updating source code to revision: 30bbab8b2e223cc7a28c69556092d405c8dc48f7
simple	07-Nov-2024 17:01:00	Fetching 'refs/heads/features/JAL-4489_clustering_and_pca_pasimap_views' from 'http://source.jalview.org/git/jalview.git'.
simple	07-Nov-2024 17:01:01	Checking out revision 30bbab8b2e223cc7a28c69556092d405c8dc48f7.
simple	07-Nov-2024 17:01:01	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1/.git'.
simple	07-Nov-2024 17:01:01	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1'...
simple	07-Nov-2024 17:01:01	done.
simple	07-Nov-2024 17:01:13	Switched to a new branch 'features/JAL-4489_clustering_and_pca_pasimap_views'
simple	07-Nov-2024 17:01:13	Branch features/JAL-4489_clustering_and_pca_pasimap_views set up to track remote branch features/JAL-4489_clustering_and_pca_pasimap_views from origin.
simple	07-Nov-2024 17:01:13	Updated source code to revision: 30bbab8b2e223cc7a28c69556092d405c8dc48f7
simple	07-Nov-2024 17:01:13	Finished task 'Checkout Default Repository' with result: Success
simple	07-Nov-2024 17:01:13	Running pre-build action: VCS Version Collector
simple	07-Nov-2024 17:01:13	Running pre-build action: Artifactory Release Staging
simple	07-Nov-2024 17:01:13	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	07-Nov-2024 17:01:13	Bamboo Artifactory Plugin version: 2.6.2
command	07-Nov-2024 17:01:13	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - features-JAL-4489_clustering_and_pca_pasimap_views - Clover and Tests #1 (JB-GDB641-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_repository_revision_number=30bbab8b2e223cc7a28c69556092d405c8dc48f7\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB641-JOB1-1\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-GDB641-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB641-JOB1\nbamboo_shortPlanName=features-JAL-4489_clustering_and_pca_pasimap_views\nbamboo_repository_46498179_git_branch=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB641-JOB1-1\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - features-JAL-4489_clustering_and_pca_pasimap_views\nbamboo_shortPlanKey=GDB641\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=30bbab8b2e223cc7a28c69556092d405c8dc48f7\nbamboo_buildTimeStamp=2024-11-07T17:01:00.737Z\nbamboo_repository_git_branch=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_buildResultKey=JB-GDB641-JOB1-1\nbamboo_repository_branch_name=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - features-JAL-4489_clustering_and_pca_pasimap_views - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=30bbab8b2e223cc7a28c69556092d405c8dc48f7\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_repository_46498179_git_username=\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=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46498179_name=Jalview Git\nbamboo_planRepository_branchDisplayName=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_repository_46498179_revision_number=30bbab8b2e223cc7a28c69556092d405c8dc48f7\nbamboo_repository_46498179_branch_name=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=features/JAL-4489_clustering_and_pca_pasimap_views\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_repository_46498179_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_plan_storageTag=plan-46301957\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-GDB641-JOB1\nbamboo_planKey=JB-GDB641\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=features/JAL-4489_clustering_and_pca_pasimap_views\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	07-Nov-2024 17:01:13	444
build	07-Nov-2024 17:01:13	Starting a Gradle Daemon (subsequent builds will be faster)
build	07-Nov-2024 17:01:22	
build	07-Nov-2024 17:01:22	> Configure project :
build	07-Nov-2024 17:01:22	Using properties from file './utils/channels/default/channel_gradle.properties'
build	07-Nov-2024 17:01:22	JALVIEW_VERSION is set to '2.11.4.1'
build	07-Nov-2024 17:01:22	HEADLESS BUILD
build	07-Nov-2024 17:01:22	J2S ENABLED
build	07-Nov-2024 17:01:23	Using a LOCAL profile.
build	07-Nov-2024 17:01:24	eclipseDir exists
build	07-Nov-2024 17:01:24	
build	07-Nov-2024 17:01:24	> Task :clean
build	07-Nov-2024 17:01:24	> Task :cleanClover
build	07-Nov-2024 17:01:24	> Task :cleanTest UP-TO-DATE
build	07-Nov-2024 17:01:27	
build	07-Nov-2024 17:01:27	> Task :cloverInstrJava
build	07-Nov-2024 17:01:27	Clover: About to instrument 1106 files
build	07-Nov-2024 17:01:27	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	07-Nov-2024 17:01:27	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1/build/clover/clover.db'.
build	07-Nov-2024 17:01:27	Processing files at 1.9 source level.
error	07-Nov-2024 17:01:31	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	07-Nov-2024 17:01:31	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	07-Nov-2024 17:01:31	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	07-Nov-2024 17:01:31	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	07-Nov-2024 17:01:31	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	07-Nov-2024 17:01:31	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
error	07-Nov-2024 17:01:31	WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body?
build	07-Nov-2024 17:01:38	Clover all over. Instrumented 1106 files (112 packages).
build	07-Nov-2024 17:01:40	
build	07-Nov-2024 17:01:40	> Task :cloverInstrTests
build	07-Nov-2024 17:01:40	Clover: About to instrument test files
build	07-Nov-2024 17:01:40	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	07-Nov-2024 17:01:40	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1/build/clover/clover.db'.
build	07-Nov-2024 17:01:40	Processing files at 1.9 source level.
build	07-Nov-2024 17:01:43	Clover all over. Instrumented 291 files (52 packages).
build	07-Nov-2024 17:01:43	1594 test methods detected.
build	07-Nov-2024 17:01:43	
build	07-Nov-2024 17:01:43	> Task :cloverInstr
build	07-Nov-2024 17:01:47	
build	07-Nov-2024 17:01:47	> Task :compileCloverJava
build	07-Nov-2024 17:01:47	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	07-Nov-2024 17:01:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrJava' uses this output of task ':compileCloverJava' 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	07-Nov-2024 17:01:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrTests' uses this output of task ':compileCloverJava' 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	07-Nov-2024 17:01:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1/build/clover/clover-instr'. Reason: Task ':compileCloverJava' uses this output of task ':cloverInstrJava' 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	07-Nov-2024 17:01:47	Setting target compatibility to 11
error	07-Nov-2024 17:02:08	/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1/build/clover/clover-instr/jalview/project/Jalview2XML.java:6772: error: cannot find symbol
error	07-Nov-2024 17:02:08	        __CLR4_4_12n9u2n9um37k1sbw.R.inc(127064);panel.getPasimapModel().setPaSiMap(pasimap);
error	07-Nov-2024 17:02:08	                                                                        ^
error	07-Nov-2024 17:02:08	  symbol:   method setPaSiMap(PaSiMap)
error	07-Nov-2024 17:02:08	  location: class PaSiMapModel
error	07-Nov-2024 17:02:10	Note: Some input files use or override a deprecated API.
error	07-Nov-2024 17:02:10	Note: Recompile with -Xlint:deprecation for details.
error	07-Nov-2024 17:02:10	Note: Some input files use unchecked or unsafe operations.
error	07-Nov-2024 17:02:10	Note: Recompile with -Xlint:unchecked for details.
error	07-Nov-2024 17:02:10	1 error
build	07-Nov-2024 17:02:10	
build	07-Nov-2024 17:02:10	> Task :compileCloverJava FAILED
build	07-Nov-2024 17:02:10	
build	07-Nov-2024 17:02:10	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	07-Nov-2024 17:02:10	
build	07-Nov-2024 17:02:10	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	07-Nov-2024 17:02:10	
build	07-Nov-2024 17:02:10	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	07-Nov-2024 17:02:10	
build	07-Nov-2024 17:02:10	Execution optimizations have been disabled for 1 invalid unit(s) of work during this build to ensure correctness.
build	07-Nov-2024 17:02:10	Please consult deprecation warnings for more details.
build	07-Nov-2024 17:02:10	6 actionable tasks: 5 executed, 1 up-to-date
error	07-Nov-2024 17:02:10	
error	07-Nov-2024 17:02:10	FAILURE: Build failed with an exception.
error	07-Nov-2024 17:02:10	
error	07-Nov-2024 17:02:10	* What went wrong:
error	07-Nov-2024 17:02:10	Execution failed for task ':compileCloverJava'.
error	07-Nov-2024 17:02:10	> Compilation failed; see the compiler error output for details.
error	07-Nov-2024 17:02:10	
error	07-Nov-2024 17:02:10	* Try:
error	07-Nov-2024 17:02:10	> Run with --stacktrace option to get the stack trace.
error	07-Nov-2024 17:02:10	> Run with --info or --debug option to get more log output.
error	07-Nov-2024 17:02:10	> Run with --scan to get full insights.
error	07-Nov-2024 17:02:10	
error	07-Nov-2024 17:02:10	* Get more help at https://help.gradle.org
error	07-Nov-2024 17:02:10	
error	07-Nov-2024 17:02:10	BUILD FAILED in 57s
simple	07-Nov-2024 17:02:11	
simple	07-Nov-2024 17:02:11	Failing task since return code of [/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test] was 1 while expected 0
simple	07-Nov-2024 17:02:11	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	07-Nov-2024 17:02:11	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	07-Nov-2024 17:02:11	Bamboo Artifactory Plugin version: 2.6.2
command	07-Nov-2024 17:02:11	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - features-JAL-4489_clustering_and_pca_pasimap_views - Clover and Tests #1 (JB-GDB641-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_repository_revision_number=30bbab8b2e223cc7a28c69556092d405c8dc48f7\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB641-JOB1-1\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-GDB641-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDB641-JOB1\nbamboo_shortPlanName=features-JAL-4489_clustering_and_pca_pasimap_views\nbamboo_repository_46498179_git_branch=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=1\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB641-JOB1-1\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - features-JAL-4489_clustering_and_pca_pasimap_views\nbamboo_shortPlanKey=GDB641\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=30bbab8b2e223cc7a28c69556092d405c8dc48f7\nbamboo_buildTimeStamp=2024-11-07T17:01:00.737Z\nbamboo_repository_git_branch=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_buildResultKey=JB-GDB641-JOB1-1\nbamboo_repository_branch_name=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - features-JAL-4489_clustering_and_pca_pasimap_views - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=30bbab8b2e223cc7a28c69556092d405c8dc48f7\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nbamboo_repository_46498179_git_username=\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=true\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46498179_name=Jalview Git\nbamboo_planRepository_branchDisplayName=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_repository_46498179_revision_number=30bbab8b2e223cc7a28c69556092d405c8dc48f7\nbamboo_repository_46498179_branch_name=features/JAL-4489_clustering_and_pca_pasimap_views\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=features/JAL-4489_clustering_and_pca_pasimap_views\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_repository_46498179_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_plan_storageTag=plan-46301957\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-GDB641-JOB1\nbamboo_planKey=JB-GDB641\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=features/JAL-4489_clustering_and_pca_pasimap_views\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	07-Nov-2024 17:02:11	444
build	07-Nov-2024 17:02:16	
build	07-Nov-2024 17:02:16	> Configure project :
build	07-Nov-2024 17:02:16	Using properties from file './utils/channels/default/channel_gradle.properties'
build	07-Nov-2024 17:02:16	JALVIEW_VERSION is set to '2.11.4.1'
build	07-Nov-2024 17:02:16	HEADLESS BUILD
build	07-Nov-2024 17:02:16	J2S ENABLED
build	07-Nov-2024 17:02:16	Using a LOCAL profile.
build	07-Nov-2024 17:02:17	eclipseDir exists
build	07-Nov-2024 17:02:19	
build	07-Nov-2024 17:02:19	> Task :cloverHtmlReport
build	07-Nov-2024 17:02:19	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	07-Nov-2024 17:02:19	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1/build/reports/clover'
build	07-Nov-2024 17:02:30	Done. Processed 116 packages in 11483ms (98ms per package).
build	07-Nov-2024 17:02:34	
build	07-Nov-2024 17:02:34	> Task :cloverXmlReport
build	07-Nov-2024 17:02:34	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	07-Nov-2024 17:02:34	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1/build/reports/clover/clover.xml'
build	07-Nov-2024 17:02:34	
build	07-Nov-2024 17:02:34	> Task :cloverReport
build	07-Nov-2024 17:02:34	
build	07-Nov-2024 17:02:34	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	07-Nov-2024 17:02:34	
build	07-Nov-2024 17:02:34	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	07-Nov-2024 17:02:34	
build	07-Nov-2024 17:02:34	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	07-Nov-2024 17:02:34	
build	07-Nov-2024 17:02:34	BUILD SUCCESSFUL in 23s
build	07-Nov-2024 17:02:34	2 actionable tasks: 2 executed
simple	07-Nov-2024 17:02:34	Finished task 'Clover Report' with result: Success
simple	07-Nov-2024 17:02:34	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	07-Nov-2024 17:02:34	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1...
simple	07-Nov-2024 17:02:34	Failing task since test cases were expected but none were found.
simple	07-Nov-2024 17:02:34	Finished task 'TestNG Parser' with result: Failed
simple	07-Nov-2024 17:02:34	Running post build plugin 'NCover Results Collector'
simple	07-Nov-2024 17:02:34	Running post build plugin 'Artifact Copier'
simple	07-Nov-2024 17:02:34	Publishing an artifact: Clover Report (System)
simple	07-Nov-2024 17:02:35	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.020 s
simple	07-Nov-2024 17:02:35	Publishing an artifact: TestNG report
error	07-Nov-2024 17:02:35	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB641-JOB1/build/reports/tests/test does not exist.
simple	07-Nov-2024 17:02:35	The artifact hasn't been successfully published after 1.373 ms
simple	07-Nov-2024 17:02:35	Running post build plugin 'Artifactory Release Management Staging'
simple	07-Nov-2024 17:02:35	Running post build plugin 'Artifactory Build Info Copier'
simple	07-Nov-2024 17:02:35	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	07-Nov-2024 17:02:35	Running post build plugin 'npm Cache Cleanup'
simple	07-Nov-2024 17:02:35	Running post build plugin 'Clover Results Collector'
simple	07-Nov-2024 17:02:35	Running post build plugin 'Docker Container Cleanup'
simple	07-Nov-2024 17:02:35	Finalising the build...
simple	07-Nov-2024 17:02:35	Stopping timer.
simple	07-Nov-2024 17:02:35	Build JB-GDB641-JOB1-1 completed.
simple	07-Nov-2024 17:02:35	Running on server: post build plugin 'NCover Results Collector'
simple	07-Nov-2024 17:02:35	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	07-Nov-2024 17:02:35	Running on server: post build plugin 'Clover Delta Calculator'
simple	07-Nov-2024 17:02:35	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	07-Nov-2024 17:02:35	All post build plugins have finished
simple	07-Nov-2024 17:02:35	Generating build results summary...
simple	07-Nov-2024 17:02:35	Saving build results to disk...
simple	07-Nov-2024 17:02:35	Logging substituted variables...
simple	07-Nov-2024 17:02:35	Indexing build results...
simple	07-Nov-2024 17:02:35	Finished building JB-GDB641-JOB1-1.