simple	04-Dec-2025 16:11:07	Build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #1 (JB-GDB734-JOB1-1) started building on agent Default Agent
simple	04-Dec-2025 16:11:07	
simple	04-Dec-2025 16:11:07	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1
simple	04-Dec-2025 16:11:07	Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #1 (JB-GDB734-JOB1-1)
simple	04-Dec-2025 16:11:07	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	04-Dec-2025 16:11:07	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1
simple	04-Dec-2025 16:11:07	Updating source code to revision: e0875267ed4b699db969bf10b30bafe83a1cbd7d
simple	04-Dec-2025 16:11:07	Fetching 'refs/heads/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	04-Dec-2025 16:11:09	Checking out revision e0875267ed4b699db969bf10b30bafe83a1cbd7d.
simple	04-Dec-2025 16:11:09	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/.git'.
simple	04-Dec-2025 16:11:09	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1'...
simple	04-Dec-2025 16:11:09	done.
simple	04-Dec-2025 16:11:16	Switched to a new branch 'bug/JAL-4107_jalviewjs_fixes_on_2_12_branch'
simple	04-Dec-2025 16:11:16	Branch bug/JAL-4107_jalviewjs_fixes_on_2_12_branch set up to track remote branch bug/JAL-4107_jalviewjs_fixes_on_2_12_branch from origin.
simple	04-Dec-2025 16:11:16	Updated source code to revision: e0875267ed4b699db969bf10b30bafe83a1cbd7d
simple	04-Dec-2025 16:11:16	Finished task 'Checkout Default Repository' with result: Success
simple	04-Dec-2025 16:11:16	Running pre-build action: VCS Version Collector
simple	04-Dec-2025 16:11:16	Running pre-build action: Artifactory Release Staging
simple	04-Dec-2025 16:11:16	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	04-Dec-2025 16:11:16	Bamboo Artifactory Plugin version: 2.6.2
command	04-Dec-2025 16:11:16	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #1 (JB-GDB734-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-GDB734-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_revision_number=e0875267ed4b699db969bf10b30bafe83a1cbd7d\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-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-GDB734-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB734-JOB1\nbamboo_repository_46498616_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498616_revision_number=e0875267ed4b699db969bf10b30bafe83a1cbd7d\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_name=Jalview Gitlab\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-GDB734-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_shortPlanKey=GDB734\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=e0875267ed4b699db969bf10b30bafe83a1cbd7d\nbamboo_buildTimeStamp=2025-12-04T16:11:07.685Z\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GDB734-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=e0875267ed4b699db969bf10b30bafe83a1cbd7d\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_46498616_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\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=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302801\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=https://gitlab.jalview.org/jalview/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-GDB734-JOB1\nbamboo_planKey=JB-GDB734\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498616_git_username=\nbamboo_repository_46498616_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_46498616_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	04-Dec-2025 16:11:16	444
build	04-Dec-2025 16:11:19	
build	04-Dec-2025 16:11:19	> Configure project :
build	04-Dec-2025 16:11:19	Using properties from file './utils/channels/default/channel_gradle.properties'
build	04-Dec-2025 16:11:19	JALVIEW_VERSION is set to '2.12.0'
build	04-Dec-2025 16:11:19	HEADLESS BUILD
build	04-Dec-2025 16:11:19	J2S ENABLED
build	04-Dec-2025 16:11:19	Using a LOCAL profile.
build	04-Dec-2025 16:11:19	eclipseDir exists
build	04-Dec-2025 16:11:19	
build	04-Dec-2025 16:11:19	> Task :clean
build	04-Dec-2025 16:11:19	> Task :cleanClover
build	04-Dec-2025 16:11:19	> Task :cleanTest UP-TO-DATE
build	04-Dec-2025 16:11:22	
build	04-Dec-2025 16:11:22	> Task :cloverInstrJava
build	04-Dec-2025 16:11:22	Clover: About to instrument 1253 files
build	04-Dec-2025 16:11:22	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	04-Dec-2025 16:11:22	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'.
build	04-Dec-2025 16:11:22	Processing files at 1.9 source level.
error	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:26	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	04-Dec-2025 16:11:27	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	04-Dec-2025 16:11:27	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	04-Dec-2025 16:11:27	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	04-Dec-2025 16:11:27	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	04-Dec-2025 16:11:27	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	04-Dec-2025 16:11:27	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	04-Dec-2025 16:11:27	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	04-Dec-2025 16:11:28	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	04-Dec-2025 16:11:28	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	04-Dec-2025 16:11:28	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	04-Dec-2025 16:11:28	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	04-Dec-2025 16:11:28	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	04-Dec-2025 16:11:28	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	04-Dec-2025 16:11:28	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	04-Dec-2025 16:11:28	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	04-Dec-2025 16:11:28	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	04-Dec-2025 16:11:28	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	04-Dec-2025 16:11:28	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	04-Dec-2025 16:11:28	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	04-Dec-2025 16:11:34	Clover all over. Instrumented 1253 files (133 packages).
build	04-Dec-2025 16:11:36	
build	04-Dec-2025 16:11:36	> Task :cloverInstrTests
build	04-Dec-2025 16:11:36	Clover: About to instrument test files
build	04-Dec-2025 16:11:36	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	04-Dec-2025 16:11:36	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'.
build	04-Dec-2025 16:11:36	Processing files at 1.9 source level.
build	04-Dec-2025 16:11:40	Clover all over. Instrumented 315 files (58 packages).
build	04-Dec-2025 16:11:40	1770 test methods detected.
build	04-Dec-2025 16:11:40	
build	04-Dec-2025 16:11:40	> Task :cloverInstr
build	04-Dec-2025 16:11:44	
build	04-Dec-2025 16:11:44	> Task :compileCloverJava
build	04-Dec-2025 16:11:44	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	04-Dec-2025 16:11:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	04-Dec-2025 16:11:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	04-Dec-2025 16:11:44	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	04-Dec-2025 16:11:44	Setting target compatibility to 11
error	04-Dec-2025 16:12:04	Note: Some input files use or override a deprecated API.
error	04-Dec-2025 16:12:04	Note: Recompile with -Xlint:deprecation for details.
error	04-Dec-2025 16:12:04	Note: Some input files use unchecked or unsafe operations.
error	04-Dec-2025 16:12:04	Note: Recompile with -Xlint:unchecked for details.
build	04-Dec-2025 16:12:11	
build	04-Dec-2025 16:12:11	> Task :processCloverResources NO-SOURCE
build	04-Dec-2025 16:12:11	> Task :cloverClasses
build	04-Dec-2025 16:12:11	> Task :copyHelp
build	04-Dec-2025 16:12:12	> Task :buildIndices
build	04-Dec-2025 16:12:12	> Task :copyResources
build	04-Dec-2025 16:12:12	> Task :copyChannelResources
build	04-Dec-2025 16:12:12	
build	04-Dec-2025 16:12:12	> Task :createBuildProperties
build	04-Dec-2025 16:12:12	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	04-Dec-2025 16:12:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-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	04-Dec-2025 16:12:12	
build	04-Dec-2025 16:12:12	> Task :buildResources
build	04-Dec-2025 16:12:13	> Task :copyDocs
build	04-Dec-2025 16:12:13	
build	04-Dec-2025 16:12:13	> Task :convertMdFiles
build	04-Dec-2025 16:12:13	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	04-Dec-2025 16:12:13	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	04-Dec-2025 16:12:13	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	04-Dec-2025 16:12:13	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
build	04-Dec-2025 16:12:13	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/building.html
build	04-Dec-2025 16:12:13	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/addingWebClient.html
build	04-Dec-2025 16:12:13	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	04-Dec-2025 16:12:13	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
build	04-Dec-2025 16:12:13	
build	04-Dec-2025 16:12:13	> Task :releasesTemplates
build	04-Dec-2025 16:12:13	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	04-Dec-2025 16:12:13	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' 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	04-Dec-2025 16:12:13	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' 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	04-Dec-2025 16:12:13	Stripping rc/test/etc for TEST
build	04-Dec-2025 16:12:13	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	04-Dec-2025 16:12:13	
build	04-Dec-2025 16:12:13	> Task :prepare
build	04-Dec-2025 16:12:15	
build	04-Dec-2025 16:12:15	> Task :compileJava
build	04-Dec-2025 16:12:15	Setting target compatibility to 11
error	04-Dec-2025 16:12:22	Note: Some input files use or override a deprecated API.
error	04-Dec-2025 16:12:22	Note: Recompile with -Xlint:deprecation for details.
error	04-Dec-2025 16:12:22	Note: Some input files use unchecked or unsafe operations.
error	04-Dec-2025 16:12:22	Note: Recompile with -Xlint:unchecked for details.
build	04-Dec-2025 16:12:24	
build	04-Dec-2025 16:12:24	> Task :compileTestJava
build	04-Dec-2025 16:12:24	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	04-Dec-2025 16:12:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes'. Reason: Task ':compileTestJava' 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	04-Dec-2025 16:12:24	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-test-instr'. Reason: Task ':compileTestJava' uses this output of task ':cloverInstrTests' 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	04-Dec-2025 16:12:24	Setting target compatibility to 11
error	04-Dec-2025 16:12:31	Note: Some input files use or override a deprecated API.
error	04-Dec-2025 16:12:31	Note: Recompile with -Xlint:deprecation for details.
error	04-Dec-2025 16:12:31	Note: Some input files use unchecked or unsafe operations.
error	04-Dec-2025 16:12:31	Note: Recompile with -Xlint:unchecked for details.
build	04-Dec-2025 16:12:33	
build	04-Dec-2025 16:12:33	> Task :processTestResources
build	04-Dec-2025 16:12:33	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	04-Dec-2025 16:12:33	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' uses this output of task ':copyDocs' 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	04-Dec-2025 16:12:33	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':buildIndices' 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	04-Dec-2025 16:12:33	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':copyHelp' 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	04-Dec-2025 16:12:33	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':releasesTemplates' 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	04-Dec-2025 16:12:33	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' 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	04-Dec-2025 16:12:33	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':copyResources' 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	04-Dec-2025 16:12:33	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':createBuildProperties' 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	04-Dec-2025 16:12:33	
build	04-Dec-2025 16:12:33	> Task :testClasses
build	04-Dec-2025 16:12:35	
build	04-Dec-2025 16:12:35	> Task :testTask0
build	04-Dec-2025 16:12:35	Running tests WITH clover
error	04-Dec-2025 16:12:37	WARNING: An illegal reflective access operation has occurred
error	04-Dec-2025 16:12:37	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	04-Dec-2025 16:12:37	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	04-Dec-2025 16:12:37	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	04-Dec-2025 16:12:37	WARNING: All illegal access operations will be denied in a future release
build	04-Dec-2025 16:18:25	
build	04-Dec-2025 16:18:25	> Task :testTask1
build	04-Dec-2025 16:18:25	Running tests WITH clover
error	04-Dec-2025 16:18:27	WARNING: An illegal reflective access operation has occurred
error	04-Dec-2025 16:18:27	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	04-Dec-2025 16:18:27	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	04-Dec-2025 16:18:27	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	04-Dec-2025 16:18:27	WARNING: All illegal access operations will be denied in a future release
build	04-Dec-2025 16:21:08	
build	04-Dec-2025 16:21:08	> Task :testTask2
build	04-Dec-2025 16:21:08	Running tests WITH clover
error	04-Dec-2025 16:21:11	WARNING: An illegal reflective access operation has occurred
error	04-Dec-2025 16:21:11	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	04-Dec-2025 16:21:11	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	04-Dec-2025 16:21:11	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	04-Dec-2025 16:21:11	WARNING: All illegal access operations will be denied in a future release
build	04-Dec-2025 16:21:14	
build	04-Dec-2025 16:21:14	> Task :testTask3
build	04-Dec-2025 16:21:14	Running tests WITH clover
error	04-Dec-2025 16:21:16	WARNING: An illegal reflective access operation has occurred
error	04-Dec-2025 16:21:16	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	04-Dec-2025 16:21:16	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	04-Dec-2025 16:21:16	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	04-Dec-2025 16:21:16	WARNING: All illegal access operations will be denied in a future release
build	04-Dec-2025 16:21:39	
build	04-Dec-2025 16:21:39	> Task :test NO-SOURCE
build	04-Dec-2025 16:21:40	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	04-Dec-2025 16:21:40	│jalview:testTask0 results: SUCCESS (2102 tests, 2102 successes, 0 failures, 0 skipped) in 5 minutes, 49.852 seconds   │
build	04-Dec-2025 16:21:40	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask0/index.html│
build	04-Dec-2025 16:21:40	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	04-Dec-2025 16:21:40	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 43.782 seconds       │
build	04-Dec-2025 16:21:40	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask1/index.html│
build	04-Dec-2025 16:21:40	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	04-Dec-2025 16:21:40	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 5.908 seconds                     │
build	04-Dec-2025 16:21:40	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask2/index.html│
build	04-Dec-2025 16:21:40	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	04-Dec-2025 16:21:40	│jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 26.908 seconds                  │
build	04-Dec-2025 16:21:40	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask3/index.html│
build	04-Dec-2025 16:21:40	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	04-Dec-2025 16:21:40	│OVERALL: results: SUCCESS (2179 tests, 2178 successes, 0 failures, 1 skipped) in 7 minutes, 126.450 seconds           │
build	04-Dec-2025 16:21:40	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	04-Dec-2025 16:21:40	
build	04-Dec-2025 16:21:40	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	04-Dec-2025 16:21:40	
build	04-Dec-2025 16:21:40	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	04-Dec-2025 16:21:40	
build	04-Dec-2025 16:21:40	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	04-Dec-2025 16:21:40	
build	04-Dec-2025 16:21:40	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	04-Dec-2025 16:21:40	Please consult deprecation warnings for more details.
build	04-Dec-2025 16:21:40	
build	04-Dec-2025 16:21:40	BUILD SUCCESSFUL in 10m 23s
build	04-Dec-2025 16:21:40	21 actionable tasks: 20 executed, 1 up-to-date
simple	04-Dec-2025 16:21:40	Finished task 'Run tests with openclover under gradle' with result: Success
simple	04-Dec-2025 16:21:40	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	04-Dec-2025 16:21:40	Bamboo Artifactory Plugin version: 2.6.2
command	04-Dec-2025 16:21:40	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #1 (JB-GDB734-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-GDB734-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_revision_number=e0875267ed4b699db969bf10b30bafe83a1cbd7d\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-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-GDB734-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB734-JOB1\nbamboo_repository_46498616_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498616_revision_number=e0875267ed4b699db969bf10b30bafe83a1cbd7d\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_name=Jalview Gitlab\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-GDB734-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_shortPlanKey=GDB734\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=e0875267ed4b699db969bf10b30bafe83a1cbd7d\nbamboo_buildTimeStamp=2025-12-04T16:11:07.685Z\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GDB734-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=e0875267ed4b699db969bf10b30bafe83a1cbd7d\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\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\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_repository_46498616_branch_name=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\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=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=false\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302801\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=https://gitlab.jalview.org/jalview/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-GDB734-JOB1\nbamboo_planKey=JB-GDB734\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498616_git_username=\nbamboo_repository_46498616_name=Jalview Gitlab\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_repository_46498616_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	04-Dec-2025 16:21:40	444
build	04-Dec-2025 16:21:48	
build	04-Dec-2025 16:21:48	> Configure project :
build	04-Dec-2025 16:21:48	Using properties from file './utils/channels/default/channel_gradle.properties'
build	04-Dec-2025 16:21:48	JALVIEW_VERSION is set to '2.12.0'
build	04-Dec-2025 16:21:48	HEADLESS BUILD
build	04-Dec-2025 16:21:48	J2S ENABLED
build	04-Dec-2025 16:21:48	Using a LOCAL profile.
build	04-Dec-2025 16:21:49	eclipseDir exists
build	04-Dec-2025 16:21:52	
build	04-Dec-2025 16:21:52	> Task :cloverHtmlReport
build	04-Dec-2025 16:21:52	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	04-Dec-2025 16:21:53	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover'
build	04-Dec-2025 16:23:00	Done. Processed 137 packages in 66283ms (483ms per package).
build	04-Dec-2025 16:23:08	
build	04-Dec-2025 16:23:08	> Task :cloverXmlReport
build	04-Dec-2025 16:23:08	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	04-Dec-2025 16:23:12	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover/clover.xml'
build	04-Dec-2025 16:23:12	
build	04-Dec-2025 16:23:12	> Task :cloverReport
build	04-Dec-2025 16:23:12	
build	04-Dec-2025 16:23:12	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	04-Dec-2025 16:23:12	
build	04-Dec-2025 16:23:12	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	04-Dec-2025 16:23:12	
build	04-Dec-2025 16:23:12	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	04-Dec-2025 16:23:12	
build	04-Dec-2025 16:23:12	BUILD SUCCESSFUL in 1m 32s
build	04-Dec-2025 16:23:12	2 actionable tasks: 2 executed
simple	04-Dec-2025 16:23:12	Finished task 'Clover Report' with result: Success
simple	04-Dec-2025 16:23:12	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	04-Dec-2025 16:23:12	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1...
simple	04-Dec-2025 16:23:13	Finished task 'TestNG Parser' with result: Success
simple	04-Dec-2025 16:23:13	Running post build plugin 'NCover Results Collector'
simple	04-Dec-2025 16:23:13	Running post build plugin 'Artifact Copier'
simple	04-Dec-2025 16:23:13	Publishing an artifact: Clover Report (System)
simple	04-Dec-2025 16:23:19	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 6.185 s
simple	04-Dec-2025 16:23:19	Publishing an artifact: TestNG report
error	04-Dec-2025 16:23:19	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/test does not exist.
simple	04-Dec-2025 16:23:19	The artifact hasn't been successfully published after 4.772 ms
simple	04-Dec-2025 16:23:19	Running post build plugin 'Artifactory Release Management Staging'
simple	04-Dec-2025 16:23:19	Running post build plugin 'Artifactory Build Info Copier'
simple	04-Dec-2025 16:23:19	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	04-Dec-2025 16:23:19	Running post build plugin 'npm Cache Cleanup'
simple	04-Dec-2025 16:23:19	Running post build plugin 'Clover Results Collector'
simple	04-Dec-2025 16:23:19	Running post build plugin 'Docker Container Cleanup'
simple	04-Dec-2025 16:23:19	Finalising the build...
simple	04-Dec-2025 16:23:19	Stopping timer.
simple	04-Dec-2025 16:23:19	Build JB-GDB734-JOB1-1 completed.
simple	04-Dec-2025 16:23:19	Running on server: post build plugin 'NCover Results Collector'
simple	04-Dec-2025 16:23:19	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	04-Dec-2025 16:23:19	Running on server: post build plugin 'Clover Delta Calculator'
simple	04-Dec-2025 16:23:19	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	04-Dec-2025 16:23:19	All post build plugins have finished
simple	04-Dec-2025 16:23:19	Generating build results summary...
simple	04-Dec-2025 16:23:20	Saving build results to disk...
simple	04-Dec-2025 16:23:20	Logging substituted variables...
simple	04-Dec-2025 16:23:20	Indexing build results...
simple	04-Dec-2025 16:23:20	Finished building JB-GDB734-JOB1-1.