simple	05-Jan-2026 05:07:16	Build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #7 (JB-GDB734-JOB1-7) started building on agent Default Agent
simple	05-Jan-2026 05:07:16	
simple	05-Jan-2026 05:07:16	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1
simple	05-Jan-2026 05:07:16	Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #7 (JB-GDB734-JOB1-7)
simple	05-Jan-2026 05:07:16	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	05-Jan-2026 05:07:16	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1
simple	05-Jan-2026 05:07:16	Updating source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5
simple	05-Jan-2026 05:07:17	Fetching 'refs/heads/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	05-Jan-2026 05:07:17	Checking out revision b6ff7e553d3ba8b32e1d2650df7860706b2a37d5.
simple	05-Jan-2026 05:07:18	Already on 'bug/JAL-4107_jalviewjs_fixes_on_2_12_branch'
simple	05-Jan-2026 05:07:18	Updated source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5
simple	05-Jan-2026 05:07:18	Finished task 'Checkout Default Repository' with result: Success
simple	05-Jan-2026 05:07:18	Running pre-build action: VCS Version Collector
simple	05-Jan-2026 05:07:18	Running pre-build action: Artifactory Release Staging
simple	05-Jan-2026 05:07:18	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	05-Jan-2026 05:07:18	Bamboo Artifactory Plugin version: 2.6.2
command	05-Jan-2026 05:07:18	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #7 (JB-GDB734-JOB1-7)'\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-JOB1-7\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=7\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-JOB1-7\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_buildTimeStamp=2026-01-05T05:06:57.638Z\nbamboo_repository_previous_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_planRepository_previousRevision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GDB734-JOB1-7\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\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\nbamboo_dependenciesDisabled=false\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_1_previousRevision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\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_ManualBuildTriggerReason_userName=jprocter\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_previous_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\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	05-Jan-2026 05:07:18	2414
build	05-Jan-2026 05:07:20	Starting a Gradle Daemon, 1 busy Daemon could not be reused, use --status for details
build	05-Jan-2026 05:07:31	
build	05-Jan-2026 05:07:31	> Configure project :
build	05-Jan-2026 05:07:31	Using properties from file './utils/channels/default/channel_gradle.properties'
build	05-Jan-2026 05:07:31	JALVIEW_VERSION is set to '2.12.0'
build	05-Jan-2026 05:07:31	HEADLESS BUILD
build	05-Jan-2026 05:07:31	J2S ENABLED
build	05-Jan-2026 05:07:32	Using a LOCAL profile.
build	05-Jan-2026 05:07:35	eclipseDir exists
build	05-Jan-2026 05:07:37	
build	05-Jan-2026 05:07:37	> Task :clean FAILED
error	05-Jan-2026 05:07:37	
error	05-Jan-2026 05:07:37	FAILURE: Build failed with an exception.
error	05-Jan-2026 05:07:37	
error	05-Jan-2026 05:07:37	* What went wrong:
error	05-Jan-2026 05:07:37	Execution failed for task ':clean'.
error	05-Jan-2026 05:07:37	> java.io.IOException: Unable to delete directory '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build'
error	05-Jan-2026 05:07:37	    Failed to delete some children. This might happen because a process has files open or has its working directory set in the target directory.
error	05-Jan-2026 05:07:37	    - /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover
error	05-Jan-2026 05:07:37	    New files were found. This might happen because a process is still writing to the target directory.
error	05-Jan-2026 05:07:37	    - /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db71ykx1z80pum_a_8bepgo_mk0p8rgs.s
error	05-Jan-2026 05:07:37	    - /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db71ykx1z80pum_c_8bepgo_mk0p8rrl.s
error	05-Jan-2026 05:07:37	    - /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db71ykx1z80pum_d_8bepgo_mk0p8rxp.s
error	05-Jan-2026 05:07:37	    - /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db71ykx1z80pum_9_i3gheq_mk0p8ku0.s
error	05-Jan-2026 05:07:37	    - /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db71ykx1z80pum_b_i3gheq_mk0p8rm0.s
error	05-Jan-2026 05:07:37	    - /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db71ykx1z80pum_9_8bepgo_mk0p8ku0.s
error	05-Jan-2026 05:07:37	    - /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db71ykx1z80pum_b_8bepgo_mk0p8rm0.s
error	05-Jan-2026 05:07:37	    - /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db71ykx1z80pum_d_i3gheq_mk0p8rxp.s
error	05-Jan-2026 05:07:37	    - /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db71ykx1z80pum_c_i3gheq_mk0p8rrl.s
error	05-Jan-2026 05:07:37	    - /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db71ykx1z80pum_a_i3gheq_mk0p8rgs.s
error	05-Jan-2026 05:07:37	
error	05-Jan-2026 05:07:37	* Try:
error	05-Jan-2026 05:07:37	> Run with --stacktrace option to get the stack trace.
error	05-Jan-2026 05:07:37	> Run with --info or --debug option to get more log output.
error	05-Jan-2026 05:07:37	> Run with --scan to get full insights.
error	05-Jan-2026 05:07:37	
error	05-Jan-2026 05:07:37	* Get more help at https://help.gradle.org
error	05-Jan-2026 05:07:37	
error	05-Jan-2026 05:07:37	BUILD FAILED in 18s
build	05-Jan-2026 05:07:37	
build	05-Jan-2026 05:07:37	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	05-Jan-2026 05:07:37	
build	05-Jan-2026 05:07:37	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	05-Jan-2026 05:07:37	
build	05-Jan-2026 05:07:37	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	05-Jan-2026 05:07:37	1 actionable task: 1 executed
simple	05-Jan-2026 05:07:37	
simple	05-Jan-2026 05:07:37	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	05-Jan-2026 05:07:37	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	05-Jan-2026 05:07:37	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	05-Jan-2026 05:07:37	Bamboo Artifactory Plugin version: 2.6.2
command	05-Jan-2026 05:07:37	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #7 (JB-GDB734-JOB1-7)'\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-JOB1-7\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=7\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-JOB1-7\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_buildTimeStamp=2026-01-05T05:06:57.638Z\nbamboo_repository_previous_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_planRepository_previousRevision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GDB734-JOB1-7\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\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\nbamboo_dependenciesDisabled=false\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=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\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_planRepository_1_previousRevision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\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_ManualBuildTriggerReason_userName=jprocter\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_previous_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\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	05-Jan-2026 05:07:37	2414
build	05-Jan-2026 05:07:43	
build	05-Jan-2026 05:07:43	> Configure project :
build	05-Jan-2026 05:07:43	Using properties from file './utils/channels/default/channel_gradle.properties'
build	05-Jan-2026 05:07:43	JALVIEW_VERSION is set to '2.12.0'
build	05-Jan-2026 05:07:43	HEADLESS BUILD
build	05-Jan-2026 05:07:43	J2S ENABLED
build	05-Jan-2026 05:07:43	Using a LOCAL profile.
build	05-Jan-2026 05:07:44	eclipseDir exists
build	05-Jan-2026 05:07:44	
build	05-Jan-2026 05:07:44	> Task :cloverHtmlReport SKIPPED
build	05-Jan-2026 05:07:44	> Task :cloverXmlReport SKIPPED
build	05-Jan-2026 05:07:44	> Task :cloverReport UP-TO-DATE
build	05-Jan-2026 05:07:44	
build	05-Jan-2026 05:07:44	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	05-Jan-2026 05:07:44	
build	05-Jan-2026 05:07:44	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	05-Jan-2026 05:07:44	
build	05-Jan-2026 05:07:44	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	05-Jan-2026 05:07:44	
build	05-Jan-2026 05:07:44	BUILD SUCCESSFUL in 6s
simple	05-Jan-2026 05:07:44	Finished task 'Clover Report' with result: Success
simple	05-Jan-2026 05:07:44	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	05-Jan-2026 05:07:44	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1...
simple	05-Jan-2026 05:07:44	Failing task since 16 failing test cases were found.
simple	05-Jan-2026 05:07:44	Finished task 'TestNG Parser' with result: Failed
simple	05-Jan-2026 05:07:44	Running post build plugin 'NCover Results Collector'
simple	05-Jan-2026 05:07:44	Running post build plugin 'Artifact Copier'
simple	05-Jan-2026 05:07:44	Publishing an artifact: Clover Report (System)
error	05-Jan-2026 05:07:44	Unable to publish artifact [Clover Report (System)]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover does not exist.
simple	05-Jan-2026 05:07:44	The artifact hasn't been successfully published after 538.2 μs
simple	05-Jan-2026 05:07:44	Publishing an artifact: TestNG report
error	05-Jan-2026 05:07:44	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	05-Jan-2026 05:07:44	The artifact hasn't been successfully published after 51.57 μs
simple	05-Jan-2026 05:07:44	Running post build plugin 'Artifactory Release Management Staging'
simple	05-Jan-2026 05:07:44	Running post build plugin 'Artifactory Build Info Copier'
simple	05-Jan-2026 05:07:44	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	05-Jan-2026 05:07:44	Running post build plugin 'npm Cache Cleanup'
simple	05-Jan-2026 05:07:44	Running post build plugin 'Clover Results Collector'
error	05-Jan-2026 05:07:44	Failed to execute plugin 'Clover Results Collector' with error: No file matches the specified pattern:build/reports/clover/clover.xml in [/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1]
simple	05-Jan-2026 05:07:44	Running post build plugin 'Docker Container Cleanup'
simple	05-Jan-2026 05:07:44	Finalising the build...
simple	05-Jan-2026 05:07:44	Stopping timer.
simple	05-Jan-2026 05:07:44	Build JB-GDB734-JOB1-7 completed.
simple	05-Jan-2026 05:07:44	Running on server: post build plugin 'NCover Results Collector'
simple	05-Jan-2026 05:07:44	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	05-Jan-2026 05:07:44	Running on server: post build plugin 'Clover Delta Calculator'
simple	05-Jan-2026 05:07:44	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	05-Jan-2026 05:07:44	All post build plugins have finished
simple	05-Jan-2026 05:07:44	Generating build results summary...
simple	05-Jan-2026 05:07:45	Saving build results to disk...
simple	05-Jan-2026 05:07:45	Logging substituted variables...
simple	05-Jan-2026 05:07:45	Indexing build results...
simple	05-Jan-2026 05:07:45	Finished building JB-GDB734-JOB1-7.
simple	05-Jan-2026 05:12:05	Build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #7 (JB-GDB734-JOB1-7) started building on agent Default Agent
simple	05-Jan-2026 05:12:05	
simple	05-Jan-2026 05:12:05	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1
simple	05-Jan-2026 05:12:05	Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #7 (JB-GDB734-JOB1-7)
simple	05-Jan-2026 05:12:05	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	05-Jan-2026 05:12:05	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1
simple	05-Jan-2026 05:12:05	Updating source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5
simple	05-Jan-2026 05:12:05	Fetching 'refs/heads/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	05-Jan-2026 05:12:05	Checking out revision b6ff7e553d3ba8b32e1d2650df7860706b2a37d5.
simple	05-Jan-2026 05:12:05	Already on 'bug/JAL-4107_jalviewjs_fixes_on_2_12_branch'
simple	05-Jan-2026 05:12:05	Updated source code to revision: b6ff7e553d3ba8b32e1d2650df7860706b2a37d5
simple	05-Jan-2026 05:12:05	Finished task 'Checkout Default Repository' with result: Success
simple	05-Jan-2026 05:12:05	Running pre-build action: VCS Version Collector
simple	05-Jan-2026 05:12:05	Running pre-build action: Artifactory Release Staging
simple	05-Jan-2026 05:12:05	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	05-Jan-2026 05:12:05	Bamboo Artifactory Plugin version: 2.6.2
command	05-Jan-2026 05:12:05	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #7 (JB-GDB734-JOB1-7)'\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-JOB1-7\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=7\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-JOB1-7\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_ManualBuildTriggerReason_stageName=Default Stage\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_buildTimeStamp=2026-01-05T05:12:05.310Z\nbamboo_repository_previous_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_planRepository_previousRevision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GDB734-JOB1-7\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_4=/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\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\nbamboo_dependenciesDisabled=false\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_1_previousRevision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\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_ManualBuildTriggerReason_userName=jprocter\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_RerunBuildTriggerReason_noOfRetries=1\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498616_git_username=\nbamboo_repository_46498616_previous_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\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	05-Jan-2026 05:12:05	2414
build	05-Jan-2026 05:12:07	
build	05-Jan-2026 05:12:07	> Configure project :
build	05-Jan-2026 05:12:07	Using properties from file './utils/channels/default/channel_gradle.properties'
build	05-Jan-2026 05:12:07	JALVIEW_VERSION is set to '2.12.0'
build	05-Jan-2026 05:12:07	HEADLESS BUILD
build	05-Jan-2026 05:12:07	J2S ENABLED
build	05-Jan-2026 05:12:07	Using a LOCAL profile.
build	05-Jan-2026 05:12:07	eclipseDir exists
build	05-Jan-2026 05:12:07	
build	05-Jan-2026 05:12:07	> Task :clean
build	05-Jan-2026 05:12:07	> Task :cleanClover
build	05-Jan-2026 05:12:07	> Task :cleanTest UP-TO-DATE
build	05-Jan-2026 05:12:09	
build	05-Jan-2026 05:12:09	> Task :cloverInstrJava
build	05-Jan-2026 05:12:09	Clover: About to instrument 1253 files
build	05-Jan-2026 05:12:09	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	05-Jan-2026 05:12:09	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'.
build	05-Jan-2026 05:12:09	Processing files at 1.9 source level.
error	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:11	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	05-Jan-2026 05:12:17	Clover all over. Instrumented 1253 files (133 packages).
build	05-Jan-2026 05:12:19	
build	05-Jan-2026 05:12:19	> Task :cloverInstrTests
build	05-Jan-2026 05:12:19	Clover: About to instrument test files
build	05-Jan-2026 05:12:19	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	05-Jan-2026 05:12:19	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/clover/clover.db'.
build	05-Jan-2026 05:12:19	Processing files at 1.9 source level.
build	05-Jan-2026 05:12:21	Clover all over. Instrumented 315 files (58 packages).
build	05-Jan-2026 05:12:21	1770 test methods detected.
build	05-Jan-2026 05:12:21	
build	05-Jan-2026 05:12:21	> Task :cloverInstr
build	05-Jan-2026 05:12:23	
build	05-Jan-2026 05:12:23	> Task :compileCloverJava
build	05-Jan-2026 05:12:23	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	05-Jan-2026 05:12:23	  - 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	05-Jan-2026 05:12:23	  - 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	05-Jan-2026 05:12:23	  - 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	05-Jan-2026 05:12:23	Setting target compatibility to 11
error	05-Jan-2026 05:12:44	Note: Some input files use or override a deprecated API.
error	05-Jan-2026 05:12:44	Note: Recompile with -Xlint:deprecation for details.
error	05-Jan-2026 05:12:44	Note: Some input files use unchecked or unsafe operations.
error	05-Jan-2026 05:12:44	Note: Recompile with -Xlint:unchecked for details.
build	05-Jan-2026 05:12:50	
build	05-Jan-2026 05:12:50	> Task :processCloverResources NO-SOURCE
build	05-Jan-2026 05:12:50	> Task :cloverClasses
build	05-Jan-2026 05:12:51	> Task :copyHelp
build	05-Jan-2026 05:12:52	> Task :buildIndices
build	05-Jan-2026 05:12:52	> Task :copyResources
build	05-Jan-2026 05:12:52	> Task :copyChannelResources
build	05-Jan-2026 05:12:52	
build	05-Jan-2026 05:12:52	> Task :createBuildProperties
build	05-Jan-2026 05:12:52	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	05-Jan-2026 05:12:52	  - 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	05-Jan-2026 05:12:52	
build	05-Jan-2026 05:12:52	> Task :buildResources
build	05-Jan-2026 05:12:52	> Task :copyDocs
build	05-Jan-2026 05:12:52	
build	05-Jan-2026 05:12:52	> Task :convertMdFiles
build	05-Jan-2026 05:12:52	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	05-Jan-2026 05:12:52	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	05-Jan-2026 05:12:52	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	05-Jan-2026 05:12:52	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
build	05-Jan-2026 05:12:52	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/building.html
build	05-Jan-2026 05:12:52	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/addingWebClient.html
build	05-Jan-2026 05:12:52	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	05-Jan-2026 05:12:52	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
build	05-Jan-2026 05:12:53	
build	05-Jan-2026 05:12:53	> Task :releasesTemplates
build	05-Jan-2026 05:12:53	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	05-Jan-2026 05:12:53	  - 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	05-Jan-2026 05:12:53	  - 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	05-Jan-2026 05:12:53	Stripping rc/test/etc for TEST
build	05-Jan-2026 05:12:53	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	05-Jan-2026 05:12:53	
build	05-Jan-2026 05:12:53	> Task :prepare
build	05-Jan-2026 05:12:55	
build	05-Jan-2026 05:12:55	> Task :compileJava
build	05-Jan-2026 05:12:55	Setting target compatibility to 11
error	05-Jan-2026 05:13:00	Note: Some input files use or override a deprecated API.
error	05-Jan-2026 05:13:00	Note: Recompile with -Xlint:deprecation for details.
error	05-Jan-2026 05:13:00	Note: Some input files use unchecked or unsafe operations.
error	05-Jan-2026 05:13:00	Note: Recompile with -Xlint:unchecked for details.
build	05-Jan-2026 05:13:05	
build	05-Jan-2026 05:13:05	> Task :compileTestJava
build	05-Jan-2026 05:13:05	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	05-Jan-2026 05:13:05	  - 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	05-Jan-2026 05:13:05	  - 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	05-Jan-2026 05:13:05	Setting target compatibility to 11
error	05-Jan-2026 05:13:10	Note: Some input files use or override a deprecated API.
error	05-Jan-2026 05:13:10	Note: Recompile with -Xlint:deprecation for details.
error	05-Jan-2026 05:13:10	Note: Some input files use unchecked or unsafe operations.
error	05-Jan-2026 05:13:10	Note: Recompile with -Xlint:unchecked for details.
build	05-Jan-2026 05:13:11	
build	05-Jan-2026 05:13:11	> Task :processTestResources
build	05-Jan-2026 05:13:11	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	05-Jan-2026 05:13:11	  - 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	05-Jan-2026 05:13:11	  - 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	05-Jan-2026 05:13:11	  - 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	05-Jan-2026 05:13:11	  - 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	05-Jan-2026 05:13:11	  - 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	05-Jan-2026 05:13:11	  - 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	05-Jan-2026 05:13:11	  - 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	05-Jan-2026 05:13:11	
build	05-Jan-2026 05:13:11	> Task :testClasses
build	05-Jan-2026 05:13:13	
build	05-Jan-2026 05:13:13	> Task :testTask0
build	05-Jan-2026 05:13:13	Running tests WITH clover
error	05-Jan-2026 05:13:15	WARNING: An illegal reflective access operation has occurred
error	05-Jan-2026 05:13:15	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	05-Jan-2026 05:13:15	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	05-Jan-2026 05:13:15	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	05-Jan-2026 05:13:15	WARNING: All illegal access operations will be denied in a future release
build	05-Jan-2026 05:17:46	
build	05-Jan-2026 05:17:46	> Task :testTask1
build	05-Jan-2026 05:17:46	Running tests WITH clover
error	05-Jan-2026 05:17:48	WARNING: An illegal reflective access operation has occurred
error	05-Jan-2026 05:17:48	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	05-Jan-2026 05:17:48	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	05-Jan-2026 05:17:48	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	05-Jan-2026 05:17:48	WARNING: All illegal access operations will be denied in a future release
build	05-Jan-2026 05:19:45	
build	05-Jan-2026 05:19:45	> Task :testTask2
build	05-Jan-2026 05:19:45	Running tests WITH clover
error	05-Jan-2026 05:19:46	WARNING: An illegal reflective access operation has occurred
error	05-Jan-2026 05:19:46	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	05-Jan-2026 05:19:46	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	05-Jan-2026 05:19:46	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	05-Jan-2026 05:19:46	WARNING: All illegal access operations will be denied in a future release
build	05-Jan-2026 05:19:50	
build	05-Jan-2026 05:19:50	> Task :testTask3
build	05-Jan-2026 05:19:50	Running tests WITH clover
error	05-Jan-2026 05:19:51	WARNING: An illegal reflective access operation has occurred
error	05-Jan-2026 05:19:51	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	05-Jan-2026 05:19:51	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	05-Jan-2026 05:19:51	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	05-Jan-2026 05:19:51	WARNING: All illegal access operations will be denied in a future release
build	05-Jan-2026 05:20:08	
build	05-Jan-2026 05:20:08	> Task :test NO-SOURCE
build	05-Jan-2026 05:20:08	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	05-Jan-2026 05:20:08	│jalview:testTask0 results: SUCCESS (2102 tests, 2102 successes, 0 failures, 0 skipped) in 4 minutes, 32.370 seconds   │
build	05-Jan-2026 05:20:08	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask0/index.html│
build	05-Jan-2026 05:20:08	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	05-Jan-2026 05:20:08	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 1 minutes, 58.746 seconds       │
build	05-Jan-2026 05:20:08	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask1/index.html│
build	05-Jan-2026 05:20:08	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	05-Jan-2026 05:20:08	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.655 seconds                     │
build	05-Jan-2026 05:20:08	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask2/index.html│
build	05-Jan-2026 05:20:08	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	05-Jan-2026 05:20:08	│jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 20.192 seconds                  │
build	05-Jan-2026 05:20:08	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/tests/testTask3/index.html│
build	05-Jan-2026 05:20:08	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	05-Jan-2026 05:20:08	│OVERALL: results: SUCCESS (2179 tests, 2178 successes, 0 failures, 1 skipped) in 5 minutes, 115.963 seconds           │
build	05-Jan-2026 05:20:08	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	05-Jan-2026 05:20:08	
build	05-Jan-2026 05:20:08	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	05-Jan-2026 05:20:08	
build	05-Jan-2026 05:20:08	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	05-Jan-2026 05:20:08	
build	05-Jan-2026 05:20:08	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	05-Jan-2026 05:20:08	
build	05-Jan-2026 05:20:08	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	05-Jan-2026 05:20:08	Please consult deprecation warnings for more details.
build	05-Jan-2026 05:20:08	
build	05-Jan-2026 05:20:08	BUILD SUCCESSFUL in 8m 2s
build	05-Jan-2026 05:20:08	21 actionable tasks: 20 executed, 1 up-to-date
simple	05-Jan-2026 05:20:09	Finished task 'Run tests with openclover under gradle' with result: Success
simple	05-Jan-2026 05:20:09	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	05-Jan-2026 05:20:09	Bamboo Artifactory Plugin version: 2.6.2
command	05-Jan-2026 05:20:09	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4107_jalviewjs_fixes_on_2_12_branch - Clover and Tests #7 (JB-GDB734-JOB1-7)'\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB734-JOB1-7\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_shortPlanName=bug-JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=7\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-JOB1-7\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_ManualBuildTriggerReason_stageName=Default Stage\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_buildTimeStamp=2026-01-05T05:12:05.310Z\nbamboo_repository_previous_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_planRepository_previousRevision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nbamboo_repository_git_branch=bug/JAL-4107_jalviewjs_fixes_on_2_12_branch\nbamboo_buildResultKey=JB-GDB734-JOB1-7\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=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_4=/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\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\nbamboo_dependenciesDisabled=false\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_1_previousRevision=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\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_ManualBuildTriggerReason_userName=jprocter\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_RerunBuildTriggerReason_noOfRetries=1\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498616_git_username=\nbamboo_repository_46498616_previous_revision_number=b6ff7e553d3ba8b32e1d2650df7860706b2a37d5\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	05-Jan-2026 05:20:09	2414
build	05-Jan-2026 05:20:13	
build	05-Jan-2026 05:20:13	> Configure project :
build	05-Jan-2026 05:20:13	Using properties from file './utils/channels/default/channel_gradle.properties'
build	05-Jan-2026 05:20:13	JALVIEW_VERSION is set to '2.12.0'
build	05-Jan-2026 05:20:13	HEADLESS BUILD
build	05-Jan-2026 05:20:13	J2S ENABLED
build	05-Jan-2026 05:20:13	Using a LOCAL profile.
build	05-Jan-2026 05:20:14	eclipseDir exists
build	05-Jan-2026 05:20:17	
build	05-Jan-2026 05:20:17	> Task :cloverHtmlReport
build	05-Jan-2026 05:20:17	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	05-Jan-2026 05:20:18	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover'
build	05-Jan-2026 05:21:09	Done. Processed 137 packages in 51633ms (376ms per package).
build	05-Jan-2026 05:21:14	
build	05-Jan-2026 05:21:14	> Task :cloverXmlReport
build	05-Jan-2026 05:21:14	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	05-Jan-2026 05:21:15	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1/build/reports/clover/clover.xml'
build	05-Jan-2026 05:21:15	
build	05-Jan-2026 05:21:15	> Task :cloverReport
build	05-Jan-2026 05:21:15	
build	05-Jan-2026 05:21:15	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	05-Jan-2026 05:21:15	
build	05-Jan-2026 05:21:15	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	05-Jan-2026 05:21:15	
build	05-Jan-2026 05:21:15	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	05-Jan-2026 05:21:15	
build	05-Jan-2026 05:21:15	BUILD SUCCESSFUL in 1m 6s
build	05-Jan-2026 05:21:15	2 actionable tasks: 2 executed
simple	05-Jan-2026 05:21:15	Finished task 'Clover Report' with result: Success
simple	05-Jan-2026 05:21:15	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	05-Jan-2026 05:21:15	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB734-JOB1...
simple	05-Jan-2026 05:21:15	Finished task 'TestNG Parser' with result: Success
simple	05-Jan-2026 05:21:15	Running post build plugin 'NCover Results Collector'
simple	05-Jan-2026 05:21:15	Running post build plugin 'Artifact Copier'
simple	05-Jan-2026 05:21:15	Publishing an artifact: Clover Report (System)
simple	05-Jan-2026 05:21:17	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.073 s
simple	05-Jan-2026 05:21:17	Publishing an artifact: TestNG report
error	05-Jan-2026 05:21:17	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	05-Jan-2026 05:21:17	The artifact hasn't been successfully published after 1.366 ms
simple	05-Jan-2026 05:21:17	Running post build plugin 'Artifactory Release Management Staging'
simple	05-Jan-2026 05:21:17	Running post build plugin 'Artifactory Build Info Copier'
simple	05-Jan-2026 05:21:17	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	05-Jan-2026 05:21:17	Running post build plugin 'npm Cache Cleanup'
simple	05-Jan-2026 05:21:17	Running post build plugin 'Clover Results Collector'
simple	05-Jan-2026 05:21:17	Running post build plugin 'Docker Container Cleanup'
simple	05-Jan-2026 05:21:17	Finalising the build...
simple	05-Jan-2026 05:21:17	Stopping timer.
simple	05-Jan-2026 05:21:17	Build JB-GDB734-JOB1-7 completed.
simple	05-Jan-2026 05:21:17	Running on server: post build plugin 'NCover Results Collector'
simple	05-Jan-2026 05:21:17	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	05-Jan-2026 05:21:17	Running on server: post build plugin 'Clover Delta Calculator'
simple	05-Jan-2026 05:21:17	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	05-Jan-2026 05:21:17	All post build plugins have finished
simple	05-Jan-2026 05:21:17	Generating build results summary...
simple	05-Jan-2026 05:21:18	Saving build results to disk...
simple	05-Jan-2026 05:21:18	Logging substituted variables...
simple	05-Jan-2026 05:21:18	Indexing build results...
simple	05-Jan-2026 05:21:18	Finished building JB-GDB734-JOB1-7.