simple	01-Dec-2025 13:17:14	Build Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests #8 (JB-GDB722-JOB1-8) started building on agent Default Agent
simple	01-Dec-2025 13:17:14	
simple	01-Dec-2025 13:17:15	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1
simple	01-Dec-2025 13:17:15	Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests #8 (JB-GDB722-JOB1-8)
simple	01-Dec-2025 13:17:15	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	01-Dec-2025 13:17:15	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1
simple	01-Dec-2025 13:17:15	Updating source code to revision: cc05d28187e3100fd060e6b7e3b1795477c23e62
simple	01-Dec-2025 13:17:15	Fetching 'refs/heads/bug/JAL-4603_export_svg_files_missing_part_of_sequence' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	01-Dec-2025 13:17:15	Checking out revision cc05d28187e3100fd060e6b7e3b1795477c23e62.
simple	01-Dec-2025 13:17:15	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	01-Dec-2025 13:17:15	   5579c74..cc05d28  bug/JAL-4603_export_svg_files_missing_part_of_sequence -> origin/bug/JAL-4603_export_svg_files_missing_part_of_sequence
simple	01-Dec-2025 13:17:15	   df9575c..6f2c311  bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest -> origin/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest
simple	01-Dec-2025 13:17:15	 * [new branch]      bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus -> origin/bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus
simple	01-Dec-2025 13:17:15	   2c0064b..e99989f  development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch
simple	01-Dec-2025 13:17:15	 * [new branch]      patch/JAL-4601_stk_ss_annots_showhide -> origin/patch/JAL-4601_stk_ss_annots_showhide
simple	01-Dec-2025 13:17:15	   86d2c84..a66e20b  releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch
simple	01-Dec-2025 13:17:15	 * [new branch]      test/JAL-4603_test_for_JAL-4603_in_progress -> origin/test/JAL-4603_test_for_JAL-4603_in_progress
simple	01-Dec-2025 13:17:15	Already on 'bug/JAL-4603_export_svg_files_missing_part_of_sequence'
simple	01-Dec-2025 13:17:15	Your branch is behind 'origin/bug/JAL-4603_export_svg_files_missing_part_of_sequence' by 62 commits, and can be fast-forwarded.
simple	01-Dec-2025 13:17:15	  (use "git pull" to update your local branch)
simple	01-Dec-2025 13:17:15	HEAD is now at cc05d28 Merge branch 'development/Release_2_11_5_Branch' into bug/JAL-4603_export_svg_files_missing_part_of_sequence
simple	01-Dec-2025 13:17:15	Updated source code to revision: cc05d28187e3100fd060e6b7e3b1795477c23e62
simple	01-Dec-2025 13:17:15	Finished task 'Checkout Default Repository' with result: Success
simple	01-Dec-2025 13:17:15	Running pre-build action: VCS Version Collector
simple	01-Dec-2025 13:17:15	Running pre-build action: Artifactory Release Staging
simple	01-Dec-2025 13:17:16	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	01-Dec-2025 13:17:16	Bamboo Artifactory Plugin version: 2.6.2
command	01-Dec-2025 13:17:16	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests #8 (JB-GDB722-JOB1-8)'\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-GDB722-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_repository_revision_number=cc05d28187e3100fd060e6b7e3b1795477c23e62\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB722-JOB1-8\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-GDB722-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB722-JOB1\nbamboo_repository_46498555_previous_revision_number=5579c7411432a1b978a885bb1addf5853f0f3fd4\nbamboo_shortPlanName=bug-JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=8\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-GDB722-JOB1-8\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498555_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - 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build	01-Dec-2025 13:17:16	444
build	01-Dec-2025 13:17:17	Starting a Gradle Daemon (subsequent builds will be faster)
build	01-Dec-2025 13:17:25	
build	01-Dec-2025 13:17:25	> Configure project :
build	01-Dec-2025 13:17:25	Using properties from file './utils/channels/default/channel_gradle.properties'
build	01-Dec-2025 13:17:25	JALVIEW_VERSION is set to '2.11.5.1'
build	01-Dec-2025 13:17:25	HEADLESS BUILD
build	01-Dec-2025 13:17:25	J2S ENABLED
build	01-Dec-2025 13:17:25	Using a LOCAL profile.
build	01-Dec-2025 13:17:26	eclipseDir exists
build	01-Dec-2025 13:17:27	
build	01-Dec-2025 13:17:27	> Task :clean
build	01-Dec-2025 13:17:27	> Task :cleanClover
build	01-Dec-2025 13:17:27	> Task :cleanTest UP-TO-DATE
build	01-Dec-2025 13:17:30	
build	01-Dec-2025 13:17:30	> Task :cloverInstrJava
build	01-Dec-2025 13:17:30	Clover: About to instrument 1109 files
build	01-Dec-2025 13:17:30	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	01-Dec-2025 13:17:30	Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover.db'.
build	01-Dec-2025 13:17:30	Processing files at 1.9 source level.
error	01-Dec-2025 13:17:33	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	01-Dec-2025 13:17:33	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	01-Dec-2025 13:17:33	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	01-Dec-2025 13:17:33	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	01-Dec-2025 13:17:33	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	01-Dec-2025 13:17:33	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	01-Dec-2025 13:17:33	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	01-Dec-2025 13:17:41	Clover all over. Instrumented 1109 files (113 packages).
build	01-Dec-2025 13:17:43	
build	01-Dec-2025 13:17:43	> Task :cloverInstrTests
build	01-Dec-2025 13:17:43	Clover: About to instrument test files
build	01-Dec-2025 13:17:43	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	01-Dec-2025 13:17:43	Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover.db'.
build	01-Dec-2025 13:17:43	Processing files at 1.9 source level.
build	01-Dec-2025 13:17:46	Clover all over. Instrumented 293 files (52 packages).
build	01-Dec-2025 13:17:46	1625 test methods detected.
build	01-Dec-2025 13:17:46	
build	01-Dec-2025 13:17:46	> Task :cloverInstr
build	01-Dec-2025 13:17:49	
build	01-Dec-2025 13:17:49	> Task :compileCloverJava
build	01-Dec-2025 13:17:49	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	01-Dec-2025 13:17:49	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:17:49	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:17:49	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:17:49	Setting target compatibility to 11
error	01-Dec-2025 13:18:12	Note: Some input files use or override a deprecated API.
error	01-Dec-2025 13:18:12	Note: Recompile with -Xlint:deprecation for details.
error	01-Dec-2025 13:18:12	Note: Some input files use unchecked or unsafe operations.
error	01-Dec-2025 13:18:12	Note: Recompile with -Xlint:unchecked for details.
build	01-Dec-2025 13:18:20	
build	01-Dec-2025 13:18:20	> Task :processCloverResources NO-SOURCE
build	01-Dec-2025 13:18:20	> Task :cloverClasses
build	01-Dec-2025 13:18:21	> Task :copyHelp
build	01-Dec-2025 13:18:22	> Task :buildIndices
build	01-Dec-2025 13:18:22	> Task :copyResources
build	01-Dec-2025 13:18:22	> Task :copyChannelResources
build	01-Dec-2025 13:18:22	
build	01-Dec-2025 13:18:22	> Task :createBuildProperties
build	01-Dec-2025 13:18:22	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	01-Dec-2025 13:18:22	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:18:22	
build	01-Dec-2025 13:18:22	> Task :buildResources
build	01-Dec-2025 13:18:22	> Task :copyDocs
build	01-Dec-2025 13:18:22	
build	01-Dec-2025 13:18:22	> Task :convertMdFiles
build	01-Dec-2025 13:18:22	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	01-Dec-2025 13:18:22	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	01-Dec-2025 13:18:22	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	01-Dec-2025 13:18:22	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/building.html
build	01-Dec-2025 13:18:22	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	01-Dec-2025 13:18:23	
build	01-Dec-2025 13:18:23	> Task :releasesTemplates
build	01-Dec-2025 13:18:23	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	01-Dec-2025 13:18:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:18:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:18:23	Stripping rc/test/etc for TEST
build	01-Dec-2025 13:18:23	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
build	01-Dec-2025 13:18:23	
build	01-Dec-2025 13:18:23	> Task :prepare
build	01-Dec-2025 13:18:25	
build	01-Dec-2025 13:18:25	> Task :compileJava
build	01-Dec-2025 13:18:25	Setting target compatibility to 11
error	01-Dec-2025 13:18:31	Note: Some input files use or override a deprecated API.
error	01-Dec-2025 13:18:31	Note: Recompile with -Xlint:deprecation for details.
error	01-Dec-2025 13:18:31	Note: Some input files use unchecked or unsafe operations.
error	01-Dec-2025 13:18:31	Note: Recompile with -Xlint:unchecked for details.
build	01-Dec-2025 13:18:36	
build	01-Dec-2025 13:18:36	> Task :compileTestJava
build	01-Dec-2025 13:18:36	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	01-Dec-2025 13:18:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:18:36	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:18:36	Setting target compatibility to 11
error	01-Dec-2025 13:18:41	Note: Some input files use or override a deprecated API.
error	01-Dec-2025 13:18:41	Note: Recompile with -Xlint:deprecation for details.
error	01-Dec-2025 13:18:41	Note: Some input files use unchecked or unsafe operations.
error	01-Dec-2025 13:18:41	Note: Recompile with -Xlint:unchecked for details.
build	01-Dec-2025 13:18:43	
build	01-Dec-2025 13:18:43	> Task :processTestResources
build	01-Dec-2025 13:18:43	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	01-Dec-2025 13:18:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' uses this output of task ':convertMdFiles' 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	01-Dec-2025 13:18:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:18:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:18:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:18:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:18:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:18:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:18:43	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-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	01-Dec-2025 13:18:43	
build	01-Dec-2025 13:18:43	> Task :testClasses
build	01-Dec-2025 13:18:45	
build	01-Dec-2025 13:18:45	> Task :testTask0
build	01-Dec-2025 13:18:45	Running tests WITH clover
error	01-Dec-2025 13:18:48	WARNING: An illegal reflective access operation has occurred
error	01-Dec-2025 13:18:48	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	01-Dec-2025 13:18:48	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	01-Dec-2025 13:18:48	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	01-Dec-2025 13:18:48	WARNING: All illegal access operations will be denied in a future release
build	01-Dec-2025 13:19:04	
build	01-Dec-2025 13:19:04	Gradle suite > Gradle test > jalview.ws.rest.RestClientTest.testGetRestClient FAILED
build	01-Dec-2025 13:19:04	    java.lang.AssertionError: expected:<|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter='-',returns='ANNOTATION'|?tool=jalview|> but was:<|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter='-',returns='ANNOTATION'|>
build	01-Dec-2025 13:19:04	        at org.testng.AssertJUnit.fail(AssertJUnit.java:59)
build	01-Dec-2025 13:19:04	        at org.testng.AssertJUnit.failNotEquals(AssertJUnit.java:364)
build	01-Dec-2025 13:19:04	        at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:80)
build	01-Dec-2025 13:19:04	        at org.testng.AssertJUnit.assertEquals(AssertJUnit.java:88)
build	01-Dec-2025 13:19:04	        at jalview.ws.rest.RestClientTest.__CLR4_4_15idrrq3qp5(RestClientTest.java:78)
build	01-Dec-2025 13:19:04	        at jalview.ws.rest.RestClientTest.testGetRestClient(RestClientTest.java:48)
error	01-Dec-2025 13:23:33	
error	01-Dec-2025 13:23:33	1829 tests completed, 1 failed
build	01-Dec-2025 13:23:33	There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask0/index.html
build	01-Dec-2025 13:23:35	
build	01-Dec-2025 13:23:35	> Task :testTask1
build	01-Dec-2025 13:23:35	Running tests WITH clover
error	01-Dec-2025 13:23:38	WARNING: An illegal reflective access operation has occurred
error	01-Dec-2025 13:23:38	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	01-Dec-2025 13:23:38	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	01-Dec-2025 13:23:38	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	01-Dec-2025 13:23:38	WARNING: All illegal access operations will be denied in a future release
build	01-Dec-2025 13:26:13	
build	01-Dec-2025 13:26:13	> Task :testTask2
build	01-Dec-2025 13:26:13	Running tests WITH clover
build	01-Dec-2025 13:26:16	
build	01-Dec-2025 13:26:16	> Task :testTask3
build	01-Dec-2025 13:26:16	Running tests WITH clover
error	01-Dec-2025 13:26:19	WARNING: An illegal reflective access operation has occurred
error	01-Dec-2025 13:26:19	WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
error	01-Dec-2025 13:26:19	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	01-Dec-2025 13:26:19	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	01-Dec-2025 13:26:19	WARNING: All illegal access operations will be denied in a future release
error	01-Dec-2025 13:27:19	
error	01-Dec-2025 13:27:19	FAILURE: Build failed with an exception.
error	01-Dec-2025 13:27:19	
error	01-Dec-2025 13:27:19	* Where:
error	01-Dec-2025 13:27:19	Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build.gradle' line: 1967
error	01-Dec-2025 13:27:19	
error	01-Dec-2025 13:27:19	* What went wrong:
error	01-Dec-2025 13:27:19	Failed tests!
error	01-Dec-2025 13:27:19	
error	01-Dec-2025 13:27:19	* Try:
error	01-Dec-2025 13:27:19	> Run with --stacktrace option to get the stack trace.
error	01-Dec-2025 13:27:19	> Run with --info or --debug option to get more log output.
error	01-Dec-2025 13:27:19	> Run with --scan to get full insights.
error	01-Dec-2025 13:27:19	
error	01-Dec-2025 13:27:19	* Get more help at https://help.gradle.org
error	01-Dec-2025 13:27:19	
error	01-Dec-2025 13:27:19	BUILD FAILED in 10m 3s
build	01-Dec-2025 13:27:19	
build	01-Dec-2025 13:27:19	> Task :test NO-SOURCE
build	01-Dec-2025 13:27:19	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	01-Dec-2025 13:27:19	│jalview:testTask0 results: FAILURE (1829 tests, 1828 successes, 1 failures, 0 skipped) in 4 minutes, 49.534 seconds   │
build	01-Dec-2025 13:27:19	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask0/index.html│
build	01-Dec-2025 13:27:19	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	01-Dec-2025 13:27:19	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 36.450 seconds       │
build	01-Dec-2025 13:27:19	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask1/index.html│
build	01-Dec-2025 13:27:19	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	01-Dec-2025 13:27:19	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.050 seconds                     │
build	01-Dec-2025 13:27:19	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask2/index.html│
build	01-Dec-2025 13:27:19	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	01-Dec-2025 13:27:19	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 4.363 seconds        │
build	01-Dec-2025 13:27:19	│Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/testTask3/index.html│
build	01-Dec-2025 13:27:19	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	01-Dec-2025 13:27:19	│OVERALL: results: FAILURE (1917 tests, 1916 successes, 1 failures, 0 skipped) in 7 minutes, 94.397 seconds            │
build	01-Dec-2025 13:27:19	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	01-Dec-2025 13:27:19	
build	01-Dec-2025 13:27:19	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	01-Dec-2025 13:27:19	
build	01-Dec-2025 13:27:19	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	01-Dec-2025 13:27:19	
build	01-Dec-2025 13:27:19	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	01-Dec-2025 13:27:19	
build	01-Dec-2025 13:27:19	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	01-Dec-2025 13:27:19	Please consult deprecation warnings for more details.
build	01-Dec-2025 13:27:19	21 actionable tasks: 20 executed, 1 up-to-date
simple	01-Dec-2025 13:27:19	
simple	01-Dec-2025 13:27:19	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	01-Dec-2025 13:27:19	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	01-Dec-2025 13:27:19	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	01-Dec-2025 13:27:19	Bamboo Artifactory Plugin version: 2.6.2
command	01-Dec-2025 13:27:19	Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests #8 (JB-GDB722-JOB1-8)'\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-GDB722-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_repository_revision_number=cc05d28187e3100fd060e6b7e3b1795477c23e62\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB722-JOB1-8\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-GDB722-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB722-JOB1\nbamboo_repository_46498555_previous_revision_number=5579c7411432a1b978a885bb1addf5853f0f3fd4\nbamboo_shortPlanName=bug-JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=8\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-GDB722-JOB1-8\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498555_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_shortPlanKey=GDB722\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=cc05d28187e3100fd060e6b7e3b1795477c23e62\nbamboo_buildTimeStamp=2025-12-01T13:17:14.539Z\nbamboo_repository_previous_revision_number=5579c7411432a1b978a885bb1addf5853f0f3fd4\nbamboo_planRepository_previousRevision=5579c7411432a1b978a885bb1addf5853f0f3fd4\nbamboo_repository_git_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_buildResultKey=JB-GDB722-JOB1-8\nbamboo_repository_branch_name=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=cc05d28187e3100fd060e6b7e3b1795477c23e62\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498555_git_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\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/\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-4603_export_svg_files_missing_part_of_sequence\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=5579c7411432a1b978a885bb1addf5853f0f3fd4\nbamboo_planRepository_branchDisplayName=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4603_export_svg_files_missing_part_of_sequence\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498555_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302681\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-GDB722-JOB1\nbamboo_planKey=JB-GDB722\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498555_name=Jalview Gitlab\nbamboo_repository_46498555_revision_number=cc05d28187e3100fd060e6b7e3b1795477c23e62\nbamboo_repository_46498555_branch_name=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	01-Dec-2025 13:27:19	444
build	01-Dec-2025 13:27:26	
build	01-Dec-2025 13:27:26	> Configure project :
build	01-Dec-2025 13:27:26	Using properties from file './utils/channels/default/channel_gradle.properties'
build	01-Dec-2025 13:27:26	JALVIEW_VERSION is set to '2.11.5.1'
build	01-Dec-2025 13:27:26	HEADLESS BUILD
build	01-Dec-2025 13:27:26	J2S ENABLED
build	01-Dec-2025 13:27:27	Using a LOCAL profile.
build	01-Dec-2025 13:27:28	eclipseDir exists
build	01-Dec-2025 13:27:30	
build	01-Dec-2025 13:27:30	> Task :cloverHtmlReport
build	01-Dec-2025 13:27:30	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	01-Dec-2025 13:27:33	Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/clover'
build	01-Dec-2025 13:28:28	Done. Processed 117 packages in 55256ms (472ms per package).
build	01-Dec-2025 13:28:34	
build	01-Dec-2025 13:28:34	> Task :cloverXmlReport
build	01-Dec-2025 13:28:34	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	01-Dec-2025 13:28:37	Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/clover/clover.xml'
build	01-Dec-2025 13:28:37	
build	01-Dec-2025 13:28:37	> Task :cloverReport
build	01-Dec-2025 13:28:37	
build	01-Dec-2025 13:28:37	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	01-Dec-2025 13:28:37	
build	01-Dec-2025 13:28:37	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	01-Dec-2025 13:28:37	
build	01-Dec-2025 13:28:37	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	01-Dec-2025 13:28:37	
build	01-Dec-2025 13:28:37	BUILD SUCCESSFUL in 1m 17s
build	01-Dec-2025 13:28:37	2 actionable tasks: 2 executed
simple	01-Dec-2025 13:28:37	Finished task 'Clover Report' with result: Success
simple	01-Dec-2025 13:28:37	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	01-Dec-2025 13:28:37	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1...
simple	01-Dec-2025 13:28:38	Failing task since 1 failing test cases were found.
simple	01-Dec-2025 13:28:38	Finished task 'TestNG Parser' with result: Failed
simple	01-Dec-2025 13:28:38	Running post build plugin 'NCover Results Collector'
simple	01-Dec-2025 13:28:38	Running post build plugin 'Artifact Copier'
simple	01-Dec-2025 13:28:38	Publishing an artifact: Clover Report (System)
simple	01-Dec-2025 13:28:43	Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 5.139 s
simple	01-Dec-2025 13:28:43	Publishing an artifact: TestNG report
error	01-Dec-2025 13:28:43	Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB722-JOB1/build/reports/tests/test does not exist.
simple	01-Dec-2025 13:28:43	The artifact hasn't been successfully published after 4.108 ms
simple	01-Dec-2025 13:28:43	Running post build plugin 'Artifactory Release Management Staging'
simple	01-Dec-2025 13:28:43	Running post build plugin 'Artifactory Build Info Copier'
simple	01-Dec-2025 13:28:43	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	01-Dec-2025 13:28:43	Running post build plugin 'npm Cache Cleanup'
simple	01-Dec-2025 13:28:43	Running post build plugin 'Clover Results Collector'
simple	01-Dec-2025 13:28:43	Running post build plugin 'Docker Container Cleanup'
simple	01-Dec-2025 13:28:43	Finalising the build...
simple	01-Dec-2025 13:28:43	Stopping timer.
simple	01-Dec-2025 13:28:43	Build JB-GDB722-JOB1-8 completed.
simple	01-Dec-2025 13:28:43	Running on server: post build plugin 'NCover Results Collector'
simple	01-Dec-2025 13:28:43	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	01-Dec-2025 13:28:43	Running on server: post build plugin 'Clover Delta Calculator'
simple	01-Dec-2025 13:28:43	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	01-Dec-2025 13:28:43	All post build plugins have finished
simple	01-Dec-2025 13:28:43	Generating build results summary...
simple	01-Dec-2025 13:28:44	Saving build results to disk...
simple	01-Dec-2025 13:28:44	Logging substituted variables...
simple	01-Dec-2025 13:28:44	Indexing build results...
simple	01-Dec-2025 13:28:44	Finished building JB-GDB722-JOB1-8.