simple	13-Feb-2026 14:16:17	Build Jalview Builds - Getdown Plan Channel - Default Job #358 (JB-GPC-JOB1-358) started building on agent Default Agent
simple	13-Feb-2026 14:16:17	
simple	13-Feb-2026 14:16:17	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1
simple	13-Feb-2026 14:16:17	Executing build Jalview Builds - Getdown Plan Channel - Default Job #358 (JB-GPC-JOB1-358)
simple	13-Feb-2026 14:16:17	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	13-Feb-2026 14:16:17	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1
simple	13-Feb-2026 14:16:17	Updating source code to revision: 42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9
simple	13-Feb-2026 14:16:17	Fetching 'refs/heads/main' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	13-Feb-2026 14:16:17	Checking out revision 42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9.
simple	13-Feb-2026 14:16:17	error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
simple	13-Feb-2026 14:16:17	error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
simple	13-Feb-2026 14:16:18	error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
simple	13-Feb-2026 14:16:18	error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
simple	13-Feb-2026 14:16:18	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	13-Feb-2026 14:16:18	   87afc89..42e19e3  main       -> origin/main
simple	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4107_jalviewjs_fixes_on_2_12_branch -> origin/bug/JAL-4107_jalviewjs_fixes_on_2_12_branch
simple	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4559_old_cli_args_in_JVL_docs -> origin/bug/JAL-4559_old_cli_args_in_JVL_docs
simple	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest -> origin/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest
simple	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4594_ss_consensus_overlap_other_annot -> origin/bug/JAL-4594_ss_consensus_overlap_other_annot
simple	13-Feb-2026 14:16:18	 * [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	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4603_Export_files_missing_part_of_sequence -> origin/bug/JAL-4603_Export_files_missing_part_of_sequence
simple	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4603_export_svg_files_missing_part_of_sequence -> origin/bug/JAL-4603_export_svg_files_missing_part_of_sequence
simple	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection -> origin/bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
simple	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4606_Jmol_incorrect_path_on_windows -> origin/bug/JAL-4606_Jmol_incorrect_path_on_windows
simple	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4610_rightColumn_wrappedWidth_fails -> origin/bug/JAL-4610_rightColumn_wrappedWidth_fails
simple	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 -> origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12
simple	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4611_SSConsensus_Preferences -> origin/bug/JAL-4611_SSConsensus_Preferences
simple	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4623_JAL-4624_PCA_for_SS -> origin/bug/JAL-4623_JAL-4624_PCA_for_SS
simple	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4624_JAL-4623_Mul_SS_in_PCA -> origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA
simple	13-Feb-2026 14:16:18	 * [new branch]      bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch -> origin/bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch
simple	13-Feb-2026 14:16:18	 * [new branch]      citation.cff -> origin/citation.cff
simple	13-Feb-2026 14:16:18	   da33043..e193345  development/JAL-4107_merge_2115_212 -> origin/development/JAL-4107_merge_2115_212
simple	13-Feb-2026 14:16:18	 * [new branch]      development/JAL-4576_ligysis -> origin/development/JAL-4576_ligysis
simple	13-Feb-2026 14:16:18	   2c0064b..5a35253  development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch
simple	13-Feb-2026 14:16:18	 * [new branch]      development/Release_2_12_Branch -> origin/development/Release_2_12_Branch
simple	13-Feb-2026 14:16:18	 * [new branch]      epic/JAL-3907_jalview_running_under_java_17 -> origin/epic/JAL-3907_jalview_running_under_java_17
simple	13-Feb-2026 14:16:18	 * [new branch]      epic/JAL-4320_gradle_upgrade_to_gradle9 -> origin/epic/JAL-4320_gradle_upgrade_to_gradle9
simple	13-Feb-2026 14:16:18	 * [new branch]      feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp -> origin/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp
simple	13-Feb-2026 14:16:18	 * [new branch]      feature/JAL-4521_Allow_PCA_tree_for_one_seq_mul_ss -> origin/feature/JAL-4521_Allow_PCA_tree_for_one_seq_mul_ss
simple	13-Feb-2026 14:16:18	 * [new branch]      feature/JAL-4602_Hide_All_SS_consensus_for_single_provider -> origin/feature/JAL-4602_Hide_All_SS_consensus_for_single_provider
simple	13-Feb-2026 14:16:18	 * [new branch]      feature/JAL-835_hhsuite_a3m_support -> origin/feature/JAL-835_hhsuite_a3m_support
simple	13-Feb-2026 14:16:18	 * [new branch]      improvement/JAL-4607_install4j_dark_mode_background_colour -> origin/improvement/JAL-4607_install4j_dark_mode_background_colour
simple	13-Feb-2026 14:16:18	 * [new branch]      improvement/JAL-4620_faster_sim_matrices -> origin/improvement/JAL-4620_faster_sim_matrices
simple	13-Feb-2026 14:16:18	 * [new branch]      patch/JAL-4107_singleThreadTests -> origin/patch/JAL-4107_singleThreadTests
simple	13-Feb-2026 14:16:18	 * [new branch]      patch/JAL-4601_stk_ss_annots_showhide -> origin/patch/JAL-4601_stk_ss_annots_showhide
simple	13-Feb-2026 14:16:18	 * [new branch]      patch/JAL-4606_again_and_again -> origin/patch/JAL-4606_again_and_again
simple	13-Feb-2026 14:16:18	 * [new branch]      patch/JAL-4626_alphafoldVersionTracker -> origin/patch/JAL-4626_alphafoldVersionTracker
simple	13-Feb-2026 14:16:18	   86d2c84..9e8107e  releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch
simple	13-Feb-2026 14:16:18	 * [new branch]      spike/JAL-4107_wrappedWidthCalcs -> origin/spike/JAL-4107_wrappedWidthCalcs
simple	13-Feb-2026 14:16:18	 * [new branch]      task/JAL-4645_JAL-4320_add_gradle_wrapper -> origin/task/JAL-4645_JAL-4320_add_gradle_wrapper
simple	13-Feb-2026 14:16:18	 * [new branch]      test/JAL-4603_test_for_JAL-4603_in_progress -> origin/test/JAL-4603_test_for_JAL-4603_in_progress
simple	13-Feb-2026 14:16:18	 * [new tag]         Release_2_11_5_1 -> Release_2_11_5_1
simple	13-Feb-2026 14:16:18	error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
simple	13-Feb-2026 14:16:18	Already on 'main'
simple	13-Feb-2026 14:16:18	Your branch is behind 'origin/main' by 103 commits, and can be fast-forwarded.
simple	13-Feb-2026 14:16:18	  (use "git pull" to update your local branch)
simple	13-Feb-2026 14:16:18	HEAD is now at 42e19e3 Merge branch 'releases/Release_2_11_5_Branch'
simple	13-Feb-2026 14:16:18	Updated source code to revision: 42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9
simple	13-Feb-2026 14:16:18	Finished task 'Checkout Default Repository' with result: Success
simple	13-Feb-2026 14:16:18	Running pre-build action: VCS Version Collector
simple	13-Feb-2026 14:16:18	Running pre-build action: Artifactory Release Staging
command	13-Feb-2026 14:16:18	Substituting variable: ${bamboo.planKey} with JB-GPC
simple	13-Feb-2026 14:16:18	Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	13-Feb-2026 14:16:18	Bamboo Artifactory Plugin version: 2.6.2
command	13-Feb-2026 14:16:18	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - Default Job #358 (JB-GPC-JOB1-358)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC clean shadowJar getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=main\nbamboo_dependency_parent_0=JB-GDB-706\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_dependency_parent_total=1\nbamboo_repository_46498248_git_branch=main\nbamboo_planRepository_1_branchDisplayName=main\nbamboo_repository_revision_number=42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC-JOB1-358\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-GPC-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GPC-JOB1\nbamboo_shortPlanName=Getdown Plan Channel\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=358\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC-JOB1-358\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown Plan Channel\nbamboo_shortPlanKey=GPC\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498248_branch_name=main\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9\nbamboo_buildTimeStamp=2026-02-13T14:16:17.303Z\nbamboo_repository_previous_revision_number=87afc897f4ab4cf704d7e1c000421e81e0464919\nbamboo_repository_git_branch=main\nbamboo_buildResultKey=JB-GPC-JOB1-358\nbamboo_repository_branch_name=main\nbamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9\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/\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=main\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46498248_previous_revision_number=87afc897f4ab4cf704d7e1c000421e81e0464919\nbamboo_repository_46498248_name=Jalview Gitlab\nbamboo_planRepository_branchDisplayName=main\nbamboo_repository_46498248_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=main\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-8978517\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_repository_46498248_git_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_46498248_revision_number=42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9\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-GPC-JOB1\nbamboo_planKey=JB-GPC\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=main\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	13-Feb-2026 14:16:20	
build	13-Feb-2026 14:16:20	> Configure project :
build	13-Feb-2026 14:16:20	Using properties from file './utils/channels/default/channel_gradle.properties'
build	13-Feb-2026 14:16:20	JALVIEW_VERSION is set to '2.11.5.1'
build	13-Feb-2026 14:16:20	HEADLESS BUILD
build	13-Feb-2026 14:16:20	J2S ENABLED
build	13-Feb-2026 14:16:20	Using a BUILD profile.
build	13-Feb-2026 14:16:20	eclipseDir exists
build	13-Feb-2026 14:16:21	
build	13-Feb-2026 14:16:21	> Task :clean
build	13-Feb-2026 14:16:21	> Task :cleanPackageDir
build	13-Feb-2026 14:16:21	> Task :copyHelp
build	13-Feb-2026 14:16:22	> Task :buildIndices
build	13-Feb-2026 14:16:22	> Task :copyResources
build	13-Feb-2026 14:16:22	> Task :copyChannelResources
build	13-Feb-2026 14:16:23	
build	13-Feb-2026 14:16:23	> Task :createBuildProperties
build	13-Feb-2026 14:16:23	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	13-Feb-2026 14:16:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-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	13-Feb-2026 14:16:23	
build	13-Feb-2026 14:16:23	> Task :buildResources
build	13-Feb-2026 14:16:23	> Task :copyDocs
build	13-Feb-2026 14:16:23	
build	13-Feb-2026 14:16:23	> Task :convertMdFiles
build	13-Feb-2026 14:16:23	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	13-Feb-2026 14:16:23	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	13-Feb-2026 14:16:23	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	13-Feb-2026 14:16:23	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/building.html
build	13-Feb-2026 14:16:23	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	13-Feb-2026 14:16:23	
build	13-Feb-2026 14:16:23	> Task :releasesTemplates
build	13-Feb-2026 14:16:23	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	13-Feb-2026 14:16:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-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	13-Feb-2026 14:16:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-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	13-Feb-2026 14:16:23	Stripping rc/test/etc for 2_11_5_1
build	13-Feb-2026 14:16:23	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md
build	13-Feb-2026 14:16:23	
build	13-Feb-2026 14:16:23	> Task :prepare
build	13-Feb-2026 14:16:25	
build	13-Feb-2026 14:16:25	> Task :compileJava
build	13-Feb-2026 14:16:25	Setting target compatibility to 11
error	13-Feb-2026 14:16:31	Note: Some input files use or override a deprecated API.
error	13-Feb-2026 14:16:31	Note: Recompile with -Xlint:deprecation for details.
error	13-Feb-2026 14:16:31	Note: Some input files use unchecked or unsafe operations.
error	13-Feb-2026 14:16:31	Note: Recompile with -Xlint:unchecked for details.
build	13-Feb-2026 14:16:32	
build	13-Feb-2026 14:16:32	> Task :processResources
build	13-Feb-2026 14:16:32	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	13-Feb-2026 14:16:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build'. Reason: Task ':processResources' 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	13-Feb-2026 14:16:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build'. Reason: Task ':processResources' 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	13-Feb-2026 14:16:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/help_build'. Reason: Task ':processResources' 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	13-Feb-2026 14:16:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/help_build'. Reason: Task ':processResources' 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	13-Feb-2026 14:16:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/help_build'. Reason: Task ':processResources' 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	13-Feb-2026 14:16:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/resources_build'. Reason: Task ':processResources' 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	13-Feb-2026 14:16:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/resources_build'. Reason: Task ':processResources' 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	13-Feb-2026 14:16:32	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/resources_build'. Reason: Task ':processResources' 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	13-Feb-2026 14:16:32	
build	13-Feb-2026 14:16:32	> Task :classes
build	13-Feb-2026 14:16:33	
build	13-Feb-2026 14:16:33	> Task :compileLinkCheck
build	13-Feb-2026 14:16:33	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	13-Feb-2026 14:16:33	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' 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	13-Feb-2026 14:16:33	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' 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	13-Feb-2026 14:16:33	
build	13-Feb-2026 14:16:33	> Task :linkCheck
build	13-Feb-2026 14:16:33	Checking help file links
build	13-Feb-2026 14:16:33	
build	13-Feb-2026 14:16:33	Results:
build	13-Feb-2026 14:16:33	161 distinct help targets
build	13-Feb-2026 14:16:33	161 help mappings
build	13-Feb-2026 14:16:33	0 invalid targets
build	13-Feb-2026 14:16:33	31 unused targets
build	13-Feb-2026 14:16:33	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	13-Feb-2026 14:16:33	    overviewprefs: html/features/preferences.html#overview
build	13-Feb-2026 14:16:33	    cdnafeatures: html/features/codingfeatures.html
build	13-Feb-2026 14:16:33	    startupprefs: html/features/preferences.html#startup
build	13-Feb-2026 14:16:33	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	13-Feb-2026 14:16:33	    io.modellerpir: html/io/modellerpir.html
build	13-Feb-2026 14:16:33	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	13-Feb-2026 14:16:33	    pdbmcviewer: html/features/pdbviewer.html
build	13-Feb-2026 14:16:33	    groovy.colours: html/features/groovy.html#groovyColours
build	13-Feb-2026 14:16:33	    seqmappings: html/features/seqmappings.html
build	13-Feb-2026 14:16:33	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	13-Feb-2026 14:16:33	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	13-Feb-2026 14:16:33	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	13-Feb-2026 14:16:33	    search: html/features/search.html
build	13-Feb-2026 14:16:33	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	13-Feb-2026 14:16:33	    alformats: html/io/fileformats.html
build	13-Feb-2026 14:16:33	    strucprefs: html/features/preferences.html#structure
build	13-Feb-2026 14:16:33	    siftsmapping: html/features/siftsmapping.html
build	13-Feb-2026 14:16:33	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	13-Feb-2026 14:16:33	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	13-Feb-2026 14:16:33	    newkeys: html/features/newkeystrokes.html
build	13-Feb-2026 14:16:33	    importvcf.attribs: html/features/importvcf.html#attribs
build	13-Feb-2026 14:16:33	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	13-Feb-2026 14:16:33	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	13-Feb-2026 14:16:33	    jalarchive: html/features/jalarchive.html
build	13-Feb-2026 14:16:33	    newsreader: html/webServices/newsreader.html
build	13-Feb-2026 14:16:33	    jalviewcltool: html/features/commandline.html#script
build	13-Feb-2026 14:16:33	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	13-Feb-2026 14:16:33	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	13-Feb-2026 14:16:33	    paematrixformat: html/io/paematrixformat.html
build	13-Feb-2026 14:16:33	    overview: html/features/overview.html
build	13-Feb-2026 14:16:33	0 invalid map urls
build	13-Feb-2026 14:16:33	0 invalid image attributes
build	13-Feb-2026 14:16:33	520 internal href links (120 with anchors)
build	13-Feb-2026 14:16:33	0 invalid internal href links
build	13-Feb-2026 14:16:33	0 invalid internal anchor links
build	13-Feb-2026 14:16:33	112 external href links
build	13-Feb-2026 14:16:33	External links not verified as internet not available
build	13-Feb-2026 14:16:33	*** Success ***
build	13-Feb-2026 14:16:34	
build	13-Feb-2026 14:16:34	> Task :jar
build	13-Feb-2026 14:16:34	> Task :syncJars
build	13-Feb-2026 14:16:34	> Task :makeDist
build	13-Feb-2026 14:16:42	> Task :shadowJar
build	13-Feb-2026 14:16:42	
build	13-Feb-2026 14:16:42	> Task :getdownImagesCopy
build	13-Feb-2026 14:16:42	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	13-Feb-2026 14:16:42	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/utils/channels/default/images'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' 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	13-Feb-2026 14:16:43	
build	13-Feb-2026 14:16:43	> Task :getdownImagesProcess
build	13-Feb-2026 14:16:43	> Task :getdownImages
build	13-Feb-2026 14:16:43	> Task :getdownWebsiteBuild
build	13-Feb-2026 14:16:45	
build	13-Feb-2026 14:16:45	> Task :getdownDigest
build	13-Feb-2026 14:16:45	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
build	13-Feb-2026 14:16:45	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	13-Feb-2026 14:16:45	
build	13-Feb-2026 14:16:45	> Task :getdown
build	13-Feb-2026 14:16:45	
build	13-Feb-2026 14:16:45	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	13-Feb-2026 14:16:45	
build	13-Feb-2026 14:16:45	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	13-Feb-2026 14:16:45	
build	13-Feb-2026 14:16:45	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	13-Feb-2026 14:16:45	
build	13-Feb-2026 14:16:45	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	13-Feb-2026 14:16:45	Please consult deprecation warnings for more details.
build	13-Feb-2026 14:16:45	
build	13-Feb-2026 14:16:45	BUILD SUCCESSFUL in 26s
build	13-Feb-2026 14:16:45	22 actionable tasks: 22 executed
error	13-Feb-2026 14:16:45	2026/02/13 14:16:43:707 WARNING Starting without install4j classes
error	13-Feb-2026 14:16:45	2026/02/13 14:16:44:407 WARNING Starting without install4j classes
simple	13-Feb-2026 14:16:45	Finished task 'Jalview distribution for Java 11' with result: Success
simple	13-Feb-2026 14:16:45	Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled
simple	13-Feb-2026 14:16:45	Running post build plugin 'NCover Results Collector'
simple	13-Feb-2026 14:16:45	Running post build plugin 'Artifact Copier'
simple	13-Feb-2026 14:16:45	Publishing an artifact: Jalview executables
simple	13-Feb-2026 14:16:45	Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 96.62 ms
simple	13-Feb-2026 14:16:45	Publishing an artifact: install4j installers
error	13-Feb-2026 14:16:45	Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/install4j does not exist.
simple	13-Feb-2026 14:16:45	The artifact hasn't been successfully published after 2.380 ms
simple	13-Feb-2026 14:16:45	Publishing an artifact: getdown-channel
error	13-Feb-2026 14:16:45	Unable to publish artifact [getdown-channel]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/getdown/website does not exist.
simple	13-Feb-2026 14:16:45	The artifact hasn't been successfully published after 81.13 μs
simple	13-Feb-2026 14:16:45	Publishing an artifact: Jalview getdown launcher
error	13-Feb-2026 14:16:45	Unable to publish artifact [Jalview getdown launcher]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/getdown/files does not exist.
simple	13-Feb-2026 14:16:45	The artifact hasn't been successfully published after 43.60 μs
simple	13-Feb-2026 14:16:45	Publishing an artifact: getdown build for website
simple	13-Feb-2026 14:16:45	Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 184.7 ms
simple	13-Feb-2026 14:16:45	Publishing an artifact: getdown build for archive
error	13-Feb-2026 14:16:45	Unable to publish artifact [getdown build for archive]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/website/docroot/old does not exist.
simple	13-Feb-2026 14:16:45	The artifact hasn't been successfully published after 79.96 μs
simple	13-Feb-2026 14:16:45	Running post build plugin 'Artifactory Release Management Staging'
simple	13-Feb-2026 14:16:45	Running post build plugin 'Artifactory Build Info Copier'
simple	13-Feb-2026 14:16:45	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	13-Feb-2026 14:16:45	Running post build plugin 'npm Cache Cleanup'
simple	13-Feb-2026 14:16:45	Running post build plugin 'Clover Results Collector'
simple	13-Feb-2026 14:16:45	Running post build plugin 'Docker Container Cleanup'
simple	13-Feb-2026 14:16:45	Finalising the build...
simple	13-Feb-2026 14:16:45	Stopping timer.
simple	13-Feb-2026 14:16:45	Build JB-GPC-JOB1-358 completed.
simple	13-Feb-2026 14:16:45	Running on server: post build plugin 'NCover Results Collector'
simple	13-Feb-2026 14:16:45	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	13-Feb-2026 14:16:45	Running on server: post build plugin 'Clover Delta Calculator'
simple	13-Feb-2026 14:16:45	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	13-Feb-2026 14:16:45	All post build plugins have finished
simple	13-Feb-2026 14:16:45	Generating build results summary...
simple	13-Feb-2026 14:16:45	Saving build results to disk...
simple	13-Feb-2026 14:16:45	Logging substituted variables...
simple	13-Feb-2026 14:16:45	Indexing build results...
simple	13-Feb-2026 14:16:45	Finished building JB-GPC-JOB1-358.