simple	17-Sep-2025 11:02:35	Build Jalview Builds - Getdown Plan Channel - Default Job #357 (JB-GPC-JOB1-357) started building on agent Default Agent
simple	17-Sep-2025 11:02:35	
simple	17-Sep-2025 11:02:35	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1
simple	17-Sep-2025 11:02:35	Executing build Jalview Builds - Getdown Plan Channel - Default Job #357 (JB-GPC-JOB1-357)
simple	17-Sep-2025 11:02:35	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	17-Sep-2025 11:02:35	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1
simple	17-Sep-2025 11:02:35	Updating source code to revision: 87afc897f4ab4cf704d7e1c000421e81e0464919
simple	17-Sep-2025 11:02:35	Fetching 'refs/heads/main' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	17-Sep-2025 11:02:36	Checking out revision 87afc897f4ab4cf704d7e1c000421e81e0464919.
simple	17-Sep-2025 11:02:36	error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
simple	17-Sep-2025 11:02:36	error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
simple	17-Sep-2025 11:02:36	error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
simple	17-Sep-2025 11:02:36	error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
simple	17-Sep-2025 11:02:36	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	17-Sep-2025 11:02:36	   a07a210..87afc89  main       -> origin/main
simple	17-Sep-2025 11:02:36	 * [new branch]      bug/JAL-4397_failing_test_on_macos_more_space_display_setting -> origin/bug/JAL-4397_failing_test_on_macos_more_space_display_setting
simple	17-Sep-2025 11:02:36	   9ce6176..8291b4c  bug/JAL-4507_Some_exported_annotations_being_reloaded_as_sequences -> origin/bug/JAL-4507_Some_exported_annotations_being_reloaded_as_sequences
simple	17-Sep-2025 11:02:36	 * [new branch]      bug/JAL-4530_applescript_to_detect_Applications_symlink -> origin/bug/JAL-4530_applescript_to_detect_Applications_symlink
simple	17-Sep-2025 11:02:36	 * [new branch]      bug/JAL-4568_r2_11_4_2_jmol_image_deadlock -> origin/bug/JAL-4568_r2_11_4_2_jmol_image_deadlock
simple	17-Sep-2025 11:02:36	 * [new branch]      development/JAL-4107_merge_2115_212 -> origin/development/JAL-4107_merge_2115_212
simple	17-Sep-2025 11:02:36	   13316f6..2c0064b  development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch
simple	17-Sep-2025 11:02:36	 * [new branch]      feature/JAL-4435_JAL-4509_JAL-4542_JAL-4518_documentation -> origin/feature/JAL-4435_JAL-4509_JAL-4542_JAL-4518_documentation
simple	17-Sep-2025 11:02:36	 * [new branch]      feature/JAL-4515_Group_colouring_as_background -> origin/feature/JAL-4515_Group_colouring_as_background
simple	17-Sep-2025 11:02:36	 * [new branch]      feature/JAL-4528_check_min_no_annotations_for_tree -> origin/feature/JAL-4528_check_min_no_annotations_for_tree
simple	17-Sep-2025 11:02:36	 * [new branch]      feature/JAL-4542_highlight_selected_annot_labels_tree_nodes -> origin/feature/JAL-4542_highlight_selected_annot_labels_tree_nodes
simple	17-Sep-2025 11:02:36	 * [new branch]      feature/JAL-4548_show_PDBID_metadata_for_annot_tree -> origin/feature/JAL-4548_show_PDBID_metadata_for_annot_tree
simple	17-Sep-2025 11:02:36	 * [new branch]      feature/JAL-4583_incorrect_seq_count_ss_consensus -> origin/feature/JAL-4583_incorrect_seq_count_ss_consensus
simple	17-Sep-2025 11:02:36	 * [new branch]      feature/JAL_4542_highlight_selected_annot_labels_tree_nodes -> origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes
simple	17-Sep-2025 11:02:36	   f2ebc57..1d05b7e  feature/JAL_4548_show_PDBID_metadata_for_annot_tree -> origin/feature/JAL_4548_show_PDBID_metadata_for_annot_tree
simple	17-Sep-2025 11:02:36	 * [new branch]      features/JAL-4219_extended_fasta_rna_ss -> origin/features/JAL-4219_extended_fasta_rna_ss
simple	17-Sep-2025 11:02:36	 * [new branch]      features/JAL-4587_colour_group_annotation -> origin/features/JAL-4587_colour_group_annotation
simple	17-Sep-2025 11:02:36	 * [new branch]      improvement/JAL-4354_allow_many_structures_to_be_loaded_and_viewed_via_command_line -> origin/improvement/JAL-4354_allow_many_structures_to_be_loaded_and_viewed_via_command_line
simple	17-Sep-2025 11:02:36	   19317e1..4a59ca7  improvement/JAL-4530_add_applescript_to_allow_installation_to_home_applications_folder -> origin/improvement/JAL-4530_add_applescript_to_allow_installation_to_home_applications_folder
simple	17-Sep-2025 11:02:36	   20d3b89..f0d0210  improvement/JAL-4541_slight_increase_in_robustness_of_analytics_from_jalview_desktop -> origin/improvement/JAL-4541_slight_increase_in_robustness_of_analytics_from_jalview_desktop
simple	17-Sep-2025 11:02:36	 * [new branch]      improvement/JAL-4560_handle_relative_paths_in_jvl_files -> origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files
simple	17-Sep-2025 11:02:36	 * [new branch]      improvement/JAL-4570_show_tree_above_alignmentview -> origin/improvement/JAL-4570_show_tree_above_alignmentview
simple	17-Sep-2025 11:02:36	 * [new branch]      patch/JAL-3987_pergroup_annotation_consensus -> origin/patch/JAL-3987_pergroup_annotation_consensus
simple	17-Sep-2025 11:02:36	 * [new branch]      patch/JAL-4414_for_2_11_5_Branch -> origin/patch/JAL-4414_for_2_11_5_Branch
simple	17-Sep-2025 11:02:36	   5b3d6da..d7fbd2a  patch/JAL-4555_sort_by_descr -> origin/patch/JAL-4555_sort_by_descr
simple	17-Sep-2025 11:02:36	 * [new branch]      patch/JAL-4590_remove_isBlank_use -> origin/patch/JAL-4590_remove_isBlank_use
simple	17-Sep-2025 11:02:36	 * [new branch]      patch_bits/JAL-4590_isBlank_PDB_ChainIssue -> origin/patch_bits/JAL-4590_isBlank_PDB_ChainIssue
simple	17-Sep-2025 11:02:36	   dd2df48..147e80c  releases/Release_2_11_4_Branch -> origin/releases/Release_2_11_4_Branch
simple	17-Sep-2025 11:02:36	 * [new branch]      releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch
simple	17-Sep-2025 11:02:36	 * [new branch]      spike/JAL-4576_ligysis_exploration -> origin/spike/JAL-4576_ligysis_exploration
simple	17-Sep-2025 11:02:36	 * [new branch]      update/JAL-4243_biotools_json_record -> origin/update/JAL-4243_biotools_json_record
simple	17-Sep-2025 11:02:36	 * [new tag]         Release_2_11_5_0 -> Release_2_11_5_0
simple	17-Sep-2025 11:02:36	error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object!
simple	17-Sep-2025 11:02:39	Your branch is behind 'origin/main' by 378 commits, and can be fast-forwarded.
simple	17-Sep-2025 11:02:39	  (use "git pull" to update your local branch)
simple	17-Sep-2025 11:02:39	Already on 'main'
simple	17-Sep-2025 11:02:40	HEAD is now at 87afc89 Merge tag 'Release_2_11_5_0'
simple	17-Sep-2025 11:02:40	Updated source code to revision: 87afc897f4ab4cf704d7e1c000421e81e0464919
simple	17-Sep-2025 11:02:40	Finished task 'Checkout Default Repository' with result: Success
simple	17-Sep-2025 11:02:40	Running pre-build action: VCS Version Collector
simple	17-Sep-2025 11:02:40	Running pre-build action: Artifactory Release Staging
command	17-Sep-2025 11:02:40	Substituting variable: ${bamboo.planKey} with JB-GPC
simple	17-Sep-2025 11:02:40	Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	17-Sep-2025 11:02:40	Bamboo Artifactory Plugin version: 2.6.2
command	17-Sep-2025 11:02:40	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - Default Job #357 (JB-GPC-JOB1-357)'\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-705\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=87afc897f4ab4cf704d7e1c000421e81e0464919\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC-JOB1-357\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=357\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-JOB1-357\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=87afc897f4ab4cf704d7e1c000421e81e0464919\nbamboo_buildTimeStamp=2025-09-17T11:02:35.766+01:00\nbamboo_repository_previous_revision_number=a07a210e39b574048817742f680ad4bbcebb590c\nbamboo_repository_git_branch=main\nbamboo_buildResultKey=JB-GPC-JOB1-357\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=87afc897f4ab4cf704d7e1c000421e81e0464919\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=a07a210e39b574048817742f680ad4bbcebb590c\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=87afc897f4ab4cf704d7e1c000421e81e0464919\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	17-Sep-2025 11:02:42	
build	17-Sep-2025 11:02:42	> Configure project :
build	17-Sep-2025 11:02:42	Using properties from file './utils/channels/default/channel_gradle.properties'
build	17-Sep-2025 11:02:42	JALVIEW_VERSION is set to '2.11.5.0'
build	17-Sep-2025 11:02:42	HEADLESS BUILD
build	17-Sep-2025 11:02:42	J2S ENABLED
build	17-Sep-2025 11:02:42	Using a BUILD profile.
build	17-Sep-2025 11:02:42	eclipseDir exists
build	17-Sep-2025 11:02:42	
build	17-Sep-2025 11:02:42	> Task :clean
build	17-Sep-2025 11:02:42	> Task :cleanPackageDir
build	17-Sep-2025 11:02:43	> Task :copyHelp
build	17-Sep-2025 11:02:44	> Task :buildIndices
build	17-Sep-2025 11:02:44	> Task :copyResources
build	17-Sep-2025 11:02:44	> Task :copyChannelResources
build	17-Sep-2025 11:02:44	
build	17-Sep-2025 11:02:44	> Task :createBuildProperties
build	17-Sep-2025 11:02:44	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	17-Sep-2025 11:02:44	  - 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	17-Sep-2025 11:02:44	
build	17-Sep-2025 11:02:44	> Task :buildResources
build	17-Sep-2025 11:02:44	> Task :copyDocs
build	17-Sep-2025 11:02:44	
build	17-Sep-2025 11:02:44	> Task :convertMdFiles
build	17-Sep-2025 11:02:44	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	17-Sep-2025 11:02:44	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	17-Sep-2025 11:02:44	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	17-Sep-2025 11:02:44	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/building.html
build	17-Sep-2025 11:02:44	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	17-Sep-2025 11:02:44	
build	17-Sep-2025 11:02:44	> Task :releasesTemplates
build	17-Sep-2025 11:02:44	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	17-Sep-2025 11:02:44	  - 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	17-Sep-2025 11:02:44	  - 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	17-Sep-2025 11:02:44	Stripping rc/test/etc for 2_11_5_0
build	17-Sep-2025 11:02:44	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_0.md
build	17-Sep-2025 11:02:44	
build	17-Sep-2025 11:02:44	> Task :prepare
build	17-Sep-2025 11:02:46	
build	17-Sep-2025 11:02:46	> Task :compileJava
build	17-Sep-2025 11:02:46	Setting target compatibility to 11
error	17-Sep-2025 11:02:53	Note: Some input files use or override a deprecated API.
error	17-Sep-2025 11:02:53	Note: Recompile with -Xlint:deprecation for details.
error	17-Sep-2025 11:02:53	Note: Some input files use unchecked or unsafe operations.
error	17-Sep-2025 11:02:53	Note: Recompile with -Xlint:unchecked for details.
build	17-Sep-2025 11:02:54	
build	17-Sep-2025 11:02:54	> Task :processResources
build	17-Sep-2025 11:02:54	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	17-Sep-2025 11:02:54	  - 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	17-Sep-2025 11:02:54	  - 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	17-Sep-2025 11:02:54	  - 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	17-Sep-2025 11:02:54	  - 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	17-Sep-2025 11:02:54	  - 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	17-Sep-2025 11:02:54	  - 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	17-Sep-2025 11:02:54	  - 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	17-Sep-2025 11:02:54	  - 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	17-Sep-2025 11:02:54	
build	17-Sep-2025 11:02:54	> Task :classes
build	17-Sep-2025 11:02:56	
build	17-Sep-2025 11:02:56	> Task :compileLinkCheck
build	17-Sep-2025 11:02:56	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	17-Sep-2025 11:02:56	  - 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	17-Sep-2025 11:02:56	  - 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	17-Sep-2025 11:02:58	
build	17-Sep-2025 11:02:58	> Task :linkCheck
build	17-Sep-2025 11:02:58	Checking help file links
build	17-Sep-2025 11:05:04	
build	17-Sep-2025 11:05:04	Results:
build	17-Sep-2025 11:05:04	161 distinct help targets
build	17-Sep-2025 11:05:04	161 help mappings
build	17-Sep-2025 11:05:04	0 invalid targets
build	17-Sep-2025 11:05:04	31 unused targets
build	17-Sep-2025 11:05:04	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	17-Sep-2025 11:05:04	    overviewprefs: html/features/preferences.html#overview
build	17-Sep-2025 11:05:04	    cdnafeatures: html/features/codingfeatures.html
build	17-Sep-2025 11:05:04	    startupprefs: html/features/preferences.html#startup
build	17-Sep-2025 11:05:04	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	17-Sep-2025 11:05:04	    io.modellerpir: html/io/modellerpir.html
build	17-Sep-2025 11:05:04	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	17-Sep-2025 11:05:04	    pdbmcviewer: html/features/pdbviewer.html
build	17-Sep-2025 11:05:04	    groovy.colours: html/features/groovy.html#groovyColours
build	17-Sep-2025 11:05:04	    seqmappings: html/features/seqmappings.html
build	17-Sep-2025 11:05:04	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	17-Sep-2025 11:05:04	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	17-Sep-2025 11:05:04	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	17-Sep-2025 11:05:04	    search: html/features/search.html
build	17-Sep-2025 11:05:04	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	17-Sep-2025 11:05:04	    alformats: html/io/fileformats.html
build	17-Sep-2025 11:05:04	    strucprefs: html/features/preferences.html#structure
build	17-Sep-2025 11:05:04	    siftsmapping: html/features/siftsmapping.html
build	17-Sep-2025 11:05:04	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	17-Sep-2025 11:05:04	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	17-Sep-2025 11:05:04	    newkeys: html/features/newkeystrokes.html
build	17-Sep-2025 11:05:04	    importvcf.attribs: html/features/importvcf.html#attribs
build	17-Sep-2025 11:05:04	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	17-Sep-2025 11:05:04	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	17-Sep-2025 11:05:04	    jalarchive: html/features/jalarchive.html
build	17-Sep-2025 11:05:04	    newsreader: html/webServices/newsreader.html
build	17-Sep-2025 11:05:04	    jalviewcltool: html/features/commandline.html#script
build	17-Sep-2025 11:05:04	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	17-Sep-2025 11:05:04	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	17-Sep-2025 11:05:04	    paematrixformat: html/io/paematrixformat.html
build	17-Sep-2025 11:05:04	    overview: html/features/overview.html
build	17-Sep-2025 11:05:04	0 invalid map urls
build	17-Sep-2025 11:05:04	0 invalid image attributes
build	17-Sep-2025 11:05:04	520 internal href links (120 with anchors)
build	17-Sep-2025 11:05:04	0 invalid internal href links
build	17-Sep-2025 11:05:04	0 invalid internal anchor links
build	17-Sep-2025 11:05:04	112 external href links
build	17-Sep-2025 11:05:04	External links not verified as internet not available
build	17-Sep-2025 11:05:04	*** Success ***
build	17-Sep-2025 11:05:04	
build	17-Sep-2025 11:05:04	> Task :jar
build	17-Sep-2025 11:05:05	> Task :syncJars
build	17-Sep-2025 11:05:05	> Task :makeDist
build	17-Sep-2025 11:05:12	> Task :shadowJar
build	17-Sep-2025 11:05:12	
build	17-Sep-2025 11:05:12	> Task :getdownImagesCopy
build	17-Sep-2025 11:05:12	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	17-Sep-2025 11:05:12	  - 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	17-Sep-2025 11:05:13	
build	17-Sep-2025 11:05:13	> Task :getdownImagesProcess
build	17-Sep-2025 11:05:13	> Task :getdownImages
build	17-Sep-2025 11:05:13	> Task :getdownWebsiteBuild
build	17-Sep-2025 11:05:14	
build	17-Sep-2025 11:05:14	> Task :getdownDigest
build	17-Sep-2025 11:05:14	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
build	17-Sep-2025 11:05:14	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	17-Sep-2025 11:05:14	
build	17-Sep-2025 11:05:14	> Task :getdown
build	17-Sep-2025 11:05:14	
build	17-Sep-2025 11:05:14	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	17-Sep-2025 11:05:14	
build	17-Sep-2025 11:05:14	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	17-Sep-2025 11:05:14	
build	17-Sep-2025 11:05:14	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	17-Sep-2025 11:05:14	
build	17-Sep-2025 11:05:14	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	17-Sep-2025 11:05:14	Please consult deprecation warnings for more details.
build	17-Sep-2025 11:05:14	
build	17-Sep-2025 11:05:14	BUILD SUCCESSFUL in 2m 34s
build	17-Sep-2025 11:05:14	22 actionable tasks: 22 executed
error	17-Sep-2025 11:05:14	2025/09/17 11:05:13:750 WARNING Starting without install4j classes
error	17-Sep-2025 11:05:14	2025/09/17 11:05:14:312 WARNING Starting without install4j classes
simple	17-Sep-2025 11:05:15	Finished task 'Jalview distribution for Java 11' with result: Success
command	17-Sep-2025 11:05:15	Substituting variable: ${bamboo.planKey} with JB-GPC
simple	17-Sep-2025 11:05:15	Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	17-Sep-2025 11:05:15	Bamboo Artifactory Plugin version: 2.6.2
command	17-Sep-2025 11:05:15	Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - Default Job #357 (JB-GPC-JOB1-357)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -x clean -PCHANNEL=BUILD -PJAVA_VERSION=1.8 -Pbamboo_planKey=JB-GPC 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-705\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=87afc897f4ab4cf704d7e1c000421e81e0464919\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC-JOB1-357\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=357\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-JOB1-357\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=87afc897f4ab4cf704d7e1c000421e81e0464919\nbamboo_buildTimeStamp=2025-09-17T11:02:35.766+01:00\nbamboo_repository_previous_revision_number=a07a210e39b574048817742f680ad4bbcebb590c\nbamboo_repository_git_branch=main\nbamboo_buildResultKey=JB-GPC-JOB1-357\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=87afc897f4ab4cf704d7e1c000421e81e0464919\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/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC clean shadowJar getdown\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=a07a210e39b574048817742f680ad4bbcebb590c\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=87afc897f4ab4cf704d7e1c000421e81e0464919\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	17-Sep-2025 11:05:16	
build	17-Sep-2025 11:05:16	> Configure project :
build	17-Sep-2025 11:05:16	Using properties from file './utils/channels/default/channel_gradle.properties'
build	17-Sep-2025 11:05:16	JALVIEW_VERSION is set to '2.11.5.0'
build	17-Sep-2025 11:05:16	HEADLESS BUILD
build	17-Sep-2025 11:05:16	J2S ENABLED
build	17-Sep-2025 11:05:16	Using a BUILD profile.
build	17-Sep-2025 11:05:16	eclipseDir exists
build	17-Sep-2025 11:05:16	
build	17-Sep-2025 11:05:16	> Task :copyHelp UP-TO-DATE
build	17-Sep-2025 11:05:17	> Task :buildIndices
build	17-Sep-2025 11:05:17	> Task :copyResources UP-TO-DATE
build	17-Sep-2025 11:05:17	> Task :copyChannelResources UP-TO-DATE
build	17-Sep-2025 11:05:17	
build	17-Sep-2025 11:05:17	> Task :createBuildProperties
build	17-Sep-2025 11:05:17	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	17-Sep-2025 11:05:17	  - 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	17-Sep-2025 11:05:17	
build	17-Sep-2025 11:05:17	> Task :buildResources
build	17-Sep-2025 11:05:17	> Task :copyDocs
build	17-Sep-2025 11:05:17	
build	17-Sep-2025 11:05:17	> Task :convertMdFiles
build	17-Sep-2025 11:05:17	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	17-Sep-2025 11:05:17	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	17-Sep-2025 11:05:17	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	17-Sep-2025 11:05:17	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/building.html
build	17-Sep-2025 11:05:17	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	17-Sep-2025 11:05:18	
build	17-Sep-2025 11:05:18	> Task :releasesTemplates
build	17-Sep-2025 11:05:18	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	17-Sep-2025 11:05:18	  - 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	17-Sep-2025 11:05:18	  - 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	17-Sep-2025 11:05:18	Stripping rc/test/etc for 2_11_5_0
build	17-Sep-2025 11:05:18	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_0.md
build	17-Sep-2025 11:05:18	
build	17-Sep-2025 11:05:18	> Task :prepare
build	17-Sep-2025 11:05:20	
build	17-Sep-2025 11:05:20	> Task :compileJava
build	17-Sep-2025 11:05:20	Setting target compatibility to 1.8
error	17-Sep-2025 11:05:26	Note: Some input files use or override a deprecated API.
error	17-Sep-2025 11:05:26	Note: Recompile with -Xlint:deprecation for details.
error	17-Sep-2025 11:05:26	Note: Some input files use unchecked or unsafe operations.
error	17-Sep-2025 11:05:26	Note: Recompile with -Xlint:unchecked for details.
build	17-Sep-2025 11:05:29	
build	17-Sep-2025 11:05:29	> Task :processResources
build	17-Sep-2025 11:05:29	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	17-Sep-2025 11:05:29	  - 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	17-Sep-2025 11:05:29	  - 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	17-Sep-2025 11:05:29	  - 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	17-Sep-2025 11:05:29	  - 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	17-Sep-2025 11:05:29	  - 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	17-Sep-2025 11:05:29	  - 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	17-Sep-2025 11:05:29	  - 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	17-Sep-2025 11:05:29	  - 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	17-Sep-2025 11:05:29	
build	17-Sep-2025 11:05:29	> Task :classes
build	17-Sep-2025 11:05:29	> Task :cleanPackageDir
build	17-Sep-2025 11:05:30	
build	17-Sep-2025 11:05:30	> Task :compileLinkCheck
build	17-Sep-2025 11:05:30	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	17-Sep-2025 11:05:30	  - 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	17-Sep-2025 11:05:30	  - 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	17-Sep-2025 11:05:32	
build	17-Sep-2025 11:05:32	> Task :linkCheck
build	17-Sep-2025 11:05:32	Checking help file links
build	17-Sep-2025 11:07:38	
build	17-Sep-2025 11:07:38	Results:
build	17-Sep-2025 11:07:38	161 distinct help targets
build	17-Sep-2025 11:07:38	161 help mappings
build	17-Sep-2025 11:07:38	0 invalid targets
build	17-Sep-2025 11:07:38	31 unused targets
build	17-Sep-2025 11:07:38	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	17-Sep-2025 11:07:38	    overviewprefs: html/features/preferences.html#overview
build	17-Sep-2025 11:07:38	    cdnafeatures: html/features/codingfeatures.html
build	17-Sep-2025 11:07:38	    startupprefs: html/features/preferences.html#startup
build	17-Sep-2025 11:07:38	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	17-Sep-2025 11:07:38	    io.modellerpir: html/io/modellerpir.html
build	17-Sep-2025 11:07:38	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	17-Sep-2025 11:07:38	    pdbmcviewer: html/features/pdbviewer.html
build	17-Sep-2025 11:07:38	    groovy.colours: html/features/groovy.html#groovyColours
build	17-Sep-2025 11:07:38	    seqmappings: html/features/seqmappings.html
build	17-Sep-2025 11:07:38	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	17-Sep-2025 11:07:38	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	17-Sep-2025 11:07:38	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	17-Sep-2025 11:07:38	    search: html/features/search.html
build	17-Sep-2025 11:07:38	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	17-Sep-2025 11:07:38	    alformats: html/io/fileformats.html
build	17-Sep-2025 11:07:38	    strucprefs: html/features/preferences.html#structure
build	17-Sep-2025 11:07:38	    siftsmapping: html/features/siftsmapping.html
build	17-Sep-2025 11:07:38	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	17-Sep-2025 11:07:38	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	17-Sep-2025 11:07:38	    newkeys: html/features/newkeystrokes.html
build	17-Sep-2025 11:07:38	    importvcf.attribs: html/features/importvcf.html#attribs
build	17-Sep-2025 11:07:38	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	17-Sep-2025 11:07:38	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	17-Sep-2025 11:07:38	    jalarchive: html/features/jalarchive.html
build	17-Sep-2025 11:07:38	    newsreader: html/webServices/newsreader.html
build	17-Sep-2025 11:07:38	    jalviewcltool: html/features/commandline.html#script
build	17-Sep-2025 11:07:38	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	17-Sep-2025 11:07:38	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	17-Sep-2025 11:07:38	    paematrixformat: html/io/paematrixformat.html
build	17-Sep-2025 11:07:38	    overview: html/features/overview.html
build	17-Sep-2025 11:07:38	0 invalid map urls
build	17-Sep-2025 11:07:38	0 invalid image attributes
build	17-Sep-2025 11:07:38	520 internal href links (120 with anchors)
build	17-Sep-2025 11:07:38	0 invalid internal href links
build	17-Sep-2025 11:07:38	0 invalid internal anchor links
build	17-Sep-2025 11:07:38	112 external href links
build	17-Sep-2025 11:07:38	External links not verified as internet not available
build	17-Sep-2025 11:07:38	*** Success ***
build	17-Sep-2025 11:07:39	
build	17-Sep-2025 11:07:39	> Task :jar
build	17-Sep-2025 11:07:39	> Task :syncJars
build	17-Sep-2025 11:07:39	> Task :makeDist
build	17-Sep-2025 11:07:45	> Task :shadowJar
build	17-Sep-2025 11:07:45	
build	17-Sep-2025 11:07:45	> Task :getdownImagesCopy
build	17-Sep-2025 11:07:45	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	17-Sep-2025 11:07:45	  - 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	17-Sep-2025 11:07:46	
build	17-Sep-2025 11:07:46	> Task :getdownImagesProcess
build	17-Sep-2025 11:07:46	> Task :getdownImages
build	17-Sep-2025 11:07:46	> Task :getdownWebsiteBuild
error	17-Sep-2025 11:07:48	2025/09/17 11:07:46:555 WARNING Starting without install4j classes
build	17-Sep-2025 11:07:48	
build	17-Sep-2025 11:07:48	> Task :getdownDigest
build	17-Sep-2025 11:07:48	Generating digest file './build/website/docroot/getdown/default/1.8/digest.txt'...
build	17-Sep-2025 11:07:48	Generating digest file './build/website/docroot/getdown/default/1.8/digest2.txt'...
error	17-Sep-2025 11:07:48	2025/09/17 11:07:47:431 WARNING Starting without install4j classes
build	17-Sep-2025 11:07:48	
build	17-Sep-2025 11:07:48	> Task :getdown
build	17-Sep-2025 11:07:48	
build	17-Sep-2025 11:07:48	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	17-Sep-2025 11:07:48	
build	17-Sep-2025 11:07:48	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	17-Sep-2025 11:07:48	
build	17-Sep-2025 11:07:48	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	17-Sep-2025 11:07:48	
build	17-Sep-2025 11:07:48	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	17-Sep-2025 11:07:48	Please consult deprecation warnings for more details.
build	17-Sep-2025 11:07:48	
build	17-Sep-2025 11:07:48	BUILD SUCCESSFUL in 2m 32s
build	17-Sep-2025 11:07:48	21 actionable tasks: 18 executed, 3 up-to-date
simple	17-Sep-2025 11:07:48	Finished task 'Jalview distribution for Java 8' with result: Success
simple	17-Sep-2025 11:07:48	Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled
simple	17-Sep-2025 11:07:48	Running post build plugin 'NCover Results Collector'
simple	17-Sep-2025 11:07:48	Running post build plugin 'Artifact Copier'
simple	17-Sep-2025 11:07:48	Publishing an artifact: Jalview executables
simple	17-Sep-2025 11:07:48	Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 260.5 ms
simple	17-Sep-2025 11:07:48	Publishing an artifact: install4j installers
error	17-Sep-2025 11:07:48	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	17-Sep-2025 11:07:48	The artifact hasn't been successfully published after 171.3 μs
simple	17-Sep-2025 11:07:48	Publishing an artifact: getdown-channel
error	17-Sep-2025 11:07:48	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	17-Sep-2025 11:07:48	The artifact hasn't been successfully published after 63.85 μs
simple	17-Sep-2025 11:07:48	Publishing an artifact: Jalview getdown launcher
error	17-Sep-2025 11:07:48	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	17-Sep-2025 11:07:48	The artifact hasn't been successfully published after 31.33 μs
simple	17-Sep-2025 11:07:48	Publishing an artifact: getdown build for website
simple	17-Sep-2025 11:07:48	Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 225.8 ms
simple	17-Sep-2025 11:07:48	Publishing an artifact: getdown build for archive
error	17-Sep-2025 11:07:48	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	17-Sep-2025 11:07:48	The artifact hasn't been successfully published after 112.0 μs
simple	17-Sep-2025 11:07:48	Running post build plugin 'Artifactory Release Management Staging'
simple	17-Sep-2025 11:07:48	Running post build plugin 'Artifactory Build Info Copier'
simple	17-Sep-2025 11:07:48	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	17-Sep-2025 11:07:48	Running post build plugin 'npm Cache Cleanup'
simple	17-Sep-2025 11:07:48	Running post build plugin 'Clover Results Collector'
simple	17-Sep-2025 11:07:48	Running post build plugin 'Docker Container Cleanup'
simple	17-Sep-2025 11:07:48	Finalising the build...
simple	17-Sep-2025 11:07:48	Stopping timer.
simple	17-Sep-2025 11:07:48	Build JB-GPC-JOB1-357 completed.
simple	17-Sep-2025 11:07:48	Running on server: post build plugin 'NCover Results Collector'
simple	17-Sep-2025 11:07:48	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	17-Sep-2025 11:07:48	Running on server: post build plugin 'Clover Delta Calculator'
simple	17-Sep-2025 11:07:48	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	17-Sep-2025 11:07:48	All post build plugins have finished
simple	17-Sep-2025 11:07:48	Generating build results summary...
simple	17-Sep-2025 11:07:48	Saving build results to disk...
simple	17-Sep-2025 11:07:48	Logging substituted variables...
simple	17-Sep-2025 11:07:48	Indexing build results...
simple	17-Sep-2025 11:07:48	Finished building JB-GPC-JOB1-357.