simple 17-Sep-2025 11:07:49 Build Jalview Builds - Getdown DEVELOP Launchers - Default Job #77 (JB-GDL-JOB1-77) started building on agent Default Agent simple 17-Sep-2025 11:07:49 simple 17-Sep-2025 11:07:49 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1 simple 17-Sep-2025 11:07:49 Executing build Jalview Builds - Getdown DEVELOP Launchers - Default Job #77 (JB-GDL-JOB1-77) simple 17-Sep-2025 11:07:49 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 17-Sep-2025 11:07:49 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1 simple 17-Sep-2025 11:07:49 Updating source code to revision: 87afc897f4ab4cf704d7e1c000421e81e0464919 simple 17-Sep-2025 11:07:50 Fetching 'refs/heads/main' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 17-Sep-2025 11:07:50 Checking out revision 87afc897f4ab4cf704d7e1c000421e81e0464919. simple 17-Sep-2025 11:07:50 error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object! simple 17-Sep-2025 11:07:50 error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object! simple 17-Sep-2025 11:07:50 error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object! simple 17-Sep-2025 11:07:50 error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object! simple 17-Sep-2025 11:07:50 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 17-Sep-2025 11:07:50 a07a210..87afc89 main -> origin/main simple 17-Sep-2025 11:07:50 * [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 11:07:50 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 11:07:50 * [new branch] bug/JAL-4530_applescript_to_detect_Applications_symlink -> origin/bug/JAL-4530_applescript_to_detect_Applications_symlink simple 17-Sep-2025 11:07:50 * [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 11:07:50 * [new branch] development/JAL-4107_merge_2115_212 -> origin/development/JAL-4107_merge_2115_212 simple 17-Sep-2025 11:07:50 13316f6..2c0064b development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch simple 17-Sep-2025 11:07:50 * [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 11:07:50 * [new branch] feature/JAL-4515_Group_colouring_as_background -> origin/feature/JAL-4515_Group_colouring_as_background simple 17-Sep-2025 11:07:50 * [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 11:07:50 * [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 11:07:50 * [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 11:07:50 * [new branch] feature/JAL-4583_incorrect_seq_count_ss_consensus -> origin/feature/JAL-4583_incorrect_seq_count_ss_consensus simple 17-Sep-2025 11:07:50 * [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 11:07:50 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 11:07:50 * [new branch] features/JAL-4219_extended_fasta_rna_ss -> origin/features/JAL-4219_extended_fasta_rna_ss simple 17-Sep-2025 11:07:50 * [new branch] features/JAL-4587_colour_group_annotation -> origin/features/JAL-4587_colour_group_annotation simple 17-Sep-2025 11:07:50 * [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 11:07:50 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 11:07:50 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 11:07:50 * [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 11:07:50 * [new branch] improvement/JAL-4570_show_tree_above_alignmentview -> origin/improvement/JAL-4570_show_tree_above_alignmentview simple 17-Sep-2025 11:07:50 * [new branch] patch/JAL-3987_pergroup_annotation_consensus -> origin/patch/JAL-3987_pergroup_annotation_consensus simple 17-Sep-2025 11:07:50 * [new branch] patch/JAL-4414_for_2_11_5_Branch -> origin/patch/JAL-4414_for_2_11_5_Branch simple 17-Sep-2025 11:07:50 5b3d6da..d7fbd2a patch/JAL-4555_sort_by_descr -> origin/patch/JAL-4555_sort_by_descr simple 17-Sep-2025 11:07:50 * [new branch] patch/JAL-4590_remove_isBlank_use -> origin/patch/JAL-4590_remove_isBlank_use simple 17-Sep-2025 11:07:50 * [new branch] patch_bits/JAL-4590_isBlank_PDB_ChainIssue -> origin/patch_bits/JAL-4590_isBlank_PDB_ChainIssue simple 17-Sep-2025 11:07:50 dd2df48..147e80c releases/Release_2_11_4_Branch -> origin/releases/Release_2_11_4_Branch simple 17-Sep-2025 11:07:50 * [new branch] releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch simple 17-Sep-2025 11:07:50 * [new branch] spike/JAL-4576_ligysis_exploration -> origin/spike/JAL-4576_ligysis_exploration simple 17-Sep-2025 11:07:50 * [new branch] update/JAL-4243_biotools_json_record -> origin/update/JAL-4243_biotools_json_record simple 17-Sep-2025 11:07:50 * [new tag] Release_2_11_5_0 -> Release_2_11_5_0 simple 17-Sep-2025 11:07:50 error: refs/remotes/origin/patch/JAL-4564_JAL-4563_urls_and_structure_args does not point to a valid object! simple 17-Sep-2025 11:07:53 Already on 'main' simple 17-Sep-2025 11:07:53 Your branch is behind 'origin/main' by 378 commits, and can be fast-forwarded. simple 17-Sep-2025 11:07:53 (use "git pull" to update your local branch) simple 17-Sep-2025 11:07:53 HEAD is now at 87afc89 Merge tag 'Release_2_11_5_0' simple 17-Sep-2025 11:07:53 Updated source code to revision: 87afc897f4ab4cf704d7e1c000421e81e0464919 simple 17-Sep-2025 11:07:53 Finished task 'Checkout Default Repository' with result: Success simple 17-Sep-2025 11:07:53 Running pre-build action: VCS Version Collector simple 17-Sep-2025 11:07:53 Running pre-build action: Artifactory Release Staging command 17-Sep-2025 11:07:54 Substituting variable: ${bamboo.planKey} with JB-GDL simple 17-Sep-2025 11:07:54 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 17-Sep-2025 11:07:54 Bamboo Artifactory Plugin version: 2.6.2 command 17-Sep-2025 11:07:54 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - Default Job #77 (JB-GDL-JOB1-77)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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_planRepository_1_branchDisplayName=main\nbamboo_repository_revision_number=87afc897f4ab4cf704d7e1c000421e81e0464919\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL-JOB1-77\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-GDL-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL-JOB1\nbamboo_shortPlanName=Getdown DEVELOP Launchers\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=77\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-GDL-JOB1-77\nbamboo_repository_46498269_git_username=\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers\nbamboo_shortPlanKey=GDL\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498269_branch_name=main\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=87afc897f4ab4cf704d7e1c000421e81e0464919\nbamboo_buildTimeStamp=2025-09-17T11:02:35.884+01:00\nbamboo_repository_previous_revision_number=a07a210e39b574048817742f680ad4bbcebb590c\nbamboo_repository_git_branch=main\nbamboo_buildResultKey=JB-GDL-JOB1-77\nbamboo_repository_branch_name=main\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498269_name=Jalview Gitlab\nbamboo_planRepository_1_revision=87afc897f4ab4cf704d7e1c000421e81e0464919\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498269_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\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_repository_46498269_git_branch=main\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_planRepository_branchDisplayName=main\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_repository_46498269_revision_number=87afc897f4ab4cf704d7e1c000421e81e0464919\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301457\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-GDL-JOB1\nbamboo_planKey=JB-GDL\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=main\nbamboo_repository_46498269_previous_revision_number=a07a210e39b574048817742f680ad4bbcebb590c\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 11:07:56 build 17-Sep-2025 11:07:56 > Configure project : build 17-Sep-2025 11:07:56 Using properties from file './utils/channels/default/channel_gradle.properties' build 17-Sep-2025 11:07:56 JALVIEW_VERSION is set to '2.11.5.0' build 17-Sep-2025 11:07:56 HEADLESS BUILD build 17-Sep-2025 11:07:56 J2S ENABLED build 17-Sep-2025 11:07:56 Using a BUILD profile. build 17-Sep-2025 11:07:56 eclipseDir exists build 17-Sep-2025 11:07:56 build 17-Sep-2025 11:07:56 > Task :clean build 17-Sep-2025 11:07:56 > Task :cleanPackageDir build 17-Sep-2025 11:07:56 > Task :getdownImagesCopy build 17-Sep-2025 11:07:56 > Task :getdownImagesProcess build 17-Sep-2025 11:07:56 > Task :getdownImages build 17-Sep-2025 11:07:56 > Task :copyHelp build 17-Sep-2025 11:07:58 > Task :buildIndices build 17-Sep-2025 11:07:58 > Task :copyResources build 17-Sep-2025 11:07:58 > Task :copyChannelResources build 17-Sep-2025 11:07:58 build 17-Sep-2025 11:07:58 > Task :createBuildProperties build 17-Sep-2025 11:07:58 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 17-Sep-2025 11:07:58 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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 11:07:58 build 17-Sep-2025 11:07:58 > Task :buildResources build 17-Sep-2025 11:07:58 > Task :copyDocs build 17-Sep-2025 11:07:58 build 17-Sep-2025 11:07:58 > Task :convertMdFiles build 17-Sep-2025 11:07:58 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 17-Sep-2025 11:07:58 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/doc_build/doc/releaseprocess.html build 17-Sep-2025 11:07:58 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 17-Sep-2025 11:07:58 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/doc_build/doc/building.html build 17-Sep-2025 11:07:58 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/doc_build/doc/jalview-projects.html build 17-Sep-2025 11:07:58 build 17-Sep-2025 11:07:58 > Task :releasesTemplates build 17-Sep-2025 11:07:58 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 17-Sep-2025 11:07:58 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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 11:07:58 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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 11:07:58 Stripping rc/test/etc for 2_11_5_0 build 17-Sep-2025 11:07:58 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_0.md build 17-Sep-2025 11:07:58 build 17-Sep-2025 11:07:58 > Task :prepare build 17-Sep-2025 11:08:00 build 17-Sep-2025 11:08:00 > Task :compileJava build 17-Sep-2025 11:08:00 Setting target compatibility to 11 error 17-Sep-2025 11:08:06 Note: Some input files use or override a deprecated API. error 17-Sep-2025 11:08:06 Note: Recompile with -Xlint:deprecation for details. error 17-Sep-2025 11:08:06 Note: Some input files use unchecked or unsafe operations. error 17-Sep-2025 11:08:06 Note: Recompile with -Xlint:unchecked for details. build 17-Sep-2025 11:08:07 build 17-Sep-2025 11:08:07 > Task :processResources build 17-Sep-2025 11:08:07 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 17-Sep-2025 11:08:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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 11:08:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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 11:08:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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 11:08:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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 11:08:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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 11:08:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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 11:08:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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 11:08:07 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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 11:08:07 build 17-Sep-2025 11:08:07 > Task :classes build 17-Sep-2025 11:08:08 build 17-Sep-2025 11:08:08 > Task :compileLinkCheck build 17-Sep-2025 11:08:08 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 17-Sep-2025 11:08:08 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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 11:08:08 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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 11:08:08 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/utils'. 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 11:08:10 build 17-Sep-2025 11:08:10 > Task :linkCheck build 17-Sep-2025 11:08:10 Checking help file links build 17-Sep-2025 11:10:16 build 17-Sep-2025 11:10:16 Results: build 17-Sep-2025 11:10:16 161 distinct help targets build 17-Sep-2025 11:10:16 161 help mappings build 17-Sep-2025 11:10:16 0 invalid targets build 17-Sep-2025 11:10:16 31 unused targets build 17-Sep-2025 11:10:16 uniprotfetcher: html/features/uniprotsequencefetcher.html build 17-Sep-2025 11:10:16 overviewprefs: html/features/preferences.html#overview build 17-Sep-2025 11:10:16 cdnafeatures: html/features/codingfeatures.html build 17-Sep-2025 11:10:16 startupprefs: html/features/preferences.html#startup build 17-Sep-2025 11:10:16 ensemblfetch: html/features/ensemblsequencefetcher.html build 17-Sep-2025 11:10:16 io.modellerpir: html/io/modellerpir.html build 17-Sep-2025 11:10:16 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 17-Sep-2025 11:10:16 pdbmcviewer: html/features/pdbviewer.html build 17-Sep-2025 11:10:16 groovy.colours: html/features/groovy.html#groovyColours build 17-Sep-2025 11:10:16 seqmappings: html/features/seqmappings.html build 17-Sep-2025 11:10:16 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 17-Sep-2025 11:10:16 splitframe.mirrorfonts: html/features/splitView.html#mirror build 17-Sep-2025 11:10:16 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 17-Sep-2025 11:10:16 search: html/features/search.html build 17-Sep-2025 11:10:16 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 17-Sep-2025 11:10:16 alformats: html/io/fileformats.html build 17-Sep-2025 11:10:16 strucprefs: html/features/preferences.html#structure build 17-Sep-2025 11:10:16 siftsmapping: html/features/siftsmapping.html build 17-Sep-2025 11:10:16 chimera.annotxfer: html/features/chimera.html#annotxfer build 17-Sep-2025 11:10:16 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 17-Sep-2025 11:10:16 newkeys: html/features/newkeystrokes.html build 17-Sep-2025 11:10:16 importvcf.attribs: html/features/importvcf.html#attribs build 17-Sep-2025 11:10:16 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 17-Sep-2025 11:10:16 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 17-Sep-2025 11:10:16 jalarchive: html/features/jalarchive.html build 17-Sep-2025 11:10:16 newsreader: html/webServices/newsreader.html build 17-Sep-2025 11:10:16 jalviewcltool: html/features/commandline.html#script build 17-Sep-2025 11:10:16 popMenuAddref: html/menus/popupMenu.html#addrefannot build 17-Sep-2025 11:10:16 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 17-Sep-2025 11:10:16 paematrixformat: html/io/paematrixformat.html build 17-Sep-2025 11:10:16 overview: html/features/overview.html build 17-Sep-2025 11:10:16 0 invalid map urls build 17-Sep-2025 11:10:16 0 invalid image attributes build 17-Sep-2025 11:10:16 520 internal href links (120 with anchors) build 17-Sep-2025 11:10:16 0 invalid internal href links build 17-Sep-2025 11:10:16 0 invalid internal anchor links build 17-Sep-2025 11:10:16 112 external href links build 17-Sep-2025 11:10:16 External links not verified as internet not available build 17-Sep-2025 11:10:16 *** Success *** build 17-Sep-2025 11:10:16 build 17-Sep-2025 11:10:16 > Task :jar build 17-Sep-2025 11:10:17 > Task :syncJars build 17-Sep-2025 11:10:17 > Task :makeDist build 17-Sep-2025 11:10:17 > Task :getdownWebsiteBuild error 17-Sep-2025 11:10:19 2025/09/17 11:10:17:667 WARNING Starting without install4j classes build 17-Sep-2025 11:10:19 error 17-Sep-2025 11:10:19 2025/09/17 11:10:18:655 WARNING Starting without install4j classes build 17-Sep-2025 11:10:19 > Task :getdownDigest build 17-Sep-2025 11:10:19 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 17-Sep-2025 11:10:19 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 17-Sep-2025 11:10:19 build 17-Sep-2025 11:10:19 > Task :getdown build 17-Sep-2025 11:10:19 build 17-Sep-2025 11:10:19 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 17-Sep-2025 11:10:19 build 17-Sep-2025 11:10:19 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 17-Sep-2025 11:10:19 build 17-Sep-2025 11:10:19 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 17-Sep-2025 11:10:19 build 17-Sep-2025 11:10:19 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 17-Sep-2025 11:10:19 Please consult deprecation warnings for more details. build 17-Sep-2025 11:10:19 build 17-Sep-2025 11:10:19 BUILD SUCCESSFUL in 2m 24s build 17-Sep-2025 11:10:19 21 actionable tasks: 21 executed simple 17-Sep-2025 11:10:19 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 17-Sep-2025 11:10:19 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 17-Sep-2025 11:10:19 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - Default Job #77 (JB-GDL-JOB1-77)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL-JOB1-77-ScriptBuildTask-5689057771421410903.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-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\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=main\nbamboo_repository_revision_number=87afc897f4ab4cf704d7e1c000421e81e0464919\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL-JOB1-77\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL-JOB1\nbamboo_shortPlanName=Getdown DEVELOP Launchers\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_buildNumber=77\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-GDL-JOB1-77\nbamboo_repository_46498269_git_username=\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers\nbamboo_shortPlanKey=GDL\nbamboo_shortJobKey=JOB1\nbamboo_repository_46498269_branch_name=main\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=87afc897f4ab4cf704d7e1c000421e81e0464919\nbamboo_buildTimeStamp=2025-09-17T11:02:35.884+01:00\nbamboo_repository_previous_revision_number=a07a210e39b574048817742f680ad4bbcebb590c\nbamboo_repository_git_branch=main\nbamboo_buildResultKey=JB-GDL-JOB1-77\nbamboo_repository_branch_name=main\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_repository_46498269_name=Jalview Gitlab\nbamboo_planRepository_1_revision=87afc897f4ab4cf704d7e1c000421e81e0464919\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498269_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\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-GDL -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_repository_46498269_git_branch=main\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_planRepository_branchDisplayName=main\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=main\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498269_revision_number=87afc897f4ab4cf704d7e1c000421e81e0464919\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301457\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\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-GDL-JOB1\nbamboo_planKey=JB-GDL\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=main\nbamboo_repository_46498269_previous_revision_number=a07a210e39b574048817742f680ad4bbcebb590c\n simple 17-Sep-2025 11:10:19 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 17-Sep-2025 11:10:19 Running post build plugin 'NCover Results Collector' simple 17-Sep-2025 11:10:19 Running post build plugin 'Artifact Copier' simple 17-Sep-2025 11:10:19 Publishing an artifact: getdown simple 17-Sep-2025 11:10:19 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 139.5 ms simple 17-Sep-2025 11:10:19 Running post build plugin 'Artifactory Release Management Staging' simple 17-Sep-2025 11:10:19 Running post build plugin 'Artifactory Build Info Copier' simple 17-Sep-2025 11:10:19 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 17-Sep-2025 11:10:19 Running post build plugin 'npm Cache Cleanup' simple 17-Sep-2025 11:10:19 Running post build plugin 'Clover Results Collector' simple 17-Sep-2025 11:10:19 Running post build plugin 'Docker Container Cleanup' simple 17-Sep-2025 11:10:19 Finalising the build... simple 17-Sep-2025 11:10:19 Stopping timer. simple 17-Sep-2025 11:10:19 Build JB-GDL-JOB1-77 completed. simple 17-Sep-2025 11:10:19 Running on server: post build plugin 'NCover Results Collector' simple 17-Sep-2025 11:10:19 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 17-Sep-2025 11:10:19 Running on server: post build plugin 'Clover Delta Calculator' simple 17-Sep-2025 11:10:19 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 17-Sep-2025 11:10:19 All post build plugins have finished simple 17-Sep-2025 11:10:19 Generating build results summary... simple 17-Sep-2025 11:10:19 Saving build results to disk... simple 17-Sep-2025 11:10:19 Logging substituted variables... simple 17-Sep-2025 11:10:19 Indexing build results... simple 17-Sep-2025 11:10:19 Finished building JB-GDL-JOB1-77.