Create a getdown channel to launch this build
Build: #358 was successful
Job: Default Job was successful
Build log
The build generated 248 lines of output. Download or view full build log
| 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 |
| 13-Feb-2026 14:16:17 | |
| 13-Feb-2026 14:16:17 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1 |
| 13-Feb-2026 14:16:17 | Executing build Jalview Builds - Getdown Plan Channel - Default Job #358 (JB-GPC-JOB1-358) |
| 13-Feb-2026 14:16:17 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 13-Feb-2026 14:16:17 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1 |
| 13-Feb-2026 14:16:17 | Updating source code to revision: 42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9 |
| 13-Feb-2026 14:16:17 | Fetching 'refs/heads/main' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 13-Feb-2026 14:16:17 | Checking out revision 42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9. |
| 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! |
| 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! |
| 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! |
| 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! |
| 13-Feb-2026 14:16:18 | From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 |
| 13-Feb-2026 14:16:18 | 87afc89..42e19e3 main -> origin/main |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 13-Feb-2026 14:16:18 | * [new branch] bug/JAL-4610_rightColumn_wrappedWidth_fails -> origin/bug/JAL-4610_rightColumn_wrappedWidth_fails |
| 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 |
| 13-Feb-2026 14:16:18 | * [new branch] bug/JAL-4611_SSConsensus_Preferences -> origin/bug/JAL-4611_SSConsensus_Preferences |
| 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 |
| 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 |
| 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 |
| 13-Feb-2026 14:16:18 | * [new branch] citation.cff -> origin/citation.cff |
| 13-Feb-2026 14:16:18 | da33043..e193345 development/JAL-4107_merge_2115_212 -> origin/development/JAL-4107_merge_2115_212 |
| 13-Feb-2026 14:16:18 | * [new branch] development/JAL-4576_ligysis -> origin/development/JAL-4576_ligysis |
| 13-Feb-2026 14:16:18 | 2c0064b..5a35253 development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch |
| 13-Feb-2026 14:16:18 | * [new branch] development/Release_2_12_Branch -> origin/development/Release_2_12_Branch |
| 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 |
| 13-Feb-2026 14:16:18 | * [new branch] epic/JAL-4320_gradle_upgrade_to_gradle9 -> origin/epic/JAL-4320_gradle_upgrade_to_gradle9 |
| 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 |
| 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 |
| 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 |
| 13-Feb-2026 14:16:18 | * [new branch] feature/JAL-835_hhsuite_a3m_support -> origin/feature/JAL-835_hhsuite_a3m_support |
| 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 |
| 13-Feb-2026 14:16:18 | * [new branch] improvement/JAL-4620_faster_sim_matrices -> origin/improvement/JAL-4620_faster_sim_matrices |
| 13-Feb-2026 14:16:18 | * [new branch] patch/JAL-4107_singleThreadTests -> origin/patch/JAL-4107_singleThreadTests |
| 13-Feb-2026 14:16:18 | * [new branch] patch/JAL-4601_stk_ss_annots_showhide -> origin/patch/JAL-4601_stk_ss_annots_showhide |
| 13-Feb-2026 14:16:18 | * [new branch] patch/JAL-4606_again_and_again -> origin/patch/JAL-4606_again_and_again |
| 13-Feb-2026 14:16:18 | * [new branch] patch/JAL-4626_alphafoldVersionTracker -> origin/patch/JAL-4626_alphafoldVersionTracker |
| 13-Feb-2026 14:16:18 | 86d2c84..9e8107e releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch |
| 13-Feb-2026 14:16:18 | * [new branch] spike/JAL-4107_wrappedWidthCalcs -> origin/spike/JAL-4107_wrappedWidthCalcs |
| 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 |
| 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 |
| 13-Feb-2026 14:16:18 | * [new tag] Release_2_11_5_1 -> Release_2_11_5_1 |
| 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! |
| 13-Feb-2026 14:16:18 | Already on 'main' |
| 13-Feb-2026 14:16:18 | Your branch is behind 'origin/main' by 103 commits, and can be fast-forwarded. |
| 13-Feb-2026 14:16:18 | (use "git pull" to update your local branch) |
| 13-Feb-2026 14:16:18 | HEAD is now at 42e19e3 Merge branch 'releases/Release_2_11_5_Branch' |
| 13-Feb-2026 14:16:18 | Updated source code to revision: 42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9 |
| 13-Feb-2026 14:16:18 | Finished task 'Checkout Default Repository' with result: Success |
| 13-Feb-2026 14:16:18 | Running pre-build action: VCS Version Collector |
| 13-Feb-2026 14:16:18 | Running pre-build action: Artifactory Release Staging |
| 13-Feb-2026 14:16:18 | Substituting variable: ${bamboo.planKey} with JB-GPC |
| 13-Feb-2026 14:16:18 | Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 13-Feb-2026 14:16:18 | Bamboo Artifactory Plugin version: 2.6.2 |
| 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)' ... running command line: /home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC clean shadowJar getdown ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=main bamboo_dependency_parent_0=JB-GDB-706 bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_dependency_parent_total=1 bamboo_repository_46498248_git_branch=main bamboo_planRepository_1_branchDisplayName=main bamboo_repository_revision_number=42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC-JOB1-358 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GPC-JOB1 bamboo_shortPlanName=Getdown Plan Channel bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=358 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC-JOB1-358 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Getdown Plan Channel bamboo_shortPlanKey=GPC bamboo_shortJobKey=JOB1 bamboo_repository_46498248_branch_name=main bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9 bamboo_buildTimeStamp=2026-02-13T14:16:17.303Z bamboo_repository_previous_revision_number=87afc897f4ab4cf704d7e1c000421e81e0464919 bamboo_repository_git_branch=main bamboo_buildResultKey=JB-GPC-JOB1-358 bamboo_repository_branch_name=main bamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9 SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Gitlab JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ LANG=en_GB.UTF-8 bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=main bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_repository_46498248_previous_revision_number=87afc897f4ab4cf704d7e1c000421e81e0464919 bamboo_repository_46498248_name=Jalview Gitlab bamboo_planRepository_branchDisplayName=main bamboo_repository_46498248_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=main _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr bamboo_plan_storageTag=plan-8978517 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_repository_46498248_git_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_46498248_revision_number=42e19e3e4596642cf42f7122e2c5e6e8a1cb20b9 bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC-JOB1 bamboo_planKey=JB-GPC bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=main PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 13-Feb-2026 14:16:20 | |
| 13-Feb-2026 14:16:20 | > Configure project : |
| 13-Feb-2026 14:16:20 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 13-Feb-2026 14:16:20 | JALVIEW_VERSION is set to '2.11.5.1' |
| 13-Feb-2026 14:16:20 | HEADLESS BUILD |
| 13-Feb-2026 14:16:20 | J2S ENABLED |
| 13-Feb-2026 14:16:20 | Using a BUILD profile. |
| 13-Feb-2026 14:16:20 | eclipseDir exists |
| 13-Feb-2026 14:16:21 | |
| 13-Feb-2026 14:16:21 | > Task :clean |
| 13-Feb-2026 14:16:21 | > Task :cleanPackageDir |
| 13-Feb-2026 14:16:21 | > Task :copyHelp |
| 13-Feb-2026 14:16:22 | > Task :buildIndices |
| 13-Feb-2026 14:16:22 | > Task :copyResources |
| 13-Feb-2026 14:16:22 | > Task :copyChannelResources |
| 13-Feb-2026 14:16:23 | |
| 13-Feb-2026 14:16:23 | > Task :createBuildProperties |
| 13-Feb-2026 14:16:23 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 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. |
| 13-Feb-2026 14:16:23 | |
| 13-Feb-2026 14:16:23 | > Task :buildResources |
| 13-Feb-2026 14:16:23 | > Task :copyDocs |
| 13-Feb-2026 14:16:23 | |
| 13-Feb-2026 14:16:23 | > Task :convertMdFiles |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 13-Feb-2026 14:16:23 | |
| 13-Feb-2026 14:16:23 | > Task :releasesTemplates |
| 13-Feb-2026 14:16:23 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 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. |
| 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. |
| 13-Feb-2026 14:16:23 | Stripping rc/test/etc for 2_11_5_1 |
| 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 |
| 13-Feb-2026 14:16:23 | |
| 13-Feb-2026 14:16:23 | > Task :prepare |
| 13-Feb-2026 14:16:25 | |
| 13-Feb-2026 14:16:25 | > Task :compileJava |
| 13-Feb-2026 14:16:25 | Setting target compatibility to 11 |
| 13-Feb-2026 14:16:31 | Note: Some input files use or override a deprecated API. |
| 13-Feb-2026 14:16:31 | Note: Recompile with -Xlint:deprecation for details. |
| 13-Feb-2026 14:16:31 | Note: Some input files use unchecked or unsafe operations. |
| 13-Feb-2026 14:16:31 | Note: Recompile with -Xlint:unchecked for details. |
| 13-Feb-2026 14:16:32 | |
| 13-Feb-2026 14:16:32 | > Task :processResources |
| 13-Feb-2026 14:16:32 | Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 13-Feb-2026 14:16:32 | |
| 13-Feb-2026 14:16:32 | > Task :classes |
| 13-Feb-2026 14:16:33 | |
| 13-Feb-2026 14:16:33 | > Task :compileLinkCheck |
| 13-Feb-2026 14:16:33 | Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: |
| 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. |
| 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. |
| 13-Feb-2026 14:16:33 | |
| 13-Feb-2026 14:16:33 | > Task :linkCheck |
| 13-Feb-2026 14:16:33 | Checking help file links |
| 13-Feb-2026 14:16:33 | |
| 13-Feb-2026 14:16:33 | Results: |
| 13-Feb-2026 14:16:33 | 161 distinct help targets |
| 13-Feb-2026 14:16:33 | 161 help mappings |
| 13-Feb-2026 14:16:33 | 0 invalid targets |
| 13-Feb-2026 14:16:33 | 31 unused targets |
| 13-Feb-2026 14:16:33 | uniprotfetcher: html/features/uniprotsequencefetcher.html |
| 13-Feb-2026 14:16:33 | overviewprefs: html/features/preferences.html#overview |
| 13-Feb-2026 14:16:33 | cdnafeatures: html/features/codingfeatures.html |
| 13-Feb-2026 14:16:33 | startupprefs: html/features/preferences.html#startup |
| 13-Feb-2026 14:16:33 | ensemblfetch: html/features/ensemblsequencefetcher.html |
| 13-Feb-2026 14:16:33 | io.modellerpir: html/io/modellerpir.html |
| 13-Feb-2026 14:16:33 | structureandpaefromfile: html/features/structurechooser.html#loadfromfile |
| 13-Feb-2026 14:16:33 | pdbmcviewer: html/features/pdbviewer.html |
| 13-Feb-2026 14:16:33 | groovy.colours: html/features/groovy.html#groovyColours |
| 13-Feb-2026 14:16:33 | seqmappings: html/features/seqmappings.html |
| 13-Feb-2026 14:16:33 | uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts |
| 13-Feb-2026 14:16:33 | splitframe.mirrorfonts: html/features/splitView.html#mirror |
| 13-Feb-2026 14:16:33 | subtMatrices.pam250: html/calculations/scorematrices.html#pam250 |
| 13-Feb-2026 14:16:33 | search: html/features/search.html |
| 13-Feb-2026 14:16:33 | viewingpdbs.reps: html/features/viewingpdbs.html#viewreps |
| 13-Feb-2026 14:16:33 | alformats: html/io/fileformats.html |
| 13-Feb-2026 14:16:33 | strucprefs: html/features/preferences.html#structure |
| 13-Feb-2026 14:16:33 | siftsmapping: html/features/siftsmapping.html |
| 13-Feb-2026 14:16:33 | chimera.annotxfer: html/features/chimera.html#annotxfer |
| 13-Feb-2026 14:16:33 | pdbfts: html/features/pdbsequencefetcher.html#pdbfts |
| 13-Feb-2026 14:16:33 | newkeys: html/features/newkeystrokes.html |
| 13-Feb-2026 14:16:33 | importvcf.attribs: html/features/importvcf.html#attribs |
| 13-Feb-2026 14:16:33 | seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature |
| 13-Feb-2026 14:16:33 | structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch |
| 13-Feb-2026 14:16:33 | jalarchive: html/features/jalarchive.html |
| 13-Feb-2026 14:16:33 | newsreader: html/webServices/newsreader.html |
| 13-Feb-2026 14:16:33 | jalviewcltool: html/features/commandline.html#script |
| 13-Feb-2026 14:16:33 | popMenuAddref: html/menus/popupMenu.html#addrefannot |
| 13-Feb-2026 14:16:33 | splitframe.virtualfeats: html/features/splitView.html#virtualfeats |
| 13-Feb-2026 14:16:33 | paematrixformat: html/io/paematrixformat.html |
| 13-Feb-2026 14:16:33 | overview: html/features/overview.html |
| 13-Feb-2026 14:16:33 | 0 invalid map urls |
| 13-Feb-2026 14:16:33 | 0 invalid image attributes |
| 13-Feb-2026 14:16:33 | 520 internal href links (120 with anchors) |
| 13-Feb-2026 14:16:33 | 0 invalid internal href links |
| 13-Feb-2026 14:16:33 | 0 invalid internal anchor links |
| 13-Feb-2026 14:16:33 | 112 external href links |
| 13-Feb-2026 14:16:33 | External links not verified as internet not available |
| 13-Feb-2026 14:16:33 | *** Success *** |
| 13-Feb-2026 14:16:34 | |
| 13-Feb-2026 14:16:34 | > Task :jar |
| 13-Feb-2026 14:16:34 | > Task :syncJars |
| 13-Feb-2026 14:16:34 | > Task :makeDist |
| 13-Feb-2026 14:16:42 | > Task :shadowJar |
| 13-Feb-2026 14:16:42 | |
| 13-Feb-2026 14:16:42 | > Task :getdownImagesCopy |
| 13-Feb-2026 14:16:42 | Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons: |
| 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. |
| 13-Feb-2026 14:16:43 | |
| 13-Feb-2026 14:16:43 | > Task :getdownImagesProcess |
| 13-Feb-2026 14:16:43 | > Task :getdownImages |
| 13-Feb-2026 14:16:43 | > Task :getdownWebsiteBuild |
| 13-Feb-2026 14:16:45 | |
| 13-Feb-2026 14:16:45 | > Task :getdownDigest |
| 13-Feb-2026 14:16:45 | Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... |
| 13-Feb-2026 14:16:45 | Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... |
| 13-Feb-2026 14:16:45 | |
| 13-Feb-2026 14:16:45 | > Task :getdown |
| 13-Feb-2026 14:16:45 | |
| 13-Feb-2026 14:16:45 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 13-Feb-2026 14:16:45 | |
| 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. |
| 13-Feb-2026 14:16:45 | |
| 13-Feb-2026 14:16:45 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 13-Feb-2026 14:16:45 | |
| 13-Feb-2026 14:16:45 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 13-Feb-2026 14:16:45 | Please consult deprecation warnings for more details. |
| 13-Feb-2026 14:16:45 | |
| 13-Feb-2026 14:16:45 | BUILD SUCCESSFUL in 26s |
| 13-Feb-2026 14:16:45 | 22 actionable tasks: 22 executed |
| 13-Feb-2026 14:16:45 | 2026/02/13 14:16:43:707 WARNING Starting without install4j classes |
| 13-Feb-2026 14:16:45 | 2026/02/13 14:16:44:407 WARNING Starting without install4j classes |
| 13-Feb-2026 14:16:45 | Finished task 'Jalview distribution for Java 11' with result: Success |
| 13-Feb-2026 14:16:45 | Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled |
| 13-Feb-2026 14:16:45 | Running post build plugin 'NCover Results Collector' |
| 13-Feb-2026 14:16:45 | Running post build plugin 'Artifact Copier' |
| 13-Feb-2026 14:16:45 | Publishing an artifact: Jalview executables |
| 13-Feb-2026 14:16:45 | Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 96.62 ms |
| 13-Feb-2026 14:16:45 | Publishing an artifact: install4j installers |
| 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. |
| 13-Feb-2026 14:16:45 | The artifact hasn't been successfully published after 2.380 ms |
| 13-Feb-2026 14:16:45 | Publishing an artifact: getdown-channel |
| 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. |
| 13-Feb-2026 14:16:45 | The artifact hasn't been successfully published after 81.13 μs |
| 13-Feb-2026 14:16:45 | Publishing an artifact: Jalview getdown launcher |
| 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. |
| 13-Feb-2026 14:16:45 | The artifact hasn't been successfully published after 43.60 μs |
| 13-Feb-2026 14:16:45 | Publishing an artifact: getdown build for website |
| 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 |
| 13-Feb-2026 14:16:45 | Publishing an artifact: getdown build for archive |
| 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. |
| 13-Feb-2026 14:16:45 | The artifact hasn't been successfully published after 79.96 μs |
| 13-Feb-2026 14:16:45 | Running post build plugin 'Artifactory Release Management Staging' |
| 13-Feb-2026 14:16:45 | Running post build plugin 'Artifactory Build Info Copier' |
| 13-Feb-2026 14:16:45 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 13-Feb-2026 14:16:45 | Running post build plugin 'npm Cache Cleanup' |
| 13-Feb-2026 14:16:45 | Running post build plugin 'Clover Results Collector' |
| 13-Feb-2026 14:16:45 | Running post build plugin 'Docker Container Cleanup' |
| 13-Feb-2026 14:16:45 | Finalising the build... |
| 13-Feb-2026 14:16:45 | Stopping timer. |
| 13-Feb-2026 14:16:45 | Build JB-GPC-JOB1-358 completed. |
| 13-Feb-2026 14:16:45 | Running on server: post build plugin 'NCover Results Collector' |
| 13-Feb-2026 14:16:45 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 13-Feb-2026 14:16:45 | Running on server: post build plugin 'Clover Delta Calculator' |
| 13-Feb-2026 14:16:45 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 13-Feb-2026 14:16:45 | All post build plugins have finished |
| 13-Feb-2026 14:16:45 | Generating build results summary... |
| 13-Feb-2026 14:16:45 | Saving build results to disk... |
| 13-Feb-2026 14:16:45 | Logging substituted variables... |
| 13-Feb-2026 14:16:45 | Indexing build results... |
| 13-Feb-2026 14:16:45 | Finished building JB-GPC-JOB1-358. |