Build: #4 failed
Job: Clover and Tests failed
Build log
The build generated 490 lines of output. Download or view full build log
| 03-Jul-2026 14:09:38 | Build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #4 (JB-GDB749-JOB1-4) started building on agent Default Agent |
| 03-Jul-2026 14:09:38 | |
| 03-Jul-2026 14:09:38 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1 |
| 03-Jul-2026 14:09:38 | Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #4 (JB-GDB749-JOB1-4) |
| 03-Jul-2026 14:09:38 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 03-Jul-2026 14:09:38 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1 |
| 03-Jul-2026 14:09:38 | Updating source code to revision: a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572 |
| 03-Jul-2026 14:09:38 | Fetching 'refs/heads/patch/JAL-4410_multimers_from_3dbeacons' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 03-Jul-2026 14:09:38 | Checking out revision a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572. |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/citation.cff does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/main does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/saved/JAL-4320_JAL-4644_refactor_directory_structure-with_nearly_working_openclover does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Archived_Release_2_7 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_10_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_2_7 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_4_0 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_4_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_4_0 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_5_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_6_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/citation.cff does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/main does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/saved/JAL-4320_JAL-4644_refactor_directory_structure-with_nearly_working_openclover does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Archived_Release_2_7 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_10_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_2_7 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_4_0 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_4_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_4_0 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_5_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_6_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/citation.cff does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/main does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/saved/JAL-4320_JAL-4644_refactor_directory_structure-with_nearly_working_openclover does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Archived_Release_2_7 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_10_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_2_7 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_4_0 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_4_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_4_0 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_5_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_6_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/citation.cff does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/main does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/saved/JAL-4320_JAL-4644_refactor_directory_structure-with_nearly_working_openclover does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Archived_Release_2_7 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_10_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_2_7 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_4_0 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_4_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_4_0 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_5_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_6_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 |
| 03-Jul-2026 14:09:38 | d9d218f..a08ed3b patch/JAL-4410_multimers_from_3dbeacons -> origin/patch/JAL-4410_multimers_from_3dbeacons |
| 03-Jul-2026 14:09:38 | * [new branch] dev/JAL-4688_gitlab_ci -> origin/dev/JAL-4688_gitlab_ci |
| 03-Jul-2026 14:09:38 | 5a35253..2a40a88 development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/bug/JAL-4647_replace_deprecated_constructors-Release_2_11_5_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/citation.cff does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL-4366_JAL-4386_JAL-4435_3di_msafromstructure_msacomp does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/main does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/patch/JAL-4658_quick_patch_for_clustering_histograms_of_counts does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/saved/JAL-4320_JAL-4644_refactor_directory_structure-with_nearly_working_openclover does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Archived_Release_2_7 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_10_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_2_7 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_4_0 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_11_4_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_4_0 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_5_1 does not point to a valid object! |
| 03-Jul-2026 14:09:38 | error: refs/tags/Release_2_6_1 does not point to a valid object! |
| 03-Jul-2026 14:09:39 | Already on 'patch/JAL-4410_multimers_from_3dbeacons' |
| 03-Jul-2026 14:09:39 | Your branch is behind 'origin/patch/JAL-4410_multimers_from_3dbeacons' by 19 commits, and can be fast-forwarded. |
| 03-Jul-2026 14:09:39 | (use "git pull" to update your local branch) |
| 03-Jul-2026 14:09:39 | HEAD is now at a08ed3b JAL-4410 testData for failing test |
| 03-Jul-2026 14:09:39 | Updated source code to revision: a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572 |
| 03-Jul-2026 14:09:39 | Finished task 'Checkout Default Repository' with result: Success |
| 03-Jul-2026 14:09:39 | Running pre-build action: VCS Version Collector |
| 03-Jul-2026 14:09:39 | Running pre-build action: Artifactory Release Staging |
| 03-Jul-2026 14:09:39 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 03-Jul-2026 14:09:39 | Bamboo Artifactory Plugin version: 2.6.2 |
| 03-Jul-2026 14:09:39 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #4 (JB-GDB749-JOB1-4)' ... running command line: /home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons bamboo_repository_revision_number=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572 bamboo_repository_48169043_previous_revision_number=d9d218fe9b518987c14acfe100646789b1dbc30f bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-4 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-GDB749-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB749-JOB1 bamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=4 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-4 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons bamboo_shortPlanKey=GDB749 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572 bamboo_buildTimeStamp=2026-07-03T14:09:38.370+01:00 bamboo_repository_previous_revision_number=d9d218fe9b518987c14acfe100646789b1dbc30f bamboo_repository_48169043_name=Jalview Gitlab bamboo_planRepository_previousRevision=d9d218fe9b518987c14acfe100646789b1dbc30f bamboo_repository_git_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_buildResultKey=JB-GDB749-JOB1-4 bamboo_repository_branch_name=patch/JAL-4410_multimers_from_3dbeacons bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572 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=patch/JAL-4410_multimers_from_3dbeacons bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_48169043_git_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=d9d218fe9b518987c14acfe100646789b1dbc30f bamboo_planRepository_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=patch/JAL-4410_multimers_from_3dbeacons _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_repository_48169043_revision_number=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572 bamboo_capability_system_builderivy_Ivy=/usr bamboo_repository_48169043_git_username= bamboo_plan_storageTag=plan-47972517 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_planRepository_type=gitv2 USER=bamboo bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache 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-GDB749-JOB1 bamboo_planKey=JB-GDB749 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=patch/JAL-4410_multimers_from_3dbeacons PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 03-Jul-2026 14:09:39 | 2477 |
| 03-Jul-2026 14:09:40 | |
| 03-Jul-2026 14:09:40 | > Configure project : |
| 03-Jul-2026 14:09:40 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 03-Jul-2026 14:09:40 | JALVIEW_VERSION is set to '2.11.5.2' |
| 03-Jul-2026 14:09:40 | HEADLESS BUILD |
| 03-Jul-2026 14:09:40 | J2S ENABLED |
| 03-Jul-2026 14:09:40 | Using a LOCAL profile. |
| 03-Jul-2026 14:09:40 | eclipseDir exists |
| 03-Jul-2026 14:09:41 | |
| 03-Jul-2026 14:09:41 | > Task :clean |
| 03-Jul-2026 14:09:41 | > Task :cleanClover |
| 03-Jul-2026 14:09:41 | > Task :cleanTest UP-TO-DATE |
| 03-Jul-2026 14:09:43 | |
| 03-Jul-2026 14:09:43 | > Task :cloverInstrJava |
| 03-Jul-2026 14:09:43 | Clover: About to instrument 1110 files |
| 03-Jul-2026 14:09:43 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 03-Jul-2026 14:09:43 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'. |
| 03-Jul-2026 14:09:43 | Processing files at 1.9 source level. |
| 03-Jul-2026 14:09:46 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 03-Jul-2026 14:09:46 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 03-Jul-2026 14:09:46 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 03-Jul-2026 14:09:46 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 03-Jul-2026 14:09:46 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 03-Jul-2026 14:09:46 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 03-Jul-2026 14:09:46 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 03-Jul-2026 14:09:53 | Clover all over. Instrumented 1110 files (113 packages). |
| 03-Jul-2026 14:09:55 | |
| 03-Jul-2026 14:09:55 | > Task :cloverInstrTests |
| 03-Jul-2026 14:09:55 | Clover: About to instrument test files |
| 03-Jul-2026 14:09:55 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 03-Jul-2026 14:09:55 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'. |
| 03-Jul-2026 14:09:55 | Processing files at 1.9 source level. |
| 03-Jul-2026 14:09:57 | Clover all over. Instrumented 293 files (52 packages). |
| 03-Jul-2026 14:09:57 | 1629 test methods detected. |
| 03-Jul-2026 14:09:57 | |
| 03-Jul-2026 14:09:57 | > Task :cloverInstr |
| 03-Jul-2026 14:09:59 | |
| 03-Jul-2026 14:09:59 | > Task :compileCloverJava |
| 03-Jul-2026 14:09:59 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 03-Jul-2026 14:09:59 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrJava' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 03-Jul-2026 14:09:59 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrTests' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 03-Jul-2026 14:09:59 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-instr'. Reason: Task ':compileCloverJava' uses this output of task ':cloverInstrJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 03-Jul-2026 14:09:59 | Setting target compatibility to 11 |
| 03-Jul-2026 14:10:12 | Note: Some input files use or override a deprecated API. |
| 03-Jul-2026 14:10:12 | Note: Recompile with -Xlint:deprecation for details. |
| 03-Jul-2026 14:10:12 | Note: Some input files use unchecked or unsafe operations. |
| 03-Jul-2026 14:10:12 | Note: Recompile with -Xlint:unchecked for details. |
| 03-Jul-2026 14:10:17 | |
| 03-Jul-2026 14:10:17 | > Task :processCloverResources NO-SOURCE |
| 03-Jul-2026 14:10:17 | > Task :cloverClasses |
| 03-Jul-2026 14:10:17 | > Task :copyHelp |
| 03-Jul-2026 14:10:18 | > Task :buildIndices |
| 03-Jul-2026 14:10:18 | > Task :copyResources |
| 03-Jul-2026 14:10:18 | > Task :copyChannelResources |
| 03-Jul-2026 14:10:18 | |
| 03-Jul-2026 14:10:18 | > Task :createBuildProperties |
| 03-Jul-2026 14:10:18 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 03-Jul-2026 14:10:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 03-Jul-2026 14:10:18 | |
| 03-Jul-2026 14:10:18 | > Task :buildResources |
| 03-Jul-2026 14:10:18 | > Task :copyDocs |
| 03-Jul-2026 14:10:18 | |
| 03-Jul-2026 14:10:18 | > Task :convertMdFiles |
| 03-Jul-2026 14:10:18 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 03-Jul-2026 14:10:18 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 03-Jul-2026 14:10:18 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 03-Jul-2026 14:10:18 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/building.html |
| 03-Jul-2026 14:10:18 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 03-Jul-2026 14:10:18 | |
| 03-Jul-2026 14:10:18 | > Task :releasesTemplates |
| 03-Jul-2026 14:10:18 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 03-Jul-2026 14:10:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 03-Jul-2026 14:10:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-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. |
| 03-Jul-2026 14:10:18 | Stripping rc/test/etc for TEST |
| 03-Jul-2026 14:10:18 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/help/markdown/whatsnew/whatsnew-TEST.md |
| 03-Jul-2026 14:10:18 | |
| 03-Jul-2026 14:10:18 | > Task :prepare |
| 03-Jul-2026 14:10:20 | |
| 03-Jul-2026 14:10:20 | > Task :compileJava |
| 03-Jul-2026 14:10:20 | Setting target compatibility to 11 |
| 03-Jul-2026 14:10:24 | Note: Some input files use or override a deprecated API. |
| 03-Jul-2026 14:10:24 | Note: Recompile with -Xlint:deprecation for details. |
| 03-Jul-2026 14:10:24 | Note: Some input files use unchecked or unsafe operations. |
| 03-Jul-2026 14:10:24 | Note: Recompile with -Xlint:unchecked for details. |
| 03-Jul-2026 14:10:27 | |
| 03-Jul-2026 14:10:27 | > Task :compileTestJava |
| 03-Jul-2026 14:10:27 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
| 03-Jul-2026 14:10:27 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes'. Reason: Task ':compileTestJava' uses this output of task ':compileCloverJava' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 03-Jul-2026 14:10:27 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-test-instr'. Reason: Task ':compileTestJava' uses this output of task ':cloverInstrTests' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 03-Jul-2026 14:10:27 | Setting target compatibility to 11 |
| 03-Jul-2026 14:10:30 | Note: Some input files use or override a deprecated API. |
| 03-Jul-2026 14:10:30 | Note: Recompile with -Xlint:deprecation for details. |
| 03-Jul-2026 14:10:30 | Note: Some input files use unchecked or unsafe operations. |
| 03-Jul-2026 14:10:30 | Note: Recompile with -Xlint:unchecked for details. |
| 03-Jul-2026 14:10:32 | |
| 03-Jul-2026 14:10:32 | > Task :processTestResources |
| 03-Jul-2026 14:10:32 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
| 03-Jul-2026 14:10:32 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 03-Jul-2026 14:10:32 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 03-Jul-2026 14:10:32 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 03-Jul-2026 14:10:32 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 03-Jul-2026 14:10:32 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 03-Jul-2026 14:10:32 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 03-Jul-2026 14:10:32 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 03-Jul-2026 14:10:32 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 03-Jul-2026 14:10:32 | |
| 03-Jul-2026 14:10:32 | > Task :testClasses |
| 03-Jul-2026 14:10:34 | |
| 03-Jul-2026 14:10:34 | > Task :testTask0 |
| 03-Jul-2026 14:10:34 | Running tests WITH clover |
| 03-Jul-2026 14:10:35 | WARNING: An illegal reflective access operation has occurred |
| 03-Jul-2026 14:10:35 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 03-Jul-2026 14:10:35 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 03-Jul-2026 14:10:35 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 03-Jul-2026 14:10:35 | WARNING: All illegal access operations will be denied in a future release |
| 03-Jul-2026 14:10:57 | |
| 03-Jul-2026 14:10:57 | Gradle suite > Gradle test > jalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructure[3](examples/AlphaFold/AF-Q5VSL9-F1-model_v4.pdb, examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_cmp.json) FAILED |
| 03-Jul-2026 14:10:57 | java.lang.AssertionError: Exception importing paefile 'examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_cmp.json' |
| 03-Jul-2026 14:10:57 | at org.testng.Assert.fail(Assert.java:83) |
| 03-Jul-2026 14:10:57 | at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_1rvd1wm3rrg(EBIAlphaFoldTest.java:96) |
| 03-Jul-2026 14:10:57 | at jalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructure(EBIAlphaFoldTest.java:67) |
| 03-Jul-2026 14:10:57 | |
| 03-Jul-2026 14:10:57 | Caused by: |
| 03-Jul-2026 14:10:57 | java.io.IOException: Stream Closed |
| 03-Jul-2026 14:10:57 | at java.base/java.io.FileInputStream.readBytes(Native Method) |
| 03-Jul-2026 14:10:57 | at java.base/java.io.FileInputStream.read(FileInputStream.java:279) |
| 03-Jul-2026 14:10:57 | at java.base/java.io.BufferedInputStream.fill(BufferedInputStream.java:252) |
| 03-Jul-2026 14:10:57 | at java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:292) |
| 03-Jul-2026 14:10:57 | at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:351) |
| 03-Jul-2026 14:10:57 | at java.base/java.io.FilterInputStream.read(FilterInputStream.java:107) |
| 03-Jul-2026 14:10:57 | at jalview.util.Platform.isGzipStream(Platform.java:602) |
| 03-Jul-2026 14:10:57 | at jalview.util.Platform.checkForGzipStream(Platform.java:644) |
| 03-Jul-2026 14:10:57 | at jalview.util.Platform.parseJSON(Platform.java:534) |
| 03-Jul-2026 14:10:57 | at jalview.ws.dbsources.EBIAlfaFold.parseJSONtoPAEContactMatrix(EBIAlfaFold.java:625) |
| 03-Jul-2026 14:10:57 | at jalview.ws.dbsources.EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(EBIAlfaFold.java:660) |
| 03-Jul-2026 14:10:57 | at jalview.ws.dbsources.EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(EBIAlfaFold.java:649) |
| 03-Jul-2026 14:10:57 | at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_1rvd1wm3rrg(EBIAlphaFoldTest.java:90) |
| 03-Jul-2026 14:10:57 | ... 1 more |
| 03-Jul-2026 14:10:59 | |
| 03-Jul-2026 14:10:59 | Gradle suite > Gradle test > jalview.ws.dbsources.EBIAlphaFoldTest.testImportPAEAndStructureForMultiChainSeqs FAILED |
| 03-Jul-2026 14:10:59 | java.lang.Error: Couln't create a mapping for this matrix. |
| 03-Jul-2026 14:10:59 | at jalview.ws.datamodel.alphafold.MappableContactMatrix.liftOver(MappableContactMatrix.java:189) |
| 03-Jul-2026 14:10:59 | at jalview.ws.datamodel.alphafold.MappableContactMatrix.liftOver(MappableContactMatrix.java:38) |
| 03-Jul-2026 14:10:59 | at mc_view.PDBChain.transferResidueAnnotation(PDBChain.java:715) |
| 03-Jul-2026 14:10:59 | at jalview.structure.StructureSelectionManager.getNWMappings(StructureSelectionManager.java:1014) |
| 03-Jul-2026 14:10:59 | at jalview.structure.StructureSelectionManager.computeMapping(StructureSelectionManager.java:749) |
| 03-Jul-2026 14:10:59 | at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_130yvgz3rsn(EBIAlphaFoldTest.java:194) |
| 03-Jul-2026 14:10:59 | at jalview.ws.dbsources.EBIAlphaFoldTest.testImportPAEAndStructureForMultiChainSeqs(EBIAlphaFoldTest.java:173) |
| 03-Jul-2026 14:14:44 | |
| 03-Jul-2026 14:14:44 | 1846 tests completed, 2 failed |
| 03-Jul-2026 14:14:44 | There were failing tests. See the report at: file:///srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask0/index.html |
| 03-Jul-2026 14:14:46 | |
| 03-Jul-2026 14:14:46 | > Task :testTask1 |
| 03-Jul-2026 14:14:46 | Running tests WITH clover |
| 03-Jul-2026 14:14:47 | WARNING: An illegal reflective access operation has occurred |
| 03-Jul-2026 14:14:47 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 03-Jul-2026 14:14:47 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 03-Jul-2026 14:14:47 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 03-Jul-2026 14:14:47 | WARNING: All illegal access operations will be denied in a future release |
| 03-Jul-2026 14:17:02 | |
| 03-Jul-2026 14:17:02 | > Task :testTask2 |
| 03-Jul-2026 14:17:02 | Running tests WITH clover |
| 03-Jul-2026 14:17:05 | |
| 03-Jul-2026 14:17:05 | > Task :testTask3 |
| 03-Jul-2026 14:17:05 | Running tests WITH clover |
| 03-Jul-2026 14:17:07 | WARNING: An illegal reflective access operation has occurred |
| 03-Jul-2026 14:17:07 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 03-Jul-2026 14:17:07 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 03-Jul-2026 14:17:07 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 03-Jul-2026 14:17:07 | WARNING: All illegal access operations will be denied in a future release |
| 03-Jul-2026 14:17:57 | |
| 03-Jul-2026 14:17:57 | > Task :test NO-SOURCE |
| 03-Jul-2026 14:17:57 | ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ |
| 03-Jul-2026 14:17:57 | │jalview:testTask0 results: FAILURE (1846 tests, 1844 successes, 2 failures, 0 skipped) in 4 minutes, 12.029 seconds │ |
| 03-Jul-2026 14:17:57 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask0/index.html│ |
| 03-Jul-2026 14:17:57 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 03-Jul-2026 14:17:57 | │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 15.600 seconds │ |
| 03-Jul-2026 14:17:57 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask1/index.html│ |
| 03-Jul-2026 14:17:57 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 03-Jul-2026 14:17:57 | │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.656 seconds │ |
| 03-Jul-2026 14:17:57 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask2/index.html│ |
| 03-Jul-2026 14:17:57 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 03-Jul-2026 14:17:57 | │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 53.088 seconds │ |
| 03-Jul-2026 14:17:57 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask3/index.html│ |
| 03-Jul-2026 14:17:57 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 03-Jul-2026 14:17:57 | │OVERALL: results: FAILURE (1934 tests, 1932 successes, 2 failures, 0 skipped) in 6 minutes, 84.373 seconds │ |
| 03-Jul-2026 14:17:57 | └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ |
| 03-Jul-2026 14:17:57 | |
| 03-Jul-2026 14:17:57 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 03-Jul-2026 14:17:57 | |
| 03-Jul-2026 14:17:57 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 03-Jul-2026 14:17:57 | |
| 03-Jul-2026 14:17:57 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 03-Jul-2026 14:17:57 | |
| 03-Jul-2026 14:17:57 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 03-Jul-2026 14:17:57 | Please consult deprecation warnings for more details. |
| 03-Jul-2026 14:17:57 | 21 actionable tasks: 20 executed, 1 up-to-date |
| 03-Jul-2026 14:17:57 | |
| 03-Jul-2026 14:17:57 | FAILURE: Build failed with an exception. |
| 03-Jul-2026 14:17:57 | |
| 03-Jul-2026 14:17:57 | * Where: |
| 03-Jul-2026 14:17:57 | Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build.gradle' line: 1967 |
| 03-Jul-2026 14:17:57 | |
| 03-Jul-2026 14:17:57 | * What went wrong: |
| 03-Jul-2026 14:17:57 | Failed tests! |
| 03-Jul-2026 14:17:57 | |
| 03-Jul-2026 14:17:57 | * Try: |
| 03-Jul-2026 14:17:57 | > Run with --stacktrace option to get the stack trace. |
| 03-Jul-2026 14:17:57 | > Run with --info or --debug option to get more log output. |
| 03-Jul-2026 14:17:57 | > Run with --scan to get full insights. |
| 03-Jul-2026 14:17:57 | |
| 03-Jul-2026 14:17:57 | * Get more help at https://help.gradle.org |
| 03-Jul-2026 14:17:57 | |
| 03-Jul-2026 14:17:57 | BUILD FAILED in 8m 17s |
| 03-Jul-2026 14:17:57 | |
| 03-Jul-2026 14:17:57 | Failing task since return code of [/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test] was 1 while expected 0 |
| 03-Jul-2026 14:17:57 | Finished task 'Run tests with openclover under gradle' with result: Failed |
| 03-Jul-2026 14:17:57 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 03-Jul-2026 14:17:57 | Bamboo Artifactory Plugin version: 2.6.2 |
| 03-Jul-2026 14:17:57 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #4 (JB-GDB749-JOB1-4)' ... running command line: /home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons bamboo_repository_revision_number=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572 bamboo_repository_48169043_previous_revision_number=d9d218fe9b518987c14acfe100646789b1dbc30f bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-4 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-GDB749-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB749-JOB1 bamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=4 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-4 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons bamboo_shortPlanKey=GDB749 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572 bamboo_buildTimeStamp=2026-07-03T14:09:38.370+01:00 bamboo_repository_previous_revision_number=d9d218fe9b518987c14acfe100646789b1dbc30f bamboo_repository_48169043_name=Jalview Gitlab bamboo_planRepository_previousRevision=d9d218fe9b518987c14acfe100646789b1dbc30f bamboo_repository_git_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_buildResultKey=JB-GDB749-JOB1-4 bamboo_repository_branch_name=patch/JAL-4410_multimers_from_3dbeacons bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572 SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Gitlab bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ LANG=en_GB.UTF-8 bamboo_buildFailed=true bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_jobFailed=true bamboo_capability_system_git_executable=/bin/git bamboo_repository_48169043_git_branch=patch/JAL-4410_multimers_from_3dbeacons bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=d9d218fe9b518987c14acfe100646789b1dbc30f bamboo_planRepository_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=patch/JAL-4410_multimers_from_3dbeacons _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_repository_48169043_revision_number=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572 bamboo_capability_system_builderivy_Ivy=/usr bamboo_repository_48169043_git_username= bamboo_plan_storageTag=plan-47972517 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_planRepository_type=gitv2 USER=bamboo bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache 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-GDB749-JOB1 bamboo_planKey=JB-GDB749 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=patch/JAL-4410_multimers_from_3dbeacons PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 03-Jul-2026 14:17:57 | 2477 |
| 03-Jul-2026 14:18:02 | |
| 03-Jul-2026 14:18:02 | > Configure project : |
| 03-Jul-2026 14:18:02 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 03-Jul-2026 14:18:02 | JALVIEW_VERSION is set to '2.11.5.2' |
| 03-Jul-2026 14:18:02 | HEADLESS BUILD |
| 03-Jul-2026 14:18:02 | J2S ENABLED |
| 03-Jul-2026 14:18:03 | Using a LOCAL profile. |
| 03-Jul-2026 14:18:04 | eclipseDir exists |
| 03-Jul-2026 14:18:06 | |
| 03-Jul-2026 14:18:06 | > Task :cloverHtmlReport |
| 03-Jul-2026 14:18:06 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 03-Jul-2026 14:18:07 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/clover' |
| 03-Jul-2026 14:18:55 | Done. Processed 117 packages in 47788ms (408ms per package). |
| 03-Jul-2026 14:19:00 | |
| 03-Jul-2026 14:19:00 | > Task :cloverXmlReport |
| 03-Jul-2026 14:19:00 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 03-Jul-2026 14:19:01 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/clover/clover.xml' |
| 03-Jul-2026 14:19:01 | |
| 03-Jul-2026 14:19:01 | > Task :cloverReport |
| 03-Jul-2026 14:19:01 | |
| 03-Jul-2026 14:19:01 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 03-Jul-2026 14:19:01 | |
| 03-Jul-2026 14:19:01 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 03-Jul-2026 14:19:01 | |
| 03-Jul-2026 14:19:01 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 03-Jul-2026 14:19:01 | |
| 03-Jul-2026 14:19:01 | BUILD SUCCESSFUL in 1m 4s |
| 03-Jul-2026 14:19:01 | 2 actionable tasks: 2 executed |
| 03-Jul-2026 14:19:01 | Finished task 'Clover Report' with result: Success |
| 03-Jul-2026 14:19:01 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 03-Jul-2026 14:19:01 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1... |
| 03-Jul-2026 14:19:01 | Failing task since 2 failing test cases were found. |
| 03-Jul-2026 14:19:01 | Finished task 'TestNG Parser' with result: Failed |
| 03-Jul-2026 14:19:01 | Running post build plugin 'NCover Results Collector' |
| 03-Jul-2026 14:19:01 | Running post build plugin 'Artifact Copier' |
| 03-Jul-2026 14:19:01 | Publishing an artifact: Clover Report (System) |
| 03-Jul-2026 14:19:03 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 2.127 s |
| 03-Jul-2026 14:19:03 | Publishing an artifact: TestNG report |
| 03-Jul-2026 14:19:03 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/test does not exist. |
| 03-Jul-2026 14:19:03 | The artifact hasn't been successfully published after 1.401 ms |
| 03-Jul-2026 14:19:03 | Running post build plugin 'Artifactory Release Management Staging' |
| 03-Jul-2026 14:19:03 | Running post build plugin 'Artifactory Build Info Copier' |
| 03-Jul-2026 14:19:03 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 03-Jul-2026 14:19:03 | Running post build plugin 'npm Cache Cleanup' |
| 03-Jul-2026 14:19:03 | Running post build plugin 'Clover Results Collector' |
| 03-Jul-2026 14:19:03 | Running post build plugin 'Docker Container Cleanup' |
| 03-Jul-2026 14:19:03 | Finalising the build... |
| 03-Jul-2026 14:19:03 | Stopping timer. |
| 03-Jul-2026 14:19:03 | Build JB-GDB749-JOB1-4 completed. |
| 03-Jul-2026 14:19:03 | Running on server: post build plugin 'NCover Results Collector' |
| 03-Jul-2026 14:19:03 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 03-Jul-2026 14:19:03 | Running on server: post build plugin 'Clover Delta Calculator' |
| 03-Jul-2026 14:19:03 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 03-Jul-2026 14:19:03 | All post build plugins have finished |
| 03-Jul-2026 14:19:03 | Generating build results summary... |
| 03-Jul-2026 14:19:04 | Saving build results to disk... |
| 03-Jul-2026 14:19:04 | Logging substituted variables... |
| 03-Jul-2026 14:19:04 | Indexing build results... |
| 03-Jul-2026 14:19:04 | Finished building JB-GDB749-JOB1-4. |