simple	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
simple	03-Jul-2026 14:09:38	
simple	03-Jul-2026 14:09:38	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1
simple	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)
simple	03-Jul-2026 14:09:38	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	03-Jul-2026 14:09:38	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1
simple	03-Jul-2026 14:09:38	Updating source code to revision: a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572
simple	03-Jul-2026 14:09:38	Fetching 'refs/heads/patch/JAL-4410_multimers_from_3dbeacons' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	03-Jul-2026 14:09:38	Checking out revision a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572.
simple	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!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object!
simple	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!
simple	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!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/citation.cff does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/main does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_4_0 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_4_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	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!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object!
simple	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!
simple	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!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/citation.cff does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/main does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_4_0 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_4_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	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!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object!
simple	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!
simple	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!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/citation.cff does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/main does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_4_0 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_4_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	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!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object!
simple	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!
simple	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!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/citation.cff does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/main does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_4_0 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_4_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	03-Jul-2026 14:09:38	   d9d218f..a08ed3b  patch/JAL-4410_multimers_from_3dbeacons -> origin/patch/JAL-4410_multimers_from_3dbeacons
simple	03-Jul-2026 14:09:38	 * [new branch]      dev/JAL-4688_gitlab_ci -> origin/dev/JAL-4688_gitlab_ci
simple	03-Jul-2026 14:09:38	   5a35253..2a40a88  development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch
simple	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!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object!
simple	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!
simple	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!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/citation.cff does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/main does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object!
simple	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!
simple	03-Jul-2026 14:09:38	error: refs/tags/Archived_Release_2_7 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Jalview_2_4_0b2 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_10_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_2_7 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_4_0 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_11_4_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_4_0 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_5_1 does not point to a valid object!
simple	03-Jul-2026 14:09:38	error: refs/tags/Release_2_6_1 does not point to a valid object!
simple	03-Jul-2026 14:09:39	Already on 'patch/JAL-4410_multimers_from_3dbeacons'
simple	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.
simple	03-Jul-2026 14:09:39	  (use "git pull" to update your local branch)
simple	03-Jul-2026 14:09:39	HEAD is now at a08ed3b JAL-4410 testData for failing test
simple	03-Jul-2026 14:09:39	Updated source code to revision: a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572
simple	03-Jul-2026 14:09:39	Finished task 'Checkout Default Repository' with result: Success
simple	03-Jul-2026 14:09:39	Running pre-build action: VCS Version Collector
simple	03-Jul-2026 14:09:39	Running pre-build action: Artifactory Release Staging
simple	03-Jul-2026 14:09:39	Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	03-Jul-2026 14:09:39	Bamboo Artifactory Plugin version: 2.6.2
command	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)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_revision_number=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572\nbamboo_repository_48169043_previous_revision_number=d9d218fe9b518987c14acfe100646789b1dbc30f\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-4\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB749-JOB1\nbamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=4\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-4\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons\nbamboo_shortPlanKey=GDB749\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572\nbamboo_buildTimeStamp=2026-07-03T14:09:38.370+01:00\nbamboo_repository_previous_revision_number=d9d218fe9b518987c14acfe100646789b1dbc30f\nbamboo_repository_48169043_name=Jalview Gitlab\nbamboo_planRepository_previousRevision=d9d218fe9b518987c14acfe100646789b1dbc30f\nbamboo_repository_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildResultKey=JB-GDB749-JOB1-4\nbamboo_repository_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_48169043_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=d9d218fe9b518987c14acfe100646789b1dbc30f\nbamboo_planRepository_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4410_multimers_from_3dbeacons\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_48169043_revision_number=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_repository_48169043_git_username=\nbamboo_plan_storageTag=plan-47972517\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1\nbamboo_planKey=JB-GDB749\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4410_multimers_from_3dbeacons\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	03-Jul-2026 14:09:39	2477
build	03-Jul-2026 14:09:40	
build	03-Jul-2026 14:09:40	> Configure project :
build	03-Jul-2026 14:09:40	Using properties from file './utils/channels/default/channel_gradle.properties'
build	03-Jul-2026 14:09:40	JALVIEW_VERSION is set to '2.11.5.2'
build	03-Jul-2026 14:09:40	HEADLESS BUILD
build	03-Jul-2026 14:09:40	J2S ENABLED
build	03-Jul-2026 14:09:40	Using a LOCAL profile.
build	03-Jul-2026 14:09:40	eclipseDir exists
build	03-Jul-2026 14:09:41	
build	03-Jul-2026 14:09:41	> Task :clean
build	03-Jul-2026 14:09:41	> Task :cleanClover
build	03-Jul-2026 14:09:41	> Task :cleanTest UP-TO-DATE
build	03-Jul-2026 14:09:43	
build	03-Jul-2026 14:09:43	> Task :cloverInstrJava
build	03-Jul-2026 14:09:43	Clover: About to instrument 1110 files
build	03-Jul-2026 14:09:43	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	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'.
build	03-Jul-2026 14:09:43	Processing files at 1.9 source level.
error	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?
error	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?
error	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?
error	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?
error	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?
error	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?
error	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?
build	03-Jul-2026 14:09:53	Clover all over. Instrumented 1110 files (113 packages).
build	03-Jul-2026 14:09:55	
build	03-Jul-2026 14:09:55	> Task :cloverInstrTests
build	03-Jul-2026 14:09:55	Clover: About to instrument test files
build	03-Jul-2026 14:09:55	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	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'.
build	03-Jul-2026 14:09:55	Processing files at 1.9 source level.
build	03-Jul-2026 14:09:57	Clover all over. Instrumented 293 files (52 packages).
build	03-Jul-2026 14:09:57	1629 test methods detected.
build	03-Jul-2026 14:09:57	
build	03-Jul-2026 14:09:57	> Task :cloverInstr
build	03-Jul-2026 14:09:59	
build	03-Jul-2026 14:09:59	> Task :compileCloverJava
build	03-Jul-2026 14:09:59	Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
build	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.
build	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.
build	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.
build	03-Jul-2026 14:09:59	Setting target compatibility to 11
error	03-Jul-2026 14:10:12	Note: Some input files use or override a deprecated API.
error	03-Jul-2026 14:10:12	Note: Recompile with -Xlint:deprecation for details.
error	03-Jul-2026 14:10:12	Note: Some input files use unchecked or unsafe operations.
error	03-Jul-2026 14:10:12	Note: Recompile with -Xlint:unchecked for details.
build	03-Jul-2026 14:10:17	
build	03-Jul-2026 14:10:17	> Task :processCloverResources NO-SOURCE
build	03-Jul-2026 14:10:17	> Task :cloverClasses
build	03-Jul-2026 14:10:17	> Task :copyHelp
build	03-Jul-2026 14:10:18	> Task :buildIndices
build	03-Jul-2026 14:10:18	> Task :copyResources
build	03-Jul-2026 14:10:18	> Task :copyChannelResources
build	03-Jul-2026 14:10:18	
build	03-Jul-2026 14:10:18	> Task :createBuildProperties
build	03-Jul-2026 14:10:18	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	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.
build	03-Jul-2026 14:10:18	
build	03-Jul-2026 14:10:18	> Task :buildResources
build	03-Jul-2026 14:10:18	> Task :copyDocs
build	03-Jul-2026 14:10:18	
build	03-Jul-2026 14:10:18	> Task :convertMdFiles
build	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
build	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
build	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
build	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
build	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
build	03-Jul-2026 14:10:18	
build	03-Jul-2026 14:10:18	> Task :releasesTemplates
build	03-Jul-2026 14:10:18	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	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.
build	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.
build	03-Jul-2026 14:10:18	Stripping rc/test/etc for TEST
build	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
build	03-Jul-2026 14:10:18	
build	03-Jul-2026 14:10:18	> Task :prepare
build	03-Jul-2026 14:10:20	
build	03-Jul-2026 14:10:20	> Task :compileJava
build	03-Jul-2026 14:10:20	Setting target compatibility to 11
error	03-Jul-2026 14:10:24	Note: Some input files use or override a deprecated API.
error	03-Jul-2026 14:10:24	Note: Recompile with -Xlint:deprecation for details.
error	03-Jul-2026 14:10:24	Note: Some input files use unchecked or unsafe operations.
error	03-Jul-2026 14:10:24	Note: Recompile with -Xlint:unchecked for details.
build	03-Jul-2026 14:10:27	
build	03-Jul-2026 14:10:27	> Task :compileTestJava
build	03-Jul-2026 14:10:27	Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
build	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.
build	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.
build	03-Jul-2026 14:10:27	Setting target compatibility to 11
error	03-Jul-2026 14:10:30	Note: Some input files use or override a deprecated API.
error	03-Jul-2026 14:10:30	Note: Recompile with -Xlint:deprecation for details.
error	03-Jul-2026 14:10:30	Note: Some input files use unchecked or unsafe operations.
error	03-Jul-2026 14:10:30	Note: Recompile with -Xlint:unchecked for details.
build	03-Jul-2026 14:10:32	
build	03-Jul-2026 14:10:32	> Task :processTestResources
build	03-Jul-2026 14:10:32	Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
build	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.
build	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.
build	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.
build	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.
build	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.
build	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.
build	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.
build	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.
build	03-Jul-2026 14:10:32	
build	03-Jul-2026 14:10:32	> Task :testClasses
build	03-Jul-2026 14:10:34	
build	03-Jul-2026 14:10:34	> Task :testTask0
build	03-Jul-2026 14:10:34	Running tests WITH clover
error	03-Jul-2026 14:10:35	WARNING: An illegal reflective access operation has occurred
error	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
error	03-Jul-2026 14:10:35	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	03-Jul-2026 14:10:35	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	03-Jul-2026 14:10:35	WARNING: All illegal access operations will be denied in a future release
build	03-Jul-2026 14:10:57	
build	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
build	03-Jul-2026 14:10:57	    java.lang.AssertionError: Exception importing paefile 'examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_cmp.json'
build	03-Jul-2026 14:10:57	        at org.testng.Assert.fail(Assert.java:83)
build	03-Jul-2026 14:10:57	        at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_1rvd1wm3rrg(EBIAlphaFoldTest.java:96)
build	03-Jul-2026 14:10:57	        at jalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructure(EBIAlphaFoldTest.java:67)
build	03-Jul-2026 14:10:57	
build	03-Jul-2026 14:10:57	        Caused by:
build	03-Jul-2026 14:10:57	        java.io.IOException: Stream Closed
build	03-Jul-2026 14:10:57	            at java.base/java.io.FileInputStream.readBytes(Native Method)
build	03-Jul-2026 14:10:57	            at java.base/java.io.FileInputStream.read(FileInputStream.java:279)
build	03-Jul-2026 14:10:57	            at java.base/java.io.BufferedInputStream.fill(BufferedInputStream.java:252)
build	03-Jul-2026 14:10:57	            at java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:292)
build	03-Jul-2026 14:10:57	            at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:351)
build	03-Jul-2026 14:10:57	            at java.base/java.io.FilterInputStream.read(FilterInputStream.java:107)
build	03-Jul-2026 14:10:57	            at jalview.util.Platform.isGzipStream(Platform.java:602)
build	03-Jul-2026 14:10:57	            at jalview.util.Platform.checkForGzipStream(Platform.java:644)
build	03-Jul-2026 14:10:57	            at jalview.util.Platform.parseJSON(Platform.java:534)
build	03-Jul-2026 14:10:57	            at jalview.ws.dbsources.EBIAlfaFold.parseJSONtoPAEContactMatrix(EBIAlfaFold.java:625)
build	03-Jul-2026 14:10:57	            at jalview.ws.dbsources.EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(EBIAlfaFold.java:660)
build	03-Jul-2026 14:10:57	            at jalview.ws.dbsources.EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(EBIAlfaFold.java:649)
build	03-Jul-2026 14:10:57	            at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_1rvd1wm3rrg(EBIAlphaFoldTest.java:90)
build	03-Jul-2026 14:10:57	            ... 1 more
build	03-Jul-2026 14:10:59	
build	03-Jul-2026 14:10:59	Gradle suite > Gradle test > jalview.ws.dbsources.EBIAlphaFoldTest.testImportPAEAndStructureForMultiChainSeqs FAILED
build	03-Jul-2026 14:10:59	    java.lang.Error: Couln't create a mapping for this matrix.
build	03-Jul-2026 14:10:59	        at jalview.ws.datamodel.alphafold.MappableContactMatrix.liftOver(MappableContactMatrix.java:189)
build	03-Jul-2026 14:10:59	        at jalview.ws.datamodel.alphafold.MappableContactMatrix.liftOver(MappableContactMatrix.java:38)
build	03-Jul-2026 14:10:59	        at mc_view.PDBChain.transferResidueAnnotation(PDBChain.java:715)
build	03-Jul-2026 14:10:59	        at jalview.structure.StructureSelectionManager.getNWMappings(StructureSelectionManager.java:1014)
build	03-Jul-2026 14:10:59	        at jalview.structure.StructureSelectionManager.computeMapping(StructureSelectionManager.java:749)
build	03-Jul-2026 14:10:59	        at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_130yvgz3rsn(EBIAlphaFoldTest.java:194)
build	03-Jul-2026 14:10:59	        at jalview.ws.dbsources.EBIAlphaFoldTest.testImportPAEAndStructureForMultiChainSeqs(EBIAlphaFoldTest.java:173)
error	03-Jul-2026 14:14:44	
error	03-Jul-2026 14:14:44	1846 tests completed, 2 failed
build	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
build	03-Jul-2026 14:14:46	
build	03-Jul-2026 14:14:46	> Task :testTask1
build	03-Jul-2026 14:14:46	Running tests WITH clover
error	03-Jul-2026 14:14:47	WARNING: An illegal reflective access operation has occurred
error	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
error	03-Jul-2026 14:14:47	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	03-Jul-2026 14:14:47	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	03-Jul-2026 14:14:47	WARNING: All illegal access operations will be denied in a future release
build	03-Jul-2026 14:17:02	
build	03-Jul-2026 14:17:02	> Task :testTask2
build	03-Jul-2026 14:17:02	Running tests WITH clover
build	03-Jul-2026 14:17:05	
build	03-Jul-2026 14:17:05	> Task :testTask3
build	03-Jul-2026 14:17:05	Running tests WITH clover
error	03-Jul-2026 14:17:07	WARNING: An illegal reflective access operation has occurred
error	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
error	03-Jul-2026 14:17:07	WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
error	03-Jul-2026 14:17:07	WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
error	03-Jul-2026 14:17:07	WARNING: All illegal access operations will be denied in a future release
build	03-Jul-2026 14:17:57	
build	03-Jul-2026 14:17:57	> Task :test NO-SOURCE
build	03-Jul-2026 14:17:57	┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
build	03-Jul-2026 14:17:57	│jalview:testTask0 results: FAILURE (1846 tests, 1844 successes, 2 failures, 0 skipped) in 4 minutes, 12.029 seconds   │
build	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│
build	03-Jul-2026 14:17:57	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	03-Jul-2026 14:17:57	│jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 15.600 seconds       │
build	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│
build	03-Jul-2026 14:17:57	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	03-Jul-2026 14:17:57	│jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.656 seconds                     │
build	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│
build	03-Jul-2026 14:17:57	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	03-Jul-2026 14:17:57	│jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 53.088 seconds                  │
build	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│
build	03-Jul-2026 14:17:57	├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
build	03-Jul-2026 14:17:57	│OVERALL: results: FAILURE (1934 tests, 1932 successes, 2 failures, 0 skipped) in 6 minutes, 84.373 seconds            │
build	03-Jul-2026 14:17:57	└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
build	03-Jul-2026 14:17:57	
build	03-Jul-2026 14:17:57	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	03-Jul-2026 14:17:57	
build	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.
build	03-Jul-2026 14:17:57	
build	03-Jul-2026 14:17:57	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	03-Jul-2026 14:17:57	
build	03-Jul-2026 14:17:57	Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
build	03-Jul-2026 14:17:57	Please consult deprecation warnings for more details.
build	03-Jul-2026 14:17:57	21 actionable tasks: 20 executed, 1 up-to-date
error	03-Jul-2026 14:17:57	
error	03-Jul-2026 14:17:57	FAILURE: Build failed with an exception.
error	03-Jul-2026 14:17:57	
error	03-Jul-2026 14:17:57	* Where:
error	03-Jul-2026 14:17:57	Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build.gradle' line: 1967
error	03-Jul-2026 14:17:57	
error	03-Jul-2026 14:17:57	* What went wrong:
error	03-Jul-2026 14:17:57	Failed tests!
error	03-Jul-2026 14:17:57	
error	03-Jul-2026 14:17:57	* Try:
error	03-Jul-2026 14:17:57	> Run with --stacktrace option to get the stack trace.
error	03-Jul-2026 14:17:57	> Run with --info or --debug option to get more log output.
error	03-Jul-2026 14:17:57	> Run with --scan to get full insights.
error	03-Jul-2026 14:17:57	
error	03-Jul-2026 14:17:57	* Get more help at https://help.gradle.org
error	03-Jul-2026 14:17:57	
error	03-Jul-2026 14:17:57	BUILD FAILED in 8m 17s
simple	03-Jul-2026 14:17:57	
simple	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
simple	03-Jul-2026 14:17:57	Finished task 'Run tests with openclover under gradle' with result: Failed
simple	03-Jul-2026 14:17:57	Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	03-Jul-2026 14:17:57	Bamboo Artifactory Plugin version: 2.6.2
command	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)'\n ... running command line: \n/home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_repository_48169043_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_revision_number=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572\nbamboo_repository_48169043_previous_revision_number=d9d218fe9b518987c14acfe100646789b1dbc30f\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-4\nJAVA_OPTS=-Xms512m -Xmx1024m    -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDB749-JOB1\nbamboo_shortPlanName=patch-JAL-4410_multimers_from_3dbeacons\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=4\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_repository_48169043_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortJobName=Clover and Tests\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB749-JOB1-4\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons\nbamboo_shortPlanKey=GDB749\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572\nbamboo_buildTimeStamp=2026-07-03T14:09:38.370+01:00\nbamboo_repository_previous_revision_number=d9d218fe9b518987c14acfe100646789b1dbc30f\nbamboo_repository_48169043_name=Jalview Gitlab\nbamboo_planRepository_previousRevision=d9d218fe9b518987c14acfe100646789b1dbc30f\nbamboo_repository_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildResultKey=JB-GDB749-JOB1-4\nbamboo_repository_branch_name=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_buildPlanName=Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=true\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_jobFailed=true\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_48169043_git_branch=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=d9d218fe9b518987c14acfe100646789b1dbc30f\nbamboo_planRepository_branchDisplayName=patch/JAL-4410_multimers_from_3dbeacons\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=patch/JAL-4410_multimers_from_3dbeacons\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_48169043_revision_number=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_repository_48169043_git_username=\nbamboo_plan_storageTag=plan-47972517\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1\nbamboo_planKey=JB-GDB749\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=patch/JAL-4410_multimers_from_3dbeacons\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	03-Jul-2026 14:17:57	2477
build	03-Jul-2026 14:18:02	
build	03-Jul-2026 14:18:02	> Configure project :
build	03-Jul-2026 14:18:02	Using properties from file './utils/channels/default/channel_gradle.properties'
build	03-Jul-2026 14:18:02	JALVIEW_VERSION is set to '2.11.5.2'
build	03-Jul-2026 14:18:02	HEADLESS BUILD
build	03-Jul-2026 14:18:02	J2S ENABLED
build	03-Jul-2026 14:18:03	Using a LOCAL profile.
build	03-Jul-2026 14:18:04	eclipseDir exists
build	03-Jul-2026 14:18:06	
build	03-Jul-2026 14:18:06	> Task :cloverHtmlReport
build	03-Jul-2026 14:18:06	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	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'
build	03-Jul-2026 14:18:55	Done. Processed 117 packages in 47788ms (408ms per package).
build	03-Jul-2026 14:19:00	
build	03-Jul-2026 14:19:00	> Task :cloverXmlReport
build	03-Jul-2026 14:19:00	OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
build	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'
build	03-Jul-2026 14:19:01	
build	03-Jul-2026 14:19:01	> Task :cloverReport
build	03-Jul-2026 14:19:01	
build	03-Jul-2026 14:19:01	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	03-Jul-2026 14:19:01	
build	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.
build	03-Jul-2026 14:19:01	
build	03-Jul-2026 14:19:01	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	03-Jul-2026 14:19:01	
build	03-Jul-2026 14:19:01	BUILD SUCCESSFUL in 1m 4s
build	03-Jul-2026 14:19:01	2 actionable tasks: 2 executed
simple	03-Jul-2026 14:19:01	Finished task 'Clover Report' with result: Success
simple	03-Jul-2026 14:19:01	Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
simple	03-Jul-2026 14:19:01	Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1...
simple	03-Jul-2026 14:19:01	Failing task since 2 failing test cases were found.
simple	03-Jul-2026 14:19:01	Finished task 'TestNG Parser' with result: Failed
simple	03-Jul-2026 14:19:01	Running post build plugin 'NCover Results Collector'
simple	03-Jul-2026 14:19:01	Running post build plugin 'Artifact Copier'
simple	03-Jul-2026 14:19:01	Publishing an artifact: Clover Report (System)
simple	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
simple	03-Jul-2026 14:19:03	Publishing an artifact: TestNG report
error	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.
simple	03-Jul-2026 14:19:03	The artifact hasn't been successfully published after 1.401 ms
simple	03-Jul-2026 14:19:03	Running post build plugin 'Artifactory Release Management Staging'
simple	03-Jul-2026 14:19:03	Running post build plugin 'Artifactory Build Info Copier'
simple	03-Jul-2026 14:19:03	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	03-Jul-2026 14:19:03	Running post build plugin 'npm Cache Cleanup'
simple	03-Jul-2026 14:19:03	Running post build plugin 'Clover Results Collector'
simple	03-Jul-2026 14:19:03	Running post build plugin 'Docker Container Cleanup'
simple	03-Jul-2026 14:19:03	Finalising the build...
simple	03-Jul-2026 14:19:03	Stopping timer.
simple	03-Jul-2026 14:19:03	Build JB-GDB749-JOB1-4 completed.
simple	03-Jul-2026 14:19:03	Running on server: post build plugin 'NCover Results Collector'
simple	03-Jul-2026 14:19:03	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	03-Jul-2026 14:19:03	Running on server: post build plugin 'Clover Delta Calculator'
simple	03-Jul-2026 14:19:03	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	03-Jul-2026 14:19:03	All post build plugins have finished
simple	03-Jul-2026 14:19:03	Generating build results summary...
simple	03-Jul-2026 14:19:04	Saving build results to disk...
simple	03-Jul-2026 14:19:04	Logging substituted variables...
simple	03-Jul-2026 14:19:04	Indexing build results...
simple	03-Jul-2026 14:19:04	Finished building JB-GDB749-JOB1-4.