simple 03-Jul-2026 14:45:38 Build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #5 (JB-GDB749-JOB1-5) started building on agent Default Agent simple 03-Jul-2026 14:45:38 simple 03-Jul-2026 14:45:38 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1 simple 03-Jul-2026 14:45:38 Executing build Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #5 (JB-GDB749-JOB1-5) simple 03-Jul-2026 14:45:38 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 03-Jul-2026 14:45:38 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1 simple 03-Jul-2026 14:45:38 Updating source code to revision: 60deee6ec835c5c8b905f7ae6196fedd20f92d01 simple 03-Jul-2026 14:45:38 Fetching 'refs/heads/patch/JAL-4410_multimers_from_3dbeacons' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 03-Jul-2026 14:45:38 Checking out revision 60deee6ec835c5c8b905f7ae6196fedd20f92d01. simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/citation.cff does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/main does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Archived_Release_2_7 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_10_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_2_7 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_4_0 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_4_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_4_0 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_5_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_6_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/citation.cff does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/main does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Archived_Release_2_7 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_10_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_2_7 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_4_0 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_4_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_4_0 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_5_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_6_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/citation.cff does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/main does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Archived_Release_2_7 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_10_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_2_7 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_4_0 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_4_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_4_0 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_5_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_6_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/citation.cff does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/main does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Archived_Release_2_7 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_10_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_2_7 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_4_0 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_4_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_4_0 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_5_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_6_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 03-Jul-2026 14:45:38 a08ed3b..60deee6 patch/JAL-4410_multimers_from_3dbeacons -> origin/patch/JAL-4410_multimers_from_3dbeacons simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4530_applescript_to_detect_Applications_symlink does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4611_SSConsensus_Preferences does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4623_JAL-4624_PCA_for_SS does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/citation.cff does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/development/JAL-4576_ligysis does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/feature/JAL-4478_multimer_pae_import does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/feature/JAL_4542_highlight_selected_annot_labels_tree_nodes does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/features/JAL-4587_colour_group_annotation does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/improvement/JAL-4560_handle_relative_paths_in_jvl_files does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/improvement/JAL-4620_faster_sim_matrices does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/main does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-3848_slivka_java_client_update_06d3659 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4107_singleThreadTests does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4414_for_2_11_5_Branch does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4478_r212_initialpatch does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4590_remove_isBlank_use does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/patch/JAL-4644_add_resources_for_testng does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/releases/Release_2_11_4_Branch does not point to a valid object! simple 03-Jul-2026 14:45:38 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 14:45:38 error: refs/remotes/origin/spike/JAL-4576_ligysis_exploration does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/spike/na_hack_JAL-4673 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/remotes/origin/test/JAL-4603_test_for_JAL-4603_in_progress does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Archived_Release_2_7 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_10_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_2_7 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_4_0 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_11_4_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_4_0 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_5_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 error: refs/tags/Release_2_6_1 does not point to a valid object! simple 03-Jul-2026 14:45:38 Already on 'patch/JAL-4410_multimers_from_3dbeacons' simple 03-Jul-2026 14:45:38 Your branch is behind 'origin/patch/JAL-4410_multimers_from_3dbeacons' by 1 commit, and can be fast-forwarded. simple 03-Jul-2026 14:45:38 (use "git pull" to update your local branch) simple 03-Jul-2026 14:45:38 HEAD is now at 60deee6 JAL-4410 (still failing) multimer test WIP simple 03-Jul-2026 14:45:38 Updated source code to revision: 60deee6ec835c5c8b905f7ae6196fedd20f92d01 simple 03-Jul-2026 14:45:38 Finished task 'Checkout Default Repository' with result: Success simple 03-Jul-2026 14:45:38 Running pre-build action: VCS Version Collector simple 03-Jul-2026 14:45:38 Running pre-build action: Artifactory Release Staging simple 03-Jul-2026 14:45:38 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 03-Jul-2026 14:45:38 Bamboo Artifactory Plugin version: 2.6.2 command 03-Jul-2026 14:45:38 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #5 (JB-GDB749-JOB1-5)'\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: 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Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=5\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-JOB1-5\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=60deee6ec835c5c8b905f7ae6196fedd20f92d01\nbamboo_buildTimeStamp=2026-07-03T14:45:38.192+01:00\nbamboo_repository_previous_revision_number=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572\nbamboo_repository_48169043_name=Jalview 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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=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572\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=60deee6ec835c5c8b905f7ae6196fedd20f92d01\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 14:45:38 2477 build 03-Jul-2026 14:45:39 build 03-Jul-2026 14:45:39 > Configure project : build 03-Jul-2026 14:45:39 Using properties from file './utils/channels/default/channel_gradle.properties' build 03-Jul-2026 14:45:39 JALVIEW_VERSION is set to '2.11.5.2' build 03-Jul-2026 14:45:39 HEADLESS BUILD build 03-Jul-2026 14:45:39 J2S ENABLED build 03-Jul-2026 14:45:39 Using a LOCAL profile. build 03-Jul-2026 14:45:39 eclipseDir exists build 03-Jul-2026 14:45:40 build 03-Jul-2026 14:45:40 > Task :clean build 03-Jul-2026 14:45:40 > Task :cleanClover build 03-Jul-2026 14:45:40 > Task :cleanTest UP-TO-DATE build 03-Jul-2026 14:45:42 build 03-Jul-2026 14:45:42 > Task :cloverInstrJava build 03-Jul-2026 14:45:42 Clover: About to instrument 1110 files build 03-Jul-2026 14:45:42 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Jul-2026 14:45:42 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'. build 03-Jul-2026 14:45:42 Processing files at 1.9 source level. error 03-Jul-2026 14:45:44 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 14:45:44 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 14:45:44 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 14:45:44 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 14:45:44 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 14:45:44 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 14:45:44 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 14:45:50 Clover all over. Instrumented 1110 files (113 packages). build 03-Jul-2026 14:45:52 build 03-Jul-2026 14:45:52 > Task :cloverInstrTests build 03-Jul-2026 14:45:52 Clover: About to instrument test files build 03-Jul-2026 14:45:52 OpenClover Version 4.4.1, built on October 11 2019 (build-1020) build 03-Jul-2026 14:45:52 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/clover/clover.db'. build 03-Jul-2026 14:45:52 Processing files at 1.9 source level. build 03-Jul-2026 14:45:54 Clover all over. Instrumented 293 files (52 packages). build 03-Jul-2026 14:45:54 1629 test methods detected. build 03-Jul-2026 14:45:54 build 03-Jul-2026 14:45:54 > Task :cloverInstr build 03-Jul-2026 14:45:56 build 03-Jul-2026 14:45:56 > Task :compileCloverJava build 03-Jul-2026 14:45:56 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: build 03-Jul-2026 14:45:56 - 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 14:45:56 - 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 14:45:56 - 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 14:45:56 Setting target compatibility to 11 error 03-Jul-2026 14:46:08 Note: Some input files use or override a deprecated API. error 03-Jul-2026 14:46:08 Note: Recompile with -Xlint:deprecation for details. error 03-Jul-2026 14:46:08 Note: Some input files use unchecked or unsafe operations. error 03-Jul-2026 14:46:08 Note: Recompile with -Xlint:unchecked for details. build 03-Jul-2026 14:46:13 build 03-Jul-2026 14:46:13 > Task :processCloverResources NO-SOURCE build 03-Jul-2026 14:46:13 > Task :cloverClasses build 03-Jul-2026 14:46:13 > Task :copyHelp build 03-Jul-2026 14:46:14 > Task :buildIndices build 03-Jul-2026 14:46:14 > Task :copyResources build 03-Jul-2026 14:46:14 > Task :copyChannelResources build 03-Jul-2026 14:46:14 build 03-Jul-2026 14:46:14 > Task :createBuildProperties build 03-Jul-2026 14:46:14 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 03-Jul-2026 14:46:14 - 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 14:46:14 build 03-Jul-2026 14:46:14 > Task :buildResources build 03-Jul-2026 14:46:15 > Task :copyDocs build 03-Jul-2026 14:46:15 build 03-Jul-2026 14:46:15 > Task :convertMdFiles build 03-Jul-2026 14:46:15 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 14:46:15 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/releaseprocess.html build 03-Jul-2026 14:46:15 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 14:46:15 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/resources/doc_build/doc/building.html build 03-Jul-2026 14:46:15 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 14:46:15 build 03-Jul-2026 14:46:15 > Task :releasesTemplates build 03-Jul-2026 14:46:15 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 03-Jul-2026 14:46:15 - 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 14:46:15 - 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 14:46:15 Stripping rc/test/etc for TEST build 03-Jul-2026 14:46:15 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/help/markdown/whatsnew/whatsnew-TEST.md build 03-Jul-2026 14:46:15 build 03-Jul-2026 14:46:15 > Task :prepare build 03-Jul-2026 14:46:17 build 03-Jul-2026 14:46:17 > Task :compileJava build 03-Jul-2026 14:46:17 Setting target compatibility to 11 error 03-Jul-2026 14:46:21 Note: Some input files use or override a deprecated API. error 03-Jul-2026 14:46:21 Note: Recompile with -Xlint:deprecation for details. error 03-Jul-2026 14:46:21 Note: Some input files use unchecked or unsafe operations. error 03-Jul-2026 14:46:21 Note: Recompile with -Xlint:unchecked for details. build 03-Jul-2026 14:46:23 build 03-Jul-2026 14:46:23 > Task :compileTestJava build 03-Jul-2026 14:46:23 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: build 03-Jul-2026 14:46:23 - 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 14:46:23 - 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 14:46:23 Setting target compatibility to 11 error 03-Jul-2026 14:46:26 Note: Some input files use or override a deprecated API. error 03-Jul-2026 14:46:26 Note: Recompile with -Xlint:deprecation for details. error 03-Jul-2026 14:46:26 Note: Some input files use unchecked or unsafe operations. error 03-Jul-2026 14:46:26 Note: Recompile with -Xlint:unchecked for details. build 03-Jul-2026 14:46:28 build 03-Jul-2026 14:46:28 > Task :processTestResources build 03-Jul-2026 14:46:28 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: build 03-Jul-2026 14:46:28 - 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 14:46:28 - 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 14:46:28 - 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 14:46:28 - 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 14:46:28 - 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 14:46:28 - 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 14:46:28 - 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 14:46:28 - 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 14:46:28 build 03-Jul-2026 14:46:28 > Task :testClasses build 03-Jul-2026 14:46:30 build 03-Jul-2026 14:46:30 > Task :testTask0 build 03-Jul-2026 14:46:30 Running tests WITH clover error 03-Jul-2026 14:46:31 WARNING: An illegal reflective access operation has occurred error 03-Jul-2026 14:46:31 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 14:46:31 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 03-Jul-2026 14:46:31 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 03-Jul-2026 14:46:31 WARNING: All illegal access operations will be denied in a future release build 03-Jul-2026 14:46:57 build 03-Jul-2026 14:46:57 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 14:46:57 java.lang.AssertionError: Exception importing paefile 'examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_cmp.json' build 03-Jul-2026 14:46:57 at org.testng.Assert.fail(Assert.java:83) build 03-Jul-2026 14:46:57 at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_1rvd1wm3rrg(EBIAlphaFoldTest.java:99) build 03-Jul-2026 14:46:57 at jalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructure(EBIAlphaFoldTest.java:70) build 03-Jul-2026 14:46:57 build 03-Jul-2026 14:46:57 Caused by: build 03-Jul-2026 14:46:57 java.io.IOException: Stream Closed build 03-Jul-2026 14:46:57 at java.base/java.io.FileInputStream.readBytes(Native Method) build 03-Jul-2026 14:46:57 at java.base/java.io.FileInputStream.read(FileInputStream.java:279) build 03-Jul-2026 14:46:57 at java.base/java.io.BufferedInputStream.fill(BufferedInputStream.java:252) build 03-Jul-2026 14:46:57 at java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:292) build 03-Jul-2026 14:46:57 at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:351) build 03-Jul-2026 14:46:57 at java.base/java.io.FilterInputStream.read(FilterInputStream.java:107) build 03-Jul-2026 14:46:57 at jalview.util.Platform.isGzipStream(Platform.java:602) build 03-Jul-2026 14:46:57 at jalview.util.Platform.checkForGzipStream(Platform.java:644) build 03-Jul-2026 14:46:57 at jalview.util.Platform.parseJSON(Platform.java:534) build 03-Jul-2026 14:46:57 at jalview.ws.dbsources.EBIAlfaFold.parseJSONtoPAEContactMatrix(EBIAlfaFold.java:627) build 03-Jul-2026 14:46:57 at jalview.ws.dbsources.EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(EBIAlfaFold.java:662) build 03-Jul-2026 14:46:57 at jalview.ws.dbsources.EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(EBIAlfaFold.java:651) build 03-Jul-2026 14:46:57 at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_1rvd1wm3rrg(EBIAlphaFoldTest.java:93) build 03-Jul-2026 14:46:57 ... 1 more build 03-Jul-2026 14:46:59 build 03-Jul-2026 14:46:59 Gradle suite > Gradle test > jalview.ws.dbsources.EBIAlphaFoldTest.testImportPAEAndStructureForMultiChainSeqs FAILED build 03-Jul-2026 14:46:59 java.lang.AssertionError: Expected to find contact list for H4_HUMAN expected object to not be null build 03-Jul-2026 14:46:59 at org.testng.Assert.fail(Assert.java:94) build 03-Jul-2026 14:46:59 at org.testng.Assert.assertNotNull(Assert.java:406) build 03-Jul-2026 14:46:59 at jalview.ws.dbsources.EBIAlphaFoldTest.__CLR4_4_130yvgz3rsn(EBIAlphaFoldTest.java:208) build 03-Jul-2026 14:46:59 at jalview.ws.dbsources.EBIAlphaFoldTest.testImportPAEAndStructureForMultiChainSeqs(EBIAlphaFoldTest.java:176) build 03-Jul-2026 14:47:35 build 03-Jul-2026 14:47:35 Gradle suite > Gradle test > jalview.gui.QuitHandlerTest.testSavedAlignmentChanges FAILED build 03-Jul-2026 14:47:35 java.lang.AssertionError: Didn't read input file examples/uniref50.fa expected object to not be null build 03-Jul-2026 14:47:35 at org.testng.Assert.fail(Assert.java:94) build 03-Jul-2026 14:47:35 at org.testng.Assert.assertNotNull(Assert.java:406) build 03-Jul-2026 14:47:35 at jalview.gui.QuitHandlerTest.__CLR4_4_1c20mrg3uf0(QuitHandlerTest.java:214) build 03-Jul-2026 14:47:35 at jalview.gui.QuitHandlerTest.testSavedAlignmentChanges(QuitHandlerTest.java:210) build 03-Jul-2026 14:47:40 build 03-Jul-2026 14:47:40 Gradle suite > Gradle test > jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy FAILED build 03-Jul-2026 14:47:40 java.lang.AssertionError: Expected occupancy to be non-null in column 5 expected object to not be null build 03-Jul-2026 14:47:40 at org.testng.Assert.fail(Assert.java:94) build 03-Jul-2026 14:47:40 at org.testng.Assert.assertNotNull(Assert.java:406) build 03-Jul-2026 14:47:40 at jalview.gui.AlignViewportTest.__CLR4_4_1lfq8443uzh(AlignViewportTest.java:478) build 03-Jul-2026 14:47:40 at jalview.gui.AlignViewportTest.testShowOrDontShowOccupancy(AlignViewportTest.java:446) error 03-Jul-2026 14:50:56 error 03-Jul-2026 14:50:56 1846 tests completed, 4 failed build 03-Jul-2026 14:50:56 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 14:50:58 build 03-Jul-2026 14:50:58 > Task :testTask1 build 03-Jul-2026 14:50:58 Running tests WITH clover error 03-Jul-2026 14:50:59 WARNING: An illegal reflective access operation has occurred error 03-Jul-2026 14:50:59 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 14:50:59 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 03-Jul-2026 14:50:59 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 03-Jul-2026 14:50:59 WARNING: All illegal access operations will be denied in a future release build 03-Jul-2026 14:53:13 build 03-Jul-2026 14:53:13 > Task :testTask2 build 03-Jul-2026 14:53:13 Running tests WITH clover build 03-Jul-2026 14:53:16 build 03-Jul-2026 14:53:16 > Task :testTask3 build 03-Jul-2026 14:53:16 Running tests WITH clover error 03-Jul-2026 14:53:18 WARNING: An illegal reflective access operation has occurred error 03-Jul-2026 14:53:18 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 14:53:18 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop error 03-Jul-2026 14:53:18 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations error 03-Jul-2026 14:53:18 WARNING: All illegal access operations will be denied in a future release build 03-Jul-2026 14:54:05 build 03-Jul-2026 14:54:05 > Task :test NO-SOURCE build 03-Jul-2026 14:54:05 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ build 03-Jul-2026 14:54:05 │jalview:testTask0 results: FAILURE (1846 tests, 1842 successes, 4 failures, 0 skipped) in 4 minutes, 28.168 seconds │ build 03-Jul-2026 14:54:05 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask0/index.html│ build 03-Jul-2026 14:54:05 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Jul-2026 14:54:05 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 14.771 seconds │ build 03-Jul-2026 14:54:05 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask1/index.html│ build 03-Jul-2026 14:54:05 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Jul-2026 14:54:05 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.164 seconds │ build 03-Jul-2026 14:54:05 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask2/index.html│ build 03-Jul-2026 14:54:05 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Jul-2026 14:54:05 │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 50.488 seconds │ build 03-Jul-2026 14:54:05 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build/reports/tests/testTask3/index.html│ build 03-Jul-2026 14:54:05 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ build 03-Jul-2026 14:54:05 │OVERALL: results: FAILURE (1934 tests, 1930 successes, 4 failures, 0 skipped) in 6 minutes, 96.591 seconds │ build 03-Jul-2026 14:54:05 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ build 03-Jul-2026 14:54:05 build 03-Jul-2026 14:54:05 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 03-Jul-2026 14:54:05 build 03-Jul-2026 14:54:05 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 14:54:05 build 03-Jul-2026 14:54:05 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 03-Jul-2026 14:54:05 build 03-Jul-2026 14:54:05 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. build 03-Jul-2026 14:54:05 Please consult deprecation warnings for more details. build 03-Jul-2026 14:54:05 21 actionable tasks: 20 executed, 1 up-to-date error 03-Jul-2026 14:54:05 error 03-Jul-2026 14:54:05 FAILURE: Build failed with an exception. error 03-Jul-2026 14:54:05 error 03-Jul-2026 14:54:05 * Where: error 03-Jul-2026 14:54:05 Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB749-JOB1/build.gradle' line: 1967 error 03-Jul-2026 14:54:05 error 03-Jul-2026 14:54:05 * What went wrong: error 03-Jul-2026 14:54:05 Failed tests! error 03-Jul-2026 14:54:05 error 03-Jul-2026 14:54:05 * Try: error 03-Jul-2026 14:54:05 > Run with --stacktrace option to get the stack trace. error 03-Jul-2026 14:54:05 > Run with --info or --debug option to get more log output. error 03-Jul-2026 14:54:05 > Run with --scan to get full insights. error 03-Jul-2026 14:54:05 error 03-Jul-2026 14:54:05 * Get more help at https://help.gradle.org error 03-Jul-2026 14:54:05 error 03-Jul-2026 14:54:05 BUILD FAILED in 8m 26s simple 03-Jul-2026 14:54:05 simple 03-Jul-2026 14:54:05 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 14:54:05 Finished task 'Run tests with openclover under gradle' with result: Failed simple 03-Jul-2026 14:54:05 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 03-Jul-2026 14:54:05 Bamboo Artifactory Plugin version: 2.6.2 command 03-Jul-2026 14:54:05 Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-4410_multimers_from_3dbeacons - Clover and Tests #5 (JB-GDB749-JOB1-5)'\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: 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Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=5\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-JOB1-5\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=60deee6ec835c5c8b905f7ae6196fedd20f92d01\nbamboo_buildTimeStamp=2026-07-03T14:45:38.192+01:00\nbamboo_repository_previous_revision_number=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572\nbamboo_repository_48169043_name=Jalview 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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=a08ed3ba56eb5141e8ca3d50ccabe79d8dc95572\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=60deee6ec835c5c8b905f7ae6196fedd20f92d01\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 14:54:05 2477 build 03-Jul-2026 14:54:11 build 03-Jul-2026 14:54:11 > Configure project : build 03-Jul-2026 14:54:11 Using properties from file './utils/channels/default/channel_gradle.properties' build 03-Jul-2026 14:54:11 JALVIEW_VERSION is set to '2.11.5.2' build 03-Jul-2026 14:54:11 HEADLESS BUILD build 03-Jul-2026 14:54:11 J2S ENABLED build 03-Jul-2026 14:54:11 Using a LOCAL profile. build 03-Jul-2026 14:54:12 eclipseDir exists build 03-Jul-2026 14:54:14 build 03-J